Starting phenix.real_space_refine on Thu Mar 5 19:33:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7edg_31070/03_2026/7edg_31070.cif Found real_map, /net/cci-nas-00/data/ceres_data/7edg_31070/03_2026/7edg_31070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7edg_31070/03_2026/7edg_31070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7edg_31070/03_2026/7edg_31070.map" model { file = "/net/cci-nas-00/data/ceres_data/7edg_31070/03_2026/7edg_31070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7edg_31070/03_2026/7edg_31070.cif" } resolution = 3.2 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= 0.054 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 108 5.16 5 C 15724 2.51 5 N 3999 2.21 5 O 4884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 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: 24715 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7922 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 51, 'TRANS': 963} Chain breaks: 7 Chain: "B" Number of atoms: 7811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1000, 7811 Classifications: {'peptide': 1000} Link IDs: {'PTRANS': 49, 'TRANS': 950} Chain breaks: 8 Chain: "C" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1008, 7879 Classifications: {'peptide': 1008} Link IDs: {'PTRANS': 50, 'TRANS': 957} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.40, per 1000 atoms: 0.22 Number of scatterers: 24715 At special positions: 0 Unit cell: (133.1, 141.9, 198, 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 108 16.00 O 4884 8.00 N 3999 7.00 C 15724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=35, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 163 " 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 614 " - pdb=" SG CYS A 646 " 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=2.04 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 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 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 163 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.04 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 614 " - pdb=" SG CYS C 646 " distance=2.03 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 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=2.03 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 E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 162 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 120 " " NAG B2003 " - " ASN B 162 " " NAG B2004 " - " ASN B 231 " " NAG B2005 " - " ASN B 328 " " NAG B2006 " - " ASN B 600 " " NAG B2007 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 120 " " NAG C2003 " - " ASN C 162 " " NAG C2004 " - " ASN C 231 " " NAG C2005 " - " ASN C 328 " " NAG C2006 " - " ASN C 600 " " NAG C2007 " - " ASN C 654 " " NAG D 1 " - " ASN A 120 " " NAG E 1 " - " ASN A 231 " " NAG F 1 " - " ASN A 279 " " NAG G 1 " - " ASN A 328 " " NAG H 1 " - " ASN A 340 " " NAG I 1 " - " ASN A 613 " " NAG J 1 " - " ASN A 706 " " NAG K 1 " - " ASN A 714 " " NAG L 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A1095 " " NAG O 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 613 " " NAG b 1 " - " ASN C 706 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 1.95 Conformation dependent library (CDL) restraints added in 1.1 seconds 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5662 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 42 sheets defined 24.3% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.818A pdb=" N LEU A 387 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 407 removed outlier: 3.661A pdb=" N GLN A 406 " --> pdb=" O ASP A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 543 Processing helix chain 'A' and resid 734 through 740 removed outlier: 3.655A pdb=" N TYR A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 744 through 751 Processing helix chain 'A' and resid 752 through 754 No H-bonds generated for 'chain 'A' and resid 752 through 754' Processing helix chain 'A' and resid 757 through 780 removed outlier: 3.768A pdb=" N ASP A 772 " --> pdb=" O ALA A 768 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 773 " --> pdb=" O VAL A 769 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR A 775 " --> pdb=" O GLN A 771 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL A 778 " --> pdb=" O ASN A 774 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE A 779 " --> pdb=" O THR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 822 Processing helix chain 'A' and resid 863 through 882 Processing helix chain 'A' and resid 894 through 905 Processing helix chain 'A' and resid 910 through 915 removed outlier: 3.784A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 915 " --> pdb=" O ASN A 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 910 through 915' Processing helix chain 'A' and resid 916 through 938 removed outlier: 3.659A pdb=" N ILE A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN A 932 " --> pdb=" O ILE A 928 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP A 933 " --> pdb=" O GLY A 929 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER A 934 " --> pdb=" O LYS A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 942 removed outlier: 3.988A pdb=" N LEU A 942 " --> pdb=" O ALA A 939 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 939 through 942' Processing helix chain 'A' and resid 946 through 962 Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.650A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 991 removed outlier: 3.975A pdb=" N GLU A 987 " --> pdb=" O PRO A 983 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N GLN A 989 " --> pdb=" O GLU A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 993 through 1030 removed outlier: 3.521A pdb=" N ARG A 997 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N GLN A 999 " --> pdb=" O THR A 995 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU A1014 " --> pdb=" O ILE A1010 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A1030 " --> pdb=" O MET A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 removed outlier: 4.415A pdb=" N GLU A1141 " --> pdb=" O PRO A1137 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 334 through 340 removed outlier: 3.951A pdb=" N VAL B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 367 Processing helix chain 'B' and resid 380 through 384 Processing helix chain 'B' and resid 402 through 407 removed outlier: 4.296A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 734 through 740 removed outlier: 3.510A pdb=" N TYR B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 743 through 751 Processing helix chain 'B' and resid 752 through 754 No H-bonds generated for 'chain 'B' and resid 752 through 754' Processing helix chain 'B' and resid 757 through 780 removed outlier: 3.660A pdb=" N PHE B 779 " --> pdb=" O THR B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.514A pdb=" N ASN B 821 " --> pdb=" O ASP B 817 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.532A pdb=" N ALA B 887 " --> pdb=" O THR B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 894 through 904 removed outlier: 3.627A pdb=" N ASN B 904 " --> pdb=" O ALA B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 907 No H-bonds generated for 'chain 'B' and resid 905 through 907' Processing helix chain 'B' and resid 910 through 915 removed outlier: 3.701A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.723A pdb=" N ILE B 931 " --> pdb=" O ALA B 927 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ASP B 933 " --> pdb=" O GLY B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 961 removed outlier: 3.533A pdb=" N GLN B 946 " --> pdb=" O LEU B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 965 Processing helix chain 'B' and resid 973 through 980 removed outlier: 3.514A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.452A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.940A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP B1143 " --> pdb=" O GLN B1139 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 334 through 340 removed outlier: 3.585A pdb=" N VAL C 338 " --> pdb=" O PRO C 334 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 367 Processing helix chain 'C' and resid 382 through 386 removed outlier: 4.139A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 382 through 386' Processing helix chain 'C' and resid 403 through 407 removed outlier: 3.524A pdb=" N ILE C 407 " --> pdb=" O VAL C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.546A pdb=" N TYR C 418 " --> pdb=" O LYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 502 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 752 through 754 No H-bonds generated for 'chain 'C' and resid 752 through 754' Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.821A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN C 761 " --> pdb=" O CYS C 757 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 762 " --> pdb=" O THR C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 822 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.586A pdb=" N ILE C 867 " --> pdb=" O THR C 863 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.604A pdb=" N ALA C 887 " --> pdb=" O THR C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 894 through 906 removed outlier: 3.694A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 915 removed outlier: 3.977A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 910 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 979 removed outlier: 3.587A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.527A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.827A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.794A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 188 " --> pdb=" O LYS A 203 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL A 190 " --> pdb=" O TYR A 201 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 199 " --> pdb=" O LYS A 192 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N SER A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) removed outlier: 9.625A pdb=" N HIS A 204 " --> pdb=" O LEU A 220 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N LEU A 220 " --> pdb=" O HIS A 204 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N VAL A 36 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.022A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N GLU C 321 " --> pdb=" O CYS C 535 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN C 537 " --> pdb=" O GLU C 321 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.724A pdb=" N THR A 271 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ASP A 287 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N LEU A 273 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LYS A 275 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.522A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.484A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 4.082A pdb=" N ASN A 351 " --> pdb=" O SER A 396 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER A 396 " --> pdb=" O ASN A 351 