Starting phenix.real_space_refine on Thu Mar 5 21:24:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v8c_31798/03_2026/7v8c_31798.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v8c_31798/03_2026/7v8c_31798.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v8c_31798/03_2026/7v8c_31798.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v8c_31798/03_2026/7v8c_31798.map" model { file = "/net/cci-nas-00/data/ceres_data/7v8c_31798/03_2026/7v8c_31798.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v8c_31798/03_2026/7v8c_31798.cif" } resolution = 3.4 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= 0.040 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 111 5.16 5 C 16030 2.51 5 N 4088 2.21 5 O 4968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 25197 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8016 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 50, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8072 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 51, 'TRANS': 980} Chain breaks: 7 Chain: "C" Number of atoms: 8059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8059 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "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: 6.09, per 1000 atoms: 0.24 Number of scatterers: 25197 At special positions: 0 Unit cell: (141.9, 146.3, 196.9, 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 111 16.00 O 4968 8.00 N 4088 7.00 C 16030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.03 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.04 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.04 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.03 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.02 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.04 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.02 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.02 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2003 " - " ASN A 234 " " NAG A2004 " - " ASN A 600 " " NAG A2005 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 328 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 613 " " NAG C2006 " - " ASN C 654 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 340 " " NAG H 1 " - " ASN A 613 " " NAG I 1 " - " ASN A 706 " " NAG J 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN A1071 " " NAG M 1 " - " ASN A1095 " " NAG N 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 340 " " NAG R 1 " - " ASN B 613 " " NAG S 1 " - " ASN B 706 " " NAG T 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1071 " " NAG W 1 " - " ASN B1095 " " NAG X 1 " - " ASN B1131 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 340 " " NAG a 1 " - " ASN C 706 " " NAG b 1 " - " ASN C 714 " " NAG c 1 " - " ASN C 798 " " NAG d 1 " - " ASN C1071 " " NAG e 1 " - " ASN C1095 " " NAG f 1 " - " ASN C1131 " Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.1% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.546A pdb=" N GLU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.377A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.190A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 407 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.551A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.837A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 Processing helix chain 'A' and resid 895 through 906 removed outlier: 4.441A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.554A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.602A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.612A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.629A pdb=" N VAL A 988 " --> pdb=" O VAL A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 4.062A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.383A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.928A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN B 385 " --> pdb=" O THR B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 407 removed outlier: 3.809A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.939A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 Processing helix chain 'B' and resid 813 through 823 Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.636A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.722A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 915 removed outlier: 4.161A pdb=" N TYR B 914 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.615A pdb=" N LEU B 981 " --> pdb=" O ILE B 977 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1029 removed outlier: 3.790A pdb=" N ALA B 986 " --> pdb=" O ASP B 982 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU B 987 " --> pdb=" O LYS B 983 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL B 988 " --> pdb=" O VAL B 984 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.690A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 346 through 350 removed outlier: 3.617A pdb=" N TRP C 350 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.886A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU C 387 " --> pdb=" O LEU C 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 381 through 387' Processing helix chain 'C' and resid 402 through 407 removed outlier: 4.199A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 435 through 440 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.857A pdb=" N THR C 635 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.997A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.599A