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 7.138A pdb=" N CYS A 358 " --> pdb=" O CYS A 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 removed outlier: 3.534A pdb=" N TYR A 470 " --> pdb=" O TYR A 486 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 562 through 563 removed outlier: 7.402A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.965A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N ILE A 667 " --> pdb=" O ILE A 663 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 698 through 699 removed outlier: 6.983A pdb=" N ALA A 698 " --> pdb=" O ILE B 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 708 through 712 removed outlier: 3.591A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 715 through 725 removed outlier: 3.564A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 731 through 732 Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1119 Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.677A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL B 264 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE B 200 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL B 224 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N SER B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.729A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 6.624A pdb=" N ILE B 323 " --> pdb=" O ASN B 539 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 removed outlier: 4.051A pdb=" N ASN B 391 " --> pdb=" O GLU B 513 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 430 " --> pdb=" O LYS B 375 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LYS B 375 " --> pdb=" O VAL B 430 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 562 through 563 removed outlier: 3.845A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.242A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 698 through 701 removed outlier: 6.551A pdb=" N ALA B 698 " --> pdb=" O ILE C 785 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N LYS C 787 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N ASN B 700 " --> pdb=" O LYS C 787 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 725 removed outlier: 3.607A pdb=" N GLY B1056 " --> pdb=" O ALA B1053 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B1047 " --> pdb=" O VAL B1062 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.521A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1073 through 1075 removed outlier: 4.004A pdb=" N ALA B1075 " --> pdb=" O PHE B1092 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE B1092 " --> pdb=" O ALA B1075 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.587A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.751A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N ASN C 61 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N TYR C 266 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N SER C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.721A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 82 through 83 removed outlier: 3.607A pdb=" N SER C 169 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 308 through 316 removed outlier: 7.034A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (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 388 through 389 removed outlier: 3.670A pdb=" N VAL C 521 " --> pdb=" O PHE C 389 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.935A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 708 through 725 removed outlier: 7.021A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 708 through 725 removed outlier: 7.021A pdb=" N GLN C1068 " --> pdb=" O ILE C 713 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N THR C1073 " --> pdb=" O SER C1094 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA C1075 " --> pdb=" O PHE C1092 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N PHE C1092 " --> pdb=" O ALA C1075 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.613A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1117 through 1119 removed outlier: 3.670A pdb=" N CYS C1079 " --> pdb=" O VAL C1130 " (cutoff:3.500A) 842 hydrogen bonds defined for protein. 2307 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 2.73 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: 7757 1.34 - 1.46: 6279 1.46 - 1.59: 11080 1.59 - 1.71: 1 1.71 - 1.83: 132 Bond restraints: 25249 Sorted by residual: bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.468 -0.062 2.00e-02 2.50e+03 9.61e+00 bond pdb=" N LYS B 851 " pdb=" CA LYS B 851 " ideal model delta sigma weight residual 1.461 1.428 0.033 1.47e-02 4.63e+03 4.98e+00 bond pdb=" CB PRO C 496 " pdb=" CG PRO C 496 " ideal model delta sigma weight residual 1.492 1.587 -0.095 5.00e-02 4.00e+02 3.64e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.60e+00 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.59e+00 ... (remaining 25244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 33931 2.58 - 5.16: 378 5.16 - 7.74: 30 7.74 - 10.33: 3 10.33 - 12.91: 4 Bond angle restraints: 34346 Sorted by residual: angle pdb=" N LYS B 851 " pdb=" CA LYS B 851 " pdb=" C LYS B 851 " ideal model delta sigma weight residual 108.54 119.93 -11.39 1.41e+00 5.03e-01 6.52e+01 angle pdb=" C THR C 205 " pdb=" N PRO C 206 " pdb=" CA PRO C 206 " ideal model delta sigma weight residual 119.84 127.91 -8.07 1.25e+00 6.40e-01 4.16e+01 angle pdb=" N THR C 205 " pdb=" CA THR C 205 " pdb=" C THR C 205 " ideal model delta sigma weight residual 109.81 122.72 -12.91 2.21e+00 2.05e-01 3.41e+01 angle pdb=" N VAL A 128 " pdb=" CA VAL A 128 " pdb=" C VAL A 128 " ideal model delta sigma weight residual 111.77 105.78 5.99 1.04e+00 9.25e-01 3.31e+01 angle pdb=" C GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 116.54 110.08 6.46 1.15e+00 7.56e-01 3.15e+01 ... (remaining 34341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.67: 14970 22.67 - 45.34: 874 45.34 - 68.00: 136 68.00 - 90.67: 41 90.67 - 113.34: 23 Dihedral angle restraints: 16044 sinusoidal: 7250 harmonic: 8794 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual 93.00 -179.83 -87.17 1 1.00e+01 1.00e-02 9.13e+01 dihedral pdb=" CB CYS A1029 " pdb=" SG CYS A1029 " pdb=" SG CYS A1040 " pdb=" CB CYS A1040 " ideal model delta sinusoidal sigma weight residual -86.00 -172.82 86.82 1 1.00e+01 1.00e-02 9.07e+01 dihedral pdb=" CB CYS B 659 " pdb=" SG CYS B 659 " pdb=" SG CYS B 668 " pdb=" CB CYS B 668 " ideal model delta sinusoidal sigma weight residual 93.00 176.82 -83.82 1 1.00e+01 1.00e-02 8.57e+01 ... (remaining 16041 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 4054 0.116 - 0.233: 70 0.233 - 0.349: 8 0.349 - 0.465: 2 0.465 - 0.581: 1 Chirality restraints: 4135 Sorted by residual: chirality pdb=" C1 NAG Z 1 " pdb=" ND2 ASN C 340 " pdb=" C2 NAG Z 1 " pdb=" O5 NAG Z 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.82 -0.58 2.00e-01 2.50e+01 8.45e+00 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN C1071 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.26e+00 chirality pdb=" C1 NAG B2002 " pdb=" ND2 ASN B 120 " pdb=" C2 NAG B2002 " pdb=" O5 NAG B2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.05e+00 ... (remaining 4132 not shown) Planarity restraints: 4384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 408 " -0.059 5.00e-02 4.00e+02 8.97e-02 1.29e+01 pdb=" N PRO A 409 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 205 " -0.056 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO C 206 " 0.144 5.00e-02 4.00e+02 pdb=" CA PRO C 206 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 206 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN C 495 " -0.052 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO C 496 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO C 496 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 496 " -0.042 5.00e-02 4.00e+02 ... (remaining 4381 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 2 2.07 - 2.78: 4946 2.78 - 3.48: 31737 3.48 - 4.19: 51599 4.19 - 4.90: 93286 Nonbonded interactions: 181570 Sorted by model distance: nonbonded pdb=" CA ASN C 185 " pdb=" CG2 THR C 205 " model vdw 1.362 3.890 nonbonded pdb=" CB ASN C 185 " pdb=" CG2 THR C 205 " model vdw 1.686 3.860 nonbonded pdb=" CB ASN C 185 " pdb=" OG1 THR C 205 " model vdw 2.079 3.440 nonbonded pdb=" O LEU C 186 " pdb=" O HIS C 204 " model vdw 2.156 3.040 nonbonded pdb=" O PHE B 131 " pdb=" OG SER B 158 " model vdw 2.164 3.040 ... (remaining 181565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 138 or resid 159 through 170 or resid 184 throu \ gh 206 or resid 215 through 240 or resid 262 through 617 or resid 638 through 67 \ 2 or resid 688 through 1143 or resid 2001 through 2004)) selection = (chain 'B' and (resid 27 through 138 or resid 159 through 170 or resid 184 throu \ gh 617 or resid 638 through 824 or resid 846 through 1143 or resid 2002 through \ 2005)) selection = (chain 'C' and (resid 27 through 138 or resid 158 or resid 160 through 170 or re \ sid 184 through 206 or resid 215 through 260 or resid 262 through 841 or resid 8 \ 48 through 1143 or resid 2002 through 2005)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.760 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 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 : 0.004 0.095 25363 Z= 0.202 Angle : 0.721 12.907 34653 Z= 0.360 Chirality : 0.050 0.581 4135 Planarity : 0.005 0.090 4336 Dihedral : 14.761 113.340 10277 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.73 % Favored : 92.90 % Rotamer: Outliers : 0.45 % Allowed : 0.34 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.16), residues: 2971 helix: 1.36 (0.23), residues: 622 sheet: 0.06 (0.20), residues: 663 loop : -1.88 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1104 TYR 0.015 0.001 TYR A1064 PHE 0.028 0.001 PHE A 903 TRP 0.030 0.002 TRP C 64 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00422 (25249) covalent geometry : angle 0.67919 (34346) SS BOND : bond 0.00428 ( 35) SS BOND : angle 1.55957 ( 70) hydrogen bonds : bond 0.14927 ( 837) hydrogen bonds : angle 6.11365 ( 2307) link_BETA1-4 : bond 0.00584 ( 31) link_BETA1-4 : angle 2.24945 ( 93) link_NAG-ASN : bond 0.00485 ( 48) link_NAG-ASN : angle 3.28062 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 0.757 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.7293 (mtt-85) cc_final: 0.7021 (mtt-85) REVERT: B 28 TYR cc_start: 0.6854 (m-10) cc_final: 0.6625 (m-10) REVERT: C 348 TYR cc_start: 0.8411 (p90) cc_final: 0.8125 (p90) REVERT: C 505 TYR cc_start: 0.7734 (m-80) cc_final: 0.7408 (m-80) outliers start: 12 outliers final: 1 residues processed: 165 average time/residue: 0.1472 time to fit residues: 40.1275 Evaluate side-chains 115 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 114 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 132 GLN ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 478 ASN B 484 ASN B 999 GLN ** C 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 391 ASN C 911 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.166714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.118132 restraints weight = 39950.267| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 