pdb=" N GLN C 771 " --> pdb=" O ILE C 767 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.582A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 904 removed outlier: 3.823A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 915 Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 981 removed outlier: 3.582A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1030 removed outlier: 4.175A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.554A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.566A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.919A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.852A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.272A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.350A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 570 through 573 removed outlier: 3.835A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.399A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.600A pdb=" N GLY A1056 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.561A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1083 through 1087 removed outlier: 4.689A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A1120 " --> pdb=" O ALA A1084 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.156A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.855A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.460A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.456A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 224 through 229 removed outlier: 5.796A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.710A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 322 through 325 removed outlier: 3.662A pdb=" N ARG B 325 " --> pdb=" O ASN B 539 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC5, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC6, first strand: chain 'B' and resid 651 through 657 removed outlier: 4.994A pdb=" N THR B 693 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN B 655 " --> pdb=" O THR B 693 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AC8, first strand: chain 'B' and resid 714 through 716 Processing sheet with id=AC9, first strand: chain 'B' and resid 714 through 716 removed outlier: 5.915A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.445A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.612A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA B1077 " --> pdb=" O VAL B1130 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1091 through 1094 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.907A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.871A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.500A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 8.499A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 308 through 313 removed outlier: 5.673A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 322 through 325 removed outlier: 3.607A pdb=" N ARG C 325 " --> pdb=" O ASN C 539 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE1, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.226A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE3, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.513A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 651 through 657 removed outlier: 3.512A pdb=" N ALA C 691 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N THR C 693 " --> pdb=" O VAL C 653 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ASN C 655 " --> pdb=" O THR C 693 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.979A pdb=" N GLN C1068 " --> pdb=" O THR C 713 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY C1056 " --> pdb=" O ALA C1053 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 732 through 733 Processing sheet with id=AE7, first strand: chain 'C' and resid 1078 through 1079 Processing sheet with id=AE8, first strand: chain 'C' and resid 1085 through 1087 Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 947 hydrogen bonds defined for protein. 2574 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.12 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7935 1.34 - 1.46: 6418 1.46 - 1.58: 11258 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25749 Sorted by residual: bond pdb=" C ILE A 739 " pdb=" N CYS A 740 " ideal model delta sigma weight residual 1.332 1.308 0.025 1.40e-02 5.10e+03 3.13e+00 bond pdb=" C LEU A 229 " pdb=" N PRO A 230 " ideal model delta sigma weight residual 1.334 1.293 0.041 2.34e-02 1.83e+03 3.03e+00 bond pdb=" C1 NAG A2001 " pdb=" O5 NAG A2001 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 25744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 33839 1.66 - 3.32: 1075 3.32 - 4.98: 98 4.98 - 6.63: 15 6.63 - 8.29: 8 Bond angle restraints: 35035 Sorted by residual: angle pdb=" N VAL B 984 " pdb=" CA VAL B 984 " pdb=" C VAL B 984 " ideal model delta sigma weight residual 106.21 109.94 -3.73 1.07e+00 8.73e-01 1.22e+01 angle pdb=" C ASN A 328 " pdb=" N ILE A 329 " pdb=" CA ILE A 329 " ideal model delta sigma weight residual 121.97 127.92 -5.95 1.80e+00 3.09e-01 1.09e+01 angle pdb=" N ASP B 198 " pdb=" CA ASP B 198 " pdb=" C ASP B 198 " ideal model delta sigma weight residual 111.17 115.42 -4.25 1.41e+00 5.03e-01 9.10e+00 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 122.82 127.00 -4.18 1.42e+00 4.96e-01 8.65e+00 angle pdb=" CA THR A1114 " pdb=" C THR A1114 " pdb=" N ASP A1115 " ideal model delta sigma weight residual 116.84 121.58 -4.74 1.71e+00 3.42e-01 7.67e+00 ... (remaining 35030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14748 17.90 - 35.81: 1212 35.81 - 53.71: 251 53.71 - 71.61: 51 71.61 - 89.51: 27 Dihedral angle restraints: 16289 sinusoidal: 7301 harmonic: 8988 Sorted by residual: dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 2.73 -88.73 1 1.00e+01 1.00e-02 9.39e+01 dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 5.04 87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS A 659 " pdb=" SG CYS A 659 " pdb=" SG CYS A 668 " pdb=" CB CYS A 668 " ideal model delta sinusoidal sigma weight residual 93.00 -179.41 -87.59 1 1.00e+01 1.00e-02 9.20e+01 ... (remaining 16286 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 4094 0.110 - 0.220: 98 0.220 - 0.330: 3 0.330 - 0.440: 2 0.440 - 0.550: 2 Chirality restraints: 4199 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.56e+00 chirality pdb=" C1 NAG V 1 " pdb=" ND2 ASN B1071 " pdb=" C2 NAG V 1 " pdb=" O5 NAG V 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" C1 NAG C2003 " pdb=" ND2 ASN C 328 " pdb=" C2 NAG C2003 " pdb=" O5 NAG C2003 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.28e+00 ... (remaining 4196 not shown) Planarity restraints: 4468 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " 0.030 2.00e-02 2.50e+03 2.81e-02 9.87e+00 pdb=" CG ASN B1071 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " -0.034 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 216 " 0.033 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO C 217 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 217 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 217 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 903 " 0.015 2.00e-02 2.50e+03 1.27e-02 2.83e+00 pdb=" CG PHE C 903 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 PHE C 903 " 0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE C 903 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 903 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 903 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 903 " 0.003 2.00e-02 2.50e+03 ... (remaining 4465 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 558 2.66 - 3.22: 24351 3.22 - 3.78: 37474 3.78 - 4.34: 49172 4.34 - 4.90: 81656 Nonbonded interactions: 193211 Sorted by model distance: nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.102 3.040 nonbonded pdb=" O PRO A 230 " pdb=" NH1 ARG C 354 " model vdw 2.109 3.120 nonbonded pdb=" O GLY C 877 " pdb=" OG SER C 881 " model vdw 2.149 3.040 nonbonded pdb=" O GLU A 658 " pdb=" OH TYR A 692 " model vdw 2.149 3.040 nonbonded pdb=" OG1 THR B 615 " pdb=" OE1 GLU B 616 " model vdw 2.169 3.040 ... (remaining 193206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 260 or resid 262 through 2005)) selection = (chain 'B' and (resid 14 through 260 or resid 262 through 618 or resid 632 throu \ gh 824 or resid 852 through 2005)) selection = (chain 'C' and (resid 14 through 618 or resid 632 through 824 or resid 852 throu \ gh 2005)) } ncs_group { reference = chain 'D' selection = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.450 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: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.030 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 0.047 25862 Z= 0.252 Angle : 0.704 12.906 35334 Z= 0.353 Chirality : 0.048 0.550 4199 Planarity : 0.003 0.051 4424 Dihedral : 13.401 89.514 10389 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.81 % Favored : 93.03 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % 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: -0.58 (0.15), residues: 3040 helix: 1.52 (0.21), residues: 685 sheet: -0.14 (0.19), residues: 698 loop : -1.35 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 354 TYR 0.021 0.001 TYR C 870 PHE 0.029 0.002 PHE C 903 TRP 0.009 0.001 TRP A 883 HIS 0.003 0.001 HIS B1061 Details of bonding type rmsd covalent geometry : bond 0.00530 (25749) covalent geometry : angle 0.66924 (35035) SS BOND : bond 0.00435 ( 40) SS BOND : angle 2.15248 ( 80) hydrogen bonds : bond 0.12147 ( 943) hydrogen bonds : angle 6.14270 ( 2574) link_BETA1-4 : bond 0.00436 ( 29) link_BETA1-4 : angle 1.95828 ( 87) link_NAG-ASN : bond 0.00478 ( 44) link_NAG-ASN : angle 2.91140 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0054 (pmm) cc_final: -0.0187 (pmm) REVERT: A 1026 MET cc_start: 0.8157 (tpp) cc_final: 0.7854 (ttp) REVERT: B 242 HIS cc_start: 0.7469 (t70) cc_final: 0.7085 (t70) REVERT: B 461 PHE cc_start: 0.9130 (m-80) cc_final: 0.8410 (m-10) REVERT: B 737 MET cc_start: 0.8202 (tpt) cc_final: 0.7955 (tpt) REVERT: B 852 PHE cc_start: 0.7695 (m-10) cc_final: 0.7430 (m-10) REVERT: B 983 LYS cc_start: 0.9382 (mmpt) cc_final: 0.9122 (tppt) REVERT: C 462 GLU cc_start: 0.8922 (tp30) cc_final: 0.8068 (tm-30) REVERT: C 1047 MET cc_start: 0.7541 (ptm) cc_final: 0.7138 (ptm) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1600 time to fit residues: 43.1032 Evaluate side-chains 93 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.8980 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 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN B 318 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 759 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.118192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.074873 restraints weight = 60678.556| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 