3.30 r_work: 0.3554 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25363 Z= 0.141 Angle : 0.638 13.050 34653 Z= 0.310 Chirality : 0.047 0.445 4135 Planarity : 0.005 0.101 4336 Dihedral : 9.636 95.845 4889 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.50 % Favored : 93.23 % Rotamer: Outliers : 0.68 % Allowed : 6.14 % Favored : 93.18 % 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: -0.88 (0.16), residues: 2971 helix: 1.46 (0.22), residues: 660 sheet: 0.11 (0.20), residues: 691 loop : -1.87 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 187 TYR 0.020 0.001 TYR C 901 PHE 0.020 0.001 PHE A1118 TRP 0.021 0.001 TRP C 64 HIS 0.008 0.001 HIS C 204 Details of bonding type rmsd covalent geometry : bond 0.00327 (25249) covalent geometry : angle 0.60061 (34346) SS BOND : bond 0.00446 ( 35) SS BOND : angle 1.47256 ( 70) hydrogen bonds : bond 0.05510 ( 837) hydrogen bonds : angle 5.00254 ( 2307) link_BETA1-4 : bond 0.00617 ( 31) link_BETA1-4 : angle 2.05001 ( 93) link_NAG-ASN : bond 0.00392 ( 48) link_NAG-ASN : angle 2.88023 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: A 187 ARG cc_start: 0.8018 (mtt-85) cc_final: 0.7697 (mtt-85) REVERT: C 348 TYR cc_start: 0.8494 (p90) cc_final: 0.8209 (p90) REVERT: C 362 TYR cc_start: 0.8332 (m-80) cc_final: 0.8108 (m-80) REVERT: C 901 TYR cc_start: 0.7577 (m-10) cc_final: 0.7003 (m-10) outliers start: 18 outliers final: 14 residues processed: 138 average time/residue: 0.1442 time to fit residues: 33.8078 Evaluate side-chains 128 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1024 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 173 optimal weight: 0.9980 chunk 169 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 148 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 253 optimal weight: 2.9990 chunk 40 optimal weight: 30.0000 chunk 294 optimal weight: 0.8980 chunk 216 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 419 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 910 GLN B 999 GLN C 391 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.165427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.116540 restraints weight = 39994.534| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 3.33 r_work: 0.3739 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3584 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 25363 Z= 0.154 Angle : 0.627 12.926 34653 Z= 0.304 Chirality : 0.047 0.427 4135 Planarity : 0.004 0.106 4336 Dihedral : 8.909 93.687 4887 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.29 % Favored : 93.47 % Rotamer: Outliers : 1.10 % Allowed : 8.68 % Favored : 90.22 % 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: -0.89 (0.16), residues: 2971 helix: 1.44 (0.22), residues: 671 sheet: 0.04 (0.19), residues: 695 loop : -1.86 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1036 TYR 0.018 0.001 TYR A1064 PHE 0.021 0.001 PHE A1118 TRP 0.020 0.001 TRP C 64 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00368 (25249) covalent geometry : angle 0.58773 (34346) SS BOND : bond 0.00525 ( 35) SS BOND : angle 1.48179 ( 70) hydrogen bonds : bond 0.05702 ( 837) hydrogen bonds : angle 4.84619 ( 2307) link_BETA1-4 : bond 0.00540 ( 31) link_BETA1-4 : angle 2.10363 ( 93) link_NAG-ASN : bond 0.00358 ( 48) link_NAG-ASN : angle 2.85535 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 120 time to evaluate : 0.808 Fit side-chains REVERT: B 875 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8200 (tt) REVERT: C 268 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: C 321 GLU cc_start: 0.7310 (OUTLIER) cc_final: 0.6976 (tp30) REVERT: C 348 TYR cc_start: 0.8587 (p90) cc_final: 0.8284 (p90) REVERT: C 505 TYR cc_start: 0.7910 (m-80) cc_final: 0.7637 (m-80) REVERT: C 901 TYR cc_start: 0.7815 (m-10) cc_final: 0.7480 (m-10) outliers start: 29 outliers final: 20 residues processed: 144 average time/residue: 0.1400 time to fit residues: 34.5589 Evaluate side-chains 133 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 294 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 20.0000 chunk 128 optimal weight: 9.9990 chunk 145 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 227 optimal weight: 8.9990 chunk 225 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 14 optimal weight: 0.3980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 419 ASN B 910 GLN B 999 GLN C 391 ASN C 910 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.165035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.115688 restraints weight = 39828.501| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 3.63 r_work: 0.3518 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 25363 Z= 0.136 Angle : 0.607 12.647 34653 Z= 0.294 Chirality : 0.046 0.414 4135 Planarity : 0.004 0.111 4336 Dihedral : 8.237 89.435 4887 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.53 % Favored : 93.23 % Rotamer: Outliers : 1.86 % Allowed : 10.31 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.84 (0.16), residues: 2971 helix: 1.52 (0.22), residues: 665 sheet: 0.08 (0.20), residues: 696 loop : -1.85 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 325 TYR 0.017 0.001 TYR A1064 PHE 0.018 0.001 PHE A1118 TRP 0.017 0.001 TRP C 64 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00321 (25249) covalent geometry : angle 0.56870 (34346) SS BOND : bond 0.00415 ( 35) SS BOND : angle 1.41194 ( 70) hydrogen bonds : bond 0.05386 ( 837) hydrogen bonds : angle 4.71560 ( 2307) link_BETA1-4 : bond 0.00553 ( 31) link_BETA1-4 : angle 2.11349 ( 93) link_NAG-ASN : bond 0.00360 ( 48) link_NAG-ASN : angle 2.76973 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 122 time to evaluate : 0.790 Fit side-chains REVERT: A 999 GLN cc_start: 0.7855 (OUTLIER) cc_final: 0.7419 (mp10) REVERT: B 728 MET cc_start: 0.8806 (ptt) cc_final: 0.8594 (ptt) REVERT: B 875 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8151 (tt) REVERT: C 268 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: C 321 GLU cc_start: 0.7344 (OUTLIER) cc_final: 0.6928 (tp30) REVERT: C 348 TYR cc_start: 0.8668 (p90) cc_final: 0.8336 (p90) REVERT: C 505 TYR cc_start: 0.7838 (m-80) cc_final: 0.7593 (m-80) REVERT: C 560 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7208 (mt0) REVERT: C 901 TYR cc_start: 0.7800 (m-10) cc_final: 0.7532 (m-10) outliers start: 49 outliers final: 32 residues processed: 162 average time/residue: 0.1304 time to fit residues: 36.9588 Evaluate side-chains 150 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 113 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1142 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 288 optimal weight: 0.7980 chunk 292 optimal weight: 0.6980 chunk 143 optimal weight: 3.9990 chunk 117 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 70 optimal weight: 0.2980 chunk 289 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 299 optimal weight: 0.0370 chunk 221 optimal weight: 0.8980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 910 GLN B 911 ASN B 999 GLN C 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.166127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.116534 restraints weight = 39718.263| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.41 r_work: 0.3543 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.075 25363 Z= 0.108 Angle : 0.590 12.526 34653 Z= 0.283 Chirality : 0.045 0.405 4135 Planarity : 0.004 0.114 4336 Dihedral : 7.701 85.634 4887 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.82 % Favored : 93.94 % Rotamer: Outliers : 1.78 % Allowed : 11.75 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.16), residues: 2971 helix: 1.61 (0.22), residues: 666 sheet: 0.14 (0.19), residues: 705 loop : -1.79 (0.15), residues: 1600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.016 0.001 TYR B1064 PHE 0.014 0.001 PHE A 165 TRP 0.013 0.001 TRP C 64 HIS 0.003 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00242 (25249) covalent geometry : angle 0.55081 (34346) SS BOND : bond 0.00366 ( 35) SS BOND : angle 1.29002 ( 70) hydrogen bonds : bond 0.04883 ( 837) hydrogen bonds : angle 4.61303 ( 2307) link_BETA1-4 : bond 0.00572 ( 31) link_BETA1-4 : angle 2.11197 ( 93) link_NAG-ASN : bond 0.00379 ( 48) link_NAG-ASN : angle 2.76141 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 123 time to evaluate : 0.862 Fit side-chains REVERT: A 999 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7375 (mp10) REVERT: B 238 LEU cc_start: 0.5304 (mt) cc_final: 0.5074 (pp) REVERT: B 875 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8136 (tt) REVERT: C 268 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7372 (tt0) REVERT: C 321 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: C 348 TYR cc_start: 0.8675 (p90) cc_final: 0.8387 (p90) REVERT: C 505 TYR cc_start: 0.7816 (m-80) cc_final: 0.7578 (m-80) REVERT: C 560 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7955 (mp10) outliers start: 47 outliers final: 30 residues processed: 163 average time/residue: 0.1266 time to fit residues: 36.1895 Evaluate side-chains 151 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 116 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 735 CYS Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 321 GLU Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 31 optimal weight: 20.0000 chunk 81 optimal weight: 1.9990 chunk 272 optimal weight: 0.1980 chunk 8 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 147 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 39 optimal weight: 0.0270 overall best weight: 0.8240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 999 GLN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.165448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.116348 restraints weight = 39867.252| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.27 r_work: 0.3533 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25363 Z= 0.125 Angle : 0.585 11.884 34653 Z= 0.284 Chirality : 0.045 0.397 4135 Planarity : 0.004 0.117 4336 Dihedral : 7.076 88.323 4887 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.19 % Favored : 93.57 % Rotamer: Outliers : 2.01 % Allowed : 12.66 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.75 (0.16), residues: 2971 helix: 1.55 (0.22), residues: 674 sheet: 0.13 (0.19), residues: 705 loop : -1.80 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 325 TYR 0.017 0.001 TYR A1064 PHE 0.018 0.001 PHE A1118 TRP 0.015 0.001 TRP C 64 HIS 0.004 0.001 HIS C1080 Details of bonding type rmsd covalent geometry : bond 0.00293 (25249) covalent geometry : angle 0.54756 (34346) SS BOND : bond 0.00412 ( 35) SS BOND : angle 1.35269 ( 70) hydrogen bonds : bond 0.05050 ( 837) hydrogen bonds : angle 4.56408 ( 2307) link_BETA1-4 : bond 0.00573 ( 31) link_BETA1-4 : angle 2.10422 ( 93) link_NAG-ASN : bond 0.00355 ( 48) link_NAG-ASN : angle 2.67102 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 119 time to evaluate : 0.875 Fit side-chains REVERT: A 999 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: A 1142 LEU cc_start: 0.8403 (tt) cc_final: 0.8139 (tp) REVERT: B 875 