3.80 r_work: 0.3226 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 25862 Z= 0.161 Angle : 0.630 13.422 35334 Z= 0.314 Chirality : 0.046 0.343 4199 Planarity : 0.004 0.047 4424 Dihedral : 7.200 57.160 4887 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.49 % Favored : 94.38 % Rotamer: Outliers : 0.63 % Allowed : 5.88 % Favored : 93.49 % 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: -0.60 (0.15), residues: 3040 helix: 1.52 (0.21), residues: 678 sheet: -0.01 (0.19), residues: 680 loop : -1.42 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 354 TYR 0.015 0.001 TYR C1064 PHE 0.025 0.002 PHE A1118 TRP 0.009 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00371 (25749) covalent geometry : angle 0.60054 (35035) SS BOND : bond 0.00711 ( 40) SS BOND : angle 1.97455 ( 80) hydrogen bonds : bond 0.04655 ( 943) hydrogen bonds : angle 5.35423 ( 2574) link_BETA1-4 : bond 0.00564 ( 29) link_BETA1-4 : angle 1.63912 ( 87) link_NAG-ASN : bond 0.00429 ( 44) link_NAG-ASN : angle 2.50590 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7899 (t0) cc_final: 0.7655 (t0) REVERT: A 153 MET cc_start: 0.0191 (pmm) cc_final: -0.0123 (pmm) REVERT: A 335 PHE cc_start: 0.7926 (m-80) cc_final: 0.7353 (m-80) REVERT: A 962 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8779 (mp10) REVERT: A 985 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8187 (pm20) REVERT: A 1026 MET cc_start: 0.8023 (tpp) cc_final: 0.7700 (ttp) REVERT: B 453 PHE cc_start: 0.8561 (m-80) cc_final: 0.7826 (m-10) REVERT: B 461 PHE cc_start: 0.8968 (m-80) cc_final: 0.8367 (m-10) REVERT: B 983 LYS cc_start: 0.9418 (mmpt) cc_final: 0.9135 (tppt) REVERT: C 462 GLU cc_start: 0.8989 (tp30) cc_final: 0.8168 (tm-30) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.1454 time to fit residues: 30.5217 Evaluate side-chains 108 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 318 GLN Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 158 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 185 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 110 optimal weight: 9.9990 chunk 270 optimal weight: 0.9990 chunk 279 optimal weight: 0.7980 chunk 114 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.118573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.075206 restraints weight = 60383.434| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.85 r_work: 0.3231 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25862 Z= 0.126 Angle : 0.585 13.172 35334 Z= 0.288 Chirality : 0.044 0.332 4199 Planarity : 0.003 0.049 4424 Dihedral : 6.576 57.517 4887 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.56 % Favored : 94.31 % Rotamer: Outliers : 0.96 % Allowed : 8.28 % Favored : 90.76 % 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: -0.49 (0.15), residues: 3040 helix: 1.49 (0.21), residues: 684 sheet: 0.11 (0.19), residues: 704 loop : -1.36 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 354 TYR 0.012 0.001 TYR B1064 PHE 0.024 0.001 PHE A 389 TRP 0.010 0.001 TRP C 104 HIS 0.007 0.001 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00286 (25749) covalent geometry : angle 0.55598 (35035) SS BOND : bond 0.00340 ( 40) SS BOND : angle 1.80920 ( 80) hydrogen bonds : bond 0.04180 ( 943) hydrogen bonds : angle 5.12329 ( 2574) link_BETA1-4 : bond 0.00519 ( 29) link_BETA1-4 : angle 1.63987 ( 87) link_NAG-ASN : bond 0.00424 ( 44) link_NAG-ASN : angle 2.41031 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0256 (pmm) cc_final: -0.0082 (pmm) REVERT: A 335 PHE cc_start: 0.7969 (m-80) cc_final: 0.7464 (m-80) REVERT: A 875 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7762 (tt) REVERT: A 985 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8141 (pm20) REVERT: A 1026 MET cc_start: 0.7977 (tpp) cc_final: 0.7635 (ttp) REVERT: B 449 LEU cc_start: 0.8930 (pt) cc_final: 0.8314 (tt) REVERT: B 453 PHE cc_start: 0.8669 (m-80) cc_final: 0.8011 (m-10) REVERT: B 461 PHE cc_start: 0.8934 (m-80) cc_final: 0.8320 (m-10) REVERT: B 983 LYS cc_start: 0.9400 (mmpt) cc_final: 0.9158 (tppt) REVERT: B 1086 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7173 (m-80) REVERT: C 449 LEU cc_start: 0.9344 (tp) cc_final: 0.9139 (tp) REVERT: C 462 GLU cc_start: 0.8934 (tp30) cc_final: 0.8257 (tm-30) REVERT: C 722 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7881 (pt0) REVERT: C 931 ILE cc_start: 0.8540 (mm) cc_final: 0.8333 (mm) outliers start: 26 outliers final: 14 residues processed: 130 average time/residue: 0.1512 time to fit residues: 33.5773 Evaluate side-chains 113 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 1094 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 263 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 303 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 134 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 210 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1007 GLN A1020 ASN B 165 ASN B 242 HIS ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 GLN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1045 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.114184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072192 restraints weight = 61156.366| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 4.55 r_work: 0.3101 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.171 25862 Z= 0.346 Angle : 0.784 13.082 35334 Z= 0.397 Chirality : 0.051 0.319 4199 Planarity : 0.005 0.052 4424 Dihedral : 6.902 58.385 4887 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.50 % Favored : 92.37 % Rotamer: Outliers : 1.92 % Allowed : 11.24 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.15), residues: 3040 helix: 0.86 (0.20), residues: 676 sheet: -0.09 (0.19), residues: 696 loop : -1.73 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 902 TYR 0.035 0.002 TYR B 91 PHE 0.047 0.003 PHE A1118 TRP 0.011 0.002 TRP A 64 HIS 0.011 0.002 HIS B 242 Details of bonding type rmsd covalent geometry : bond 0.00824 (25749) covalent geometry : angle 0.75781 (35035) SS BOND : bond 0.00897 ( 40) SS BOND : angle 2.36876 ( 80) hydrogen bonds : bond 0.05759 ( 943) hydrogen bonds : angle 5.68014 ( 2574) link_BETA1-4 : bond 0.00472 ( 29) link_BETA1-4 : angle 1.72620 ( 87) link_NAG-ASN : bond 0.00441 ( 44) link_NAG-ASN : angle 2.62570 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 112 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0696 (pmm) cc_final: 0.0275 (mpp) REVERT: A 694 MET cc_start: 0.7998 (mtp) cc_final: 0.7712 (mpp) REVERT: A 875 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7299 (tt) REVERT: A 985 GLU cc_start: 0.8478 (pm20) cc_final: 0.8268 (pm20) REVERT: B 318 GLN cc_start: 0.8063 (mm-40) cc_final: 0.7562 (mm-40) REVERT: B 449 LEU cc_start: 0.9010 (pt) cc_final: 0.8415 (tt) REVERT: B 453 PHE cc_start: 0.8616 (m-80) cc_final: 0.7955 (m-80) REVERT: B 461 PHE cc_start: 0.8842 (m-80) cc_final: 0.8230 (m-10) REVERT: B 983 LYS cc_start: 0.9454 (mmpt) cc_final: 0.9148 (tppt) REVERT: B 1086 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7433 (m-10) REVERT: C 462 GLU cc_start: 0.8978 (tp30) cc_final: 0.8327 (tm-30) outliers start: 52 outliers final: 33 residues processed: 157 average time/residue: 0.1327 time to fit residues: 36.0286 Evaluate side-chains 134 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 653 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 722 GLU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1094 SER Chi-restraints excluded: chain C residue 1102 THR Chi-restraints excluded: chain C residue 1127 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 125 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 191 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 221 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 137 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 239 GLN ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.116999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.073857 restraints weight = 60335.007| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 3.75 r_work: 0.3200 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25862 Z= 0.125 Angle : 0.611 12.887 35334 Z= 0.301 Chirality : 0.045 0.322 4199 Planarity : 0.003 0.054 4424 Dihedral : 6.359 57.809 4887 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.69 % Favored : 94.18 % Rotamer: Outliers : 1.81 % Allowed : 12.31 % Favored : 85.88 % 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: -0.72 (0.15), residues: 3040 helix: 1.40 (0.21), residues: 667 sheet: 0.04 (0.20), residues: 691 loop : -1.55 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 354 TYR 0.013 0.001 TYR A 276 PHE 0.022 0.001 PHE A 389 TRP 0.014 0.001 TRP C 104 HIS 0.005 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00281 (25749) covalent geometry : angle 0.58107 (35035) SS BOND : bond 0.00517 ( 40) SS BOND : angle 2.23858 ( 80) hydrogen bonds : bond 0.04278 ( 943) hydrogen bonds : angle 5.25332 ( 2574) link_BETA1-4 : bond 0.00518 ( 29) link_BETA1-4 : angle 1.60611 ( 87) link_NAG-ASN : bond 0.00396 ( 44) link_NAG-ASN : angle 2.37381 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 102 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0406 (pmm) cc_final: -0.0037 (mpp) REVERT: A 875 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 985 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8154 (mp0) REVERT: A 1026 MET cc_start: 0.8024 (tpp) cc_final: 0.7522 (ttp) REVERT: B 318 GLN cc_start: 0.7976 (mm-40) cc_final: 0.7494 (mm-40) REVERT: B 449 LEU cc_start: 0.8985 (pt) cc_final: 0.8382 (tt) REVERT: B 453 PHE cc_start: 0.8634 (m-80) cc_final: 0.7988 (m-80) REVERT: B 461 PHE cc_start: 0.8901 (m-80) cc_final: 0.8281 (m-10) REVERT: B 983 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9145 (tppt) REVERT: B 1086 PHE cc_start: 0.7656 (OUTLIER) cc_final: 0.7249 (m-80) REVERT: B 1129 ILE cc_start: 0.7858 (OUTLIER) cc_final: 0.7642 (tp) REVERT: C 462 GLU cc_start: 0.8927 (tp30) cc_final: 0.8173 (tm-30) outliers start: 49 outliers final: 26 residues processed: 143 average time/residue: 0.1415 time to fit residues: 34.6773 Evaluate side-chains 128 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 98 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 486 TYR Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 303 optimal weight: 0.8980 chunk 250 optimal weight: 4.9990 chunk 180 optimal weight: 0.6980 chunk 46 optimal weight: 8.9990 chunk 174 optimal weight: 0.2980 chunk 58 optimal weight: 0.0070 chunk 102 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 140 optimal weight: 30.0000 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 962 GLN ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 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 = 0.4113 r_free = 0.4113 target = 0.129106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.085587 restraints weight = 59812.695| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.83 