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8171 (tt) REVERT: C 268 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: C 348 TYR cc_start: 0.8729 (p90) cc_final: 0.8413 (p90) REVERT: C 560 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7301 (mt0) REVERT: C 901 TYR cc_start: 0.7571 (m-10) cc_final: 0.7110 (m-80) outliers start: 53 outliers final: 35 residues processed: 163 average time/residue: 0.1268 time to fit residues: 36.4360 Evaluate side-chains 152 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 113 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 36 optimal weight: 30.0000 chunk 25 optimal weight: 0.0070 chunk 196 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1055 HIS B 999 GLN C 85 ASN C 391 ASN C 748 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.165368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.114527 restraints weight = 39808.222| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 3.49 r_work: 0.3525 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 25363 Z= 0.125 Angle : 0.587 11.634 34653 Z= 0.283 Chirality : 0.045 0.387 4135 Planarity : 0.004 0.118 4336 Dihedral : 6.766 78.141 4887 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.96 % Favored : 93.84 % Rotamer: Outliers : 2.12 % Allowed : 12.93 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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 (0.16), residues: 2971 helix: 1.54 (0.22), residues: 681 sheet: 0.17 (0.19), residues: 699 loop : -1.77 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 325 TYR 0.016 0.001 TYR A1064 PHE 0.017 0.001 PHE A1118 TRP 0.014 0.001 TRP C 64 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00295 (25249) covalent geometry : angle 0.55062 (34346) SS BOND : bond 0.00388 ( 35) SS BOND : angle 1.30913 ( 70) hydrogen bonds : bond 0.05070 ( 837) hydrogen bonds : angle 4.50420 ( 2307) link_BETA1-4 : bond 0.00558 ( 31) link_BETA1-4 : angle 2.06740 ( 93) link_NAG-ASN : bond 0.00357 ( 48) link_NAG-ASN : angle 2.62692 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 118 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: A 999 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7407 (mp10) REVERT: B 875 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8125 (tt) REVERT: B 1104 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7819 (tpp80) REVERT: C 197 TYR cc_start: 0.7801 (m-10) cc_final: 0.7378 (m-80) REVERT: C 268 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7344 (tt0) REVERT: C 348 TYR cc_start: 0.8727 (p90) cc_final: 0.8424 (p90) REVERT: C 560 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7267 (mt0) outliers start: 56 outliers final: 41 residues processed: 168 average time/residue: 0.1311 time to fit residues: 38.5789 Evaluate side-chains 160 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1104 ARG Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 391 ASN Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 41 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 252 optimal weight: 0.0770 chunk 82 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 chunk 244 optimal weight: 1.9990 chunk 126 optimal weight: 10.0000 chunk 142 optimal weight: 8.9990 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 ASN B 999 GLN C 85 ASN C 391 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.164426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.113633 restraints weight = 39802.280| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.44 r_work: 0.3509 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25363 Z= 0.152 Angle : 0.605 11.569 34653 Z= 0.294 Chirality : 0.046 0.385 4135 Planarity : 0.004 0.119 4336 Dihedral : 6.662 71.869 4887 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 2.12 % Allowed : 13.12 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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 (0.16), residues: 2971 helix: 1.50 (0.21), residues: 682 sheet: 0.13 (0.19), residues: 702 loop : -1.79 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.018 0.001 TYR A1064 PHE 0.022 0.001 PHE A1118 TRP 0.015 0.001 TRP C 64 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00365 (25249) covalent geometry : angle 0.56945 (34346) SS BOND : bond 0.00486 ( 35) SS BOND : angle 1.38076 ( 70) hydrogen bonds : bond 0.05430 ( 837) hydrogen bonds : angle 4.54375 ( 2307) link_BETA1-4 : bond 0.00553 ( 31) link_BETA1-4 : angle 2.07240 ( 93) link_NAG-ASN : bond 0.00350 ( 48) link_NAG-ASN : angle 2.65171 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 119 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 999 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7470 (mp10) REVERT: B 640 PHE cc_start: 0.7676 (t80) cc_final: 0.7117 (t80) REVERT: B 728 MET cc_start: 0.8815 (ptt) cc_final: 0.8606 (ptt) REVERT: B 875 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8188 (tt) REVERT: B 1104 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7814 (tpp80) REVERT: C 125 VAL cc_start: 0.7735 (m) cc_final: 0.7345 (p) REVERT: C 197 TYR cc_start: 0.7827 (m-10) cc_final: 0.7432 (m-80) REVERT: C 268 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: C 348 TYR cc_start: 0.8756 (p90) cc_final: 0.8488 (p90) REVERT: C 560 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7289 (mt0) outliers start: 56 outliers final: 40 residues processed: 167 average time/residue: 0.1380 time to fit residues: 39.9196 Evaluate side-chains 160 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 115 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1104 