r_work: 0.3208 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25862 Z= 0.117 Angle : 0.590 13.099 35334 Z= 0.288 Chirality : 0.044 0.304 4199 Planarity : 0.003 0.053 4424 Dihedral : 6.030 57.663 4887 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.72 % Favored : 94.08 % Rotamer: Outliers : 1.81 % Allowed : 12.98 % Favored : 85.21 % 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: -0.59 (0.15), residues: 3040 helix: 1.55 (0.21), residues: 672 sheet: 0.06 (0.20), residues: 661 loop : -1.44 (0.15), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 214 TYR 0.012 0.001 TYR A1064 PHE 0.022 0.001 PHE A 389 TRP 0.013 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00265 (25749) covalent geometry : angle 0.56087 (35035) SS BOND : bond 0.00325 ( 40) SS BOND : angle 2.07185 ( 80) hydrogen bonds : bond 0.03924 ( 943) hydrogen bonds : angle 5.07089 ( 2574) link_BETA1-4 : bond 0.00517 ( 29) link_BETA1-4 : angle 1.60024 ( 87) link_NAG-ASN : bond 0.00404 ( 44) link_NAG-ASN : angle 2.30613 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 107 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0267 (pmm) cc_final: -0.0224 (mpp) REVERT: A 875 LEU cc_start: 0.8108 (OUTLIER) cc_final: 0.7884 (tt) REVERT: A 985 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8173 (mp0) REVERT: A 1026 MET cc_start: 0.8032 (tpp) cc_final: 0.7506 (ttp) REVERT: B 318 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7513 (mm-40) REVERT: B 449 LEU cc_start: 0.8895 (pt) cc_final: 0.8278 (tt) REVERT: B 453 PHE cc_start: 0.8471 (m-80) cc_final: 0.7946 (m-10) REVERT: B 461 PHE cc_start: 0.8655 (m-80) cc_final: 0.8166 (m-10) REVERT: B 983 LYS cc_start: 0.9458 (mmpt) cc_final: 0.9168 (tppt) REVERT: B 1086 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7329 (m-80) REVERT: C 462 GLU cc_start: 0.8940 (tp30) cc_final: 0.8170 (tm-30) REVERT: C 1086 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.7004 (m-80) outliers start: 49 outliers final: 37 residues processed: 147 average time/residue: 0.1373 time to fit residues: 35.1382 Evaluate side-chains 139 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 112 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 139 optimal weight: 9.9990 chunk 217 optimal weight: 6.9990 chunk 100 optimal weight: 0.8980 chunk 123 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.127033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.085019 restraints weight = 58614.075| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.52 r_work: 0.3137 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 25862 Z= 0.216 Angle : 0.656 12.979 35334 Z= 0.325 Chirality : 0.046 0.298 4199 Planarity : 0.004 0.053 4424 Dihedral : 6.189 58.069 4887 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.25 % Favored : 93.55 % Rotamer: Outliers : 2.14 % Allowed : 13.68 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.15), residues: 3040 helix: 1.32 (0.20), residues: 673 sheet: -0.03 (0.20), residues: 706 loop : -1.55 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 902 TYR 0.021 0.001 TYR B 91 PHE 0.035 0.002 PHE A1118 TRP 0.009 0.002 TRP C 64 HIS 0.008 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00513 (25749) covalent geometry : angle 0.62966 (35035) SS BOND : bond 0.00567 ( 40) SS BOND : angle 2.15672 ( 80) hydrogen bonds : bond 0.04628 ( 943) hydrogen bonds : angle 5.24696 ( 2574) link_BETA1-4 : bond 0.00507 ( 29) link_BETA1-4 : angle 1.62615 ( 87) link_NAG-ASN : bond 0.00379 ( 44) link_NAG-ASN : angle 2.35333 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 103 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0727 (pmm) cc_final: 0.0258 (mpp) REVERT: A 875 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7515 (tt) REVERT: A 985 GLU cc_start: 0.8377 (pm20) cc_final: 0.8176 (mp0) REVERT: A 1026 MET cc_start: 0.8164 (tpp) cc_final: 0.7625 (ttp) REVERT: B 318 GLN cc_start: 0.8026 (mm-40) cc_final: 0.7548 (mm-40) REVERT: B 449 LEU cc_start: 0.8957 (pt) cc_final: 0.8340 (tt) REVERT: B 453 PHE cc_start: 0.8656 (m-80) cc_final: 0.7984 (m-80) REVERT: B 461 PHE cc_start: 0.8867 (m-80) cc_final: 0.8296 (m-10) REVERT: B 983 LYS cc_start: 0.9456 (mmpt) cc_final: 0.9191 (tppt) REVERT: B 1086 PHE cc_start: 0.7983 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: C 462 GLU cc_start: 0.8963 (tp30) cc_final: 0.8233 (tm-30) REVERT: C 1047 MET cc_start: 0.8204 (ptm) cc_final: 0.7929 (ptm) outliers start: 58 outliers final: 39 residues processed: 151 average time/residue: 0.1246 time to fit residues: 33.3828 Evaluate side-chains 139 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 98 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 594 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 259 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 chunk 160 optimal weight: 0.9990 chunk 195 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 54 optimal weight: 0.8980 chunk 282 optimal weight: 0.9980 chunk 139 optimal weight: 10.0000 chunk 286 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1008 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 ASN ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.128772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086179 restraints weight = 59674.420| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 4.65 r_work: 0.3175 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25862 Z= 0.120 Angle : 0.592 13.015 35334 Z= 0.289 Chirality : 0.044 0.293 4199 Planarity : 0.003 0.054 4424 Dihedral : 5.964 57.762 4887 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.39 % Favored : 94.44 % Rotamer: Outliers : 2.18 % Allowed : 13.79 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.15), residues: 3040 helix: 1.50 (0.21), residues: 674 sheet: -0.01 (0.20), residues: 676 loop : -1.40 (0.15), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 354 TYR 0.013 0.001 TYR A1064 PHE 0.022 0.001 PHE A 389 TRP 0.013 0.001 TRP C 104 HIS 0.005 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00273 (25749) covalent geometry : angle 0.56492 (35035) SS BOND : bond 0.00344 ( 40) SS BOND : angle 1.98685 ( 80) hydrogen bonds : bond 0.03933 ( 943) hydrogen bonds : angle 5.05665 ( 2574) link_BETA1-4 : bond 0.00521 ( 29) link_BETA1-4 : angle 1.58619 ( 87) link_NAG-ASN : bond 0.00396 ( 44) link_NAG-ASN : angle 2.25779 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 101 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0708 (pmm) cc_final: 0.0265 (mpp) REVERT: A 310 TYR cc_start: 0.8389 (m-80) cc_final: 0.8068 (m-80) REVERT: A 875 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7669 (tt) REVERT: A 985 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: A 998 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 1026 MET cc_start: 0.8133 (tpp) cc_final: 0.7608 (ttp) REVERT: A 1086 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.7023 (m-80) REVERT: B 318 GLN cc_start: 0.8017 (mm-40) cc_final: 0.7524 (mm-40) REVERT: B 449 LEU cc_start: 0.8985 (pt) cc_final: 0.8400 (tt) REVERT: B 453 PHE cc_start: 0.8676 (m-80) cc_final: 0.8037 (m-80) REVERT: B 461 PHE cc_start: 0.8817 (m-80) cc_final: 0.8254 (m-10) REVERT: B 983 LYS cc_start: 0.9439 (mmpt) cc_final: 0.9173 (tppt) REVERT: B 1086 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: C 29 THR cc_start: 0.7326 (OUTLIER) cc_final: 0.7019 (p) REVERT: C 153 MET cc_start: 0.1127 (OUTLIER) cc_final: 0.0701 (ptp) REVERT: C 462 GLU cc_start: 0.8961 (tp30) cc_final: 0.8170 (tm-30) REVERT: C 1047 MET cc_start: 0.8148 (ptm) cc_final: 0.7860 (ptm) REVERT: C 1086 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.7033 (m-80) outliers start: 59 outliers final: 44 residues processed: 151 average time/residue: 0.1333 time to fit residues: 35.0825 Evaluate side-chains 152 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 100 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1086 PHE Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 146 optimal weight: 20.0000 chunk 303 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 231 optimal weight: 2.9990 chunk 131 optimal weight: 8.9990 chunk 237 optimal weight: 5.9990 chunk 5 optimal weight: 0.0980 chunk 282 optimal weight: 0.2980 chunk 218 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.128814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084867 restraints weight = 59464.729| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 4.00 r_work: 0.3191 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25862 Z= 0.126 Angle : 0.587 12.881 35334 Z= 0.287 Chirality : 0.044 0.293 4199 Planarity : 0.003 0.053 4424 Dihedral : 5.850 57.697 4887 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.62 % Favored : 94.21 % Rotamer: Outliers : 2.00 % Allowed : 13.94 % Favored : 84.07 % 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: -0.54 (0.15), residues: 3040 helix: 1.53 (0.21), residues: 675 sheet: 0.03 (0.20), residues: 659 loop : -1.36 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 354 TYR 0.013 0.001 TYR A1064 PHE 0.023 0.001 PHE B1118 TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00292 (25749) covalent geometry : angle 0.56013 (35035) SS BOND : bond 0.00341 ( 40) SS BOND : angle 1.95174 ( 80) hydrogen bonds : bond 0.03883 ( 943) hydrogen bonds : angle 4.99641 ( 2574) link_BETA1-4 : bond 0.00509 ( 29) link_BETA1-4 : angle 1.57850 ( 87) link_NAG-ASN : bond 0.00388 ( 44) link_NAG-ASN : angle 2.22713 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.0610 (pmm) cc_final: 0.0183 (mpp) REVERT: A 310 TYR cc_start: 0.8462 (m-80) cc_final: 0.8162 (m-80) REVERT: A 985 GLU cc_start: 0.8294 (pm20) cc_final: 0.8065 (mp0) REVERT: A 998 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8349 (mm) REVERT: A 1026 MET cc_start: 0.8124 (tpp) cc_final: 0.7562 (ttp) REVERT: B 318 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7484 (mm-40) REVERT: B 449 LEU cc_start: 0.8996 (pt) cc_final: 0.8387 (tt) REVERT: B 453 PHE cc_start: 0.8716 (m-80) cc_final: 0.8121 (m-80) REVERT: B 461 PHE cc_start: 0.8850 (m-80) cc_final: 0.8257 (m-10) REVERT: B 1086 PHE cc_start: 0.7693 (OUTLIER) cc_final: 0.7336 (m-80) REVERT: C 29 THR cc_start: 0.7392 (OUTLIER) cc_final: 0.7095 (p) REVERT: C 153 MET cc_start: 0.1482 (OUTLIER) cc_final: 0.0964 (ptp) REVERT: C 462 GLU cc_start: 0.8971 (tp30) cc_final: 0.8177 (tm-30) REVERT: C 985 GLU cc_start: 0.7934 (pm20) cc_final: 0.7640 (pm20) REVERT: C 1047 MET cc_start: 0.8130 (ptm) cc_final: 0.7904 (ptm) REVERT: C 1086 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.6987 (m-80) outliers start: 54 outliers final: 44 residues processed: 152 average time/residue: 0.1400 time to fit residues: 37.2344 Evaluate side-chains 147 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 98 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 866 MET Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1086 PHE Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 131 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 228 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 242 optimal weight: 9.9990 chunk 155 optimal weight: 0.2980 chunk 129 optimal weight: 7.9990 chunk 144 optimal weight: 20.0000 chunk 99 optimal weight: 2.9990 chunk 44 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.126664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082900 restraints weight = 60216.159| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.83 r_work: 0.3160 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 25862 Z= 0.236 Angle : 0.678 12.915 35334 Z= 0.336 Chirality : 0.047 0.289 4199 Planarity : 0.004 0.053 4424 Dihedral : 6.150 58.220 4887 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.61 % Favored : 93.19 % Rotamer: Outliers : 2.00 % Allowed : 14.23 % Favored : 83.77 % 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: -0.77 (0.15), residues: 3040 helix: 1.28 (0.20), residues: 672 sheet: -0.08 (0.20), residues: 700 loop : -1.51 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 343 TYR 0.022 0.002 TYR B 91 PHE 0.037 0.002 PHE A1118 TRP 0.013 0.002 TRP C 64 HIS 0.008 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00561 (25749) covalent geometry : angle 0.65336 (35035) SS BOND : bond 0.00543 ( 40) SS BOND : angle 2.16623 ( 80) hydrogen bonds : bond 0.04706 ( 943) hydrogen bonds : angle 5.26981 ( 2574) link_BETA1-4 : bond 0.00478 ( 29) link_BETA1-4 : angle 1.61511 ( 87) link_NAG-ASN : bond 0.00376 ( 44) link_NAG-ASN : angle 2.29971 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 106 time to evaluate : 0.913 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.0903 (pmm) cc_final: 0.0508 (mpp) REVERT: A 985 GLU cc_start: 0.8305 (pm20) cc_final: 0.8093 (mp0) REVERT: A 1026 MET cc_start: 0.8121 (tpp) cc_final: 0.7505 (ttp) REVERT: B 318 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7520 (mm-40) REVERT: B 449 LEU cc_start: 0.8747 (pt) cc_final: 0.8189 (tt) REVERT: B 452 LEU cc_start: 0.8828 (pt) cc_final: 0.8263 (pt) REVERT: B 453 PHE cc_start: 0.8561 (m-80) cc_final: 0.8020 (m-80) REVERT: B 461 PHE cc_start: 0.8596 (m-80) cc_final: 0.8118 (m-10) REVERT: B 1086 PHE cc_start: 0.7965 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: C 29 THR cc_start: 0.7356 (OUTLIER) cc_final: 0.7021 (p) REVERT: C 153 MET cc_start: 0.1524 (OUTLIER) cc_final: 0.1048 (ptp) REVERT: C 462 GLU cc_start: 0.8983 (tp30) cc_final: 0.8294 (tm-30) REVERT: C 985 GLU cc_start: 0.7910 (pm20) cc_final: 0.7664 (pm20) outliers start: 54 outliers final: 44 residues processed: 151 average time/residue: 0.1312 time to fit residues: 35.1287 Evaluate side-chains 150 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 103 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 366 TYR Chi-restraints excluded: chain A residue 392 VAL Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 852 PHE Chi-restraints excluded: chain A residue 863 THR Chi-restraints excluded: chain A residue 903 PHE Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 22 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 530 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 614 CYS Chi-restraints excluded: chain B residue 653 VAL Chi-restraints excluded: chain B residue 742 ASP Chi-restraints excluded: chain B residue 903 PHE Chi-restraints excluded: chain B residue 973 VAL Chi-restraints excluded: chain B residue 1086 PHE Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 153 MET Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 315 PHE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 509 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 737 MET Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 855 LEU Chi-restraints excluded: chain C residue 870 TYR Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 899 MET Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 263 optimal weight: 6.9990 chunk 227 optimal weight: 0.9980 chunk 252 optimal weight: 5.9990 chunk 273 optimal weight: 0.5980 chunk 184 optimal weight: 4.9990 chunk 185 optimal weight: 2.9990 chunk 165 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.128100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084711 restraints weight = 60104.227| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 4.51 r_work: 0.3157 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 25862 Z= 0.151 Angle : 0.617 12.954 35334 Z= 0.302 Chirality : 0.045 0.281 4199 Planarity : 0.003 0.053 4424 Dihedral : 6.006 57.914 4887 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.76 % Favored : 94.05 % Rotamer: Outliers : 1.81 % Allowed : 14.49 % Favored : 83.70 % 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: -0.66 (0.15), residues: 3040 helix: 1.41 (0.21), residues: 669 sheet: 0.01 (0.20), residues: 699 loop : -1.46 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 405 TYR 0.014 0.001 TYR B 276 PHE 0.024 0.001 PHE B1118 TRP 0.012 0.001 TRP C 104 HIS 0.004 0.001 HIS B1085 Details of bonding type rmsd covalent geometry : bond 0.00355 (25749) covalent geometry : angle 0.59132 (35035) SS BOND : bond 0.00401 ( 40) SS BOND : angle 2.00995 ( 80) hydrogen bonds : bond 0.04132 ( 943) hydrogen bonds : angle 5.11146 ( 2574) link_BETA1-4 : bond 0.00498 ( 29) link_BETA1-4 : angle 1.57554 ( 87) link_NAG-ASN : bond 0.00372 ( 44) link_NAG-ASN : angle 2.23076 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7734.14 seconds wall clock time: 132 minutes 33.67 seconds (7953.67 seconds total)