ARG Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 142 optimal weight: 9.9990 chunk 24 optimal weight: 0.1980 chunk 245 optimal weight: 1.9990 chunk 226 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 242 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 289 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 999 GLN C 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.163805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.112671 restraints weight = 40018.187| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.52 r_work: 0.3504 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 25363 Z= 0.157 Angle : 0.615 11.735 34653 Z= 0.299 Chirality : 0.046 0.378 4135 Planarity : 0.004 0.120 4336 Dihedral : 6.484 59.939 4887 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.36 % Favored : 93.47 % Rotamer: Outliers : 2.08 % Allowed : 13.27 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.78 (0.16), residues: 2971 helix: 1.47 (0.21), residues: 686 sheet: 0.11 (0.19), residues: 704 loop : -1.81 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 325 TYR 0.020 0.001 TYR C 418 PHE 0.022 0.001 PHE C1118 TRP 0.015 0.001 TRP C 64 HIS 0.005 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00375 (25249) covalent geometry : angle 0.58001 (34346) SS BOND : bond 0.00441 ( 35) SS BOND : angle 1.41355 ( 70) hydrogen bonds : bond 0.05658 ( 837) hydrogen bonds : angle 4.57474 ( 2307) link_BETA1-4 : bond 0.00543 ( 31) link_BETA1-4 : angle 2.07378 ( 93) link_NAG-ASN : bond 0.00354 ( 48) link_NAG-ASN : angle 2.67130 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 116 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 999 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7534 (mp10) REVERT: B 640 PHE cc_start: 0.7738 (t80) cc_final: 0.7259 (t80) REVERT: B 875 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8196 (tt) REVERT: B 1104 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7407 (mpp80) REVERT: C 125 VAL cc_start: 0.7769 (m) cc_final: 0.7372 (p) REVERT: C 197 TYR cc_start: 0.7818 (m-10) cc_final: 0.7423 (m-80) REVERT: C 268 GLN cc_start: 0.7640 (OUTLIER) cc_final: 0.7418 (tt0) REVERT: C 362 TYR cc_start: 0.8451 (m-80) cc_final: 0.8166 (m-80) REVERT: C 505 TYR cc_start: 0.7893 (m-80) cc_final: 0.7654 (m-80) REVERT: C 560 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7251 (mt0) outliers start: 55 outliers final: 43 residues processed: 163 average time/residue: 0.1362 time to fit residues: 38.7289 Evaluate side-chains 162 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 114 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1104 ARG Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 268 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 475 THR Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 140 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 272 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 240 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 910 GLN B 999 GLN C 85 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.164715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.111403 restraints weight = 39755.907| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 3.04 r_work: 0.3534 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 25363 Z= 0.128 Angle : 0.598 11.757 34653 Z= 0.289 Chirality : 0.045 0.375 4135 Planarity : 0.004 0.121 4336 Dihedral : 6.245 57.681 4887 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.40 % Favored : 93.47 % Rotamer: Outliers : 2.01 % Allowed : 13.42 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.68 % 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: -0.70 (0.16), residues: 2971 helix: 1.52 (0.22), residues: 682 sheet: 0.15 (0.19), residues: 702 loop : -1.74 (0.15), residues: 1587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 454 TYR 0.017 0.001 TYR A1064 PHE 0.018 0.001 PHE A1118 TRP 0.013 0.001 TRP C 64 HIS 0.004 0.001 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00301 (25249) covalent geometry : angle 0.56325 (34346) SS BOND : bond 0.00394 ( 35) SS BOND : angle 1.31376 ( 70) hydrogen bonds : bond 0.05209 ( 837) hydrogen bonds : angle 4.51966 ( 2307) link_BETA1-4 : bond 0.00571 ( 31) link_BETA1-4 : angle 2.07979 ( 93) link_NAG-ASN : bond 0.00374 ( 48) link_NAG-ASN : angle 2.61376 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5942 Ramachandran restraints generated. 2971 Oldfield, 0 Emsley, 2971 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 121 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: A 999 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: B 383 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7936 (tttt) REVERT: B 640 PHE cc_start: 0.7700 (t80) cc_final: 0.7228 (t80) REVERT: B 875 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8164 (tt) REVERT: C 125 VAL cc_start: 0.7737 (m) cc_final: 0.7349 (p) REVERT: C 197 TYR cc_start: 0.7781 (m-10) cc_final: 0.7419 (m-80) REVERT: C 362 TYR cc_start: 0.8454 (m-80) cc_final: 0.8177 (m-80) REVERT: C 505 TYR cc_start: 0.7839 (m-80) cc_final: 0.7608 (m-80) REVERT: C 560 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7298 (mt0) REVERT: C 901 TYR cc_start: 0.7564 (m-10) cc_final: 0.7252 (m-80) outliers start: 53 outliers final: 44 residues processed: 166 average time/residue: 0.1351 time to fit residues: 38.8599 Evaluate side-chains 163 residues out of total 2638 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 205 THR Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 974 LEU Chi-restraints excluded: chain A residue 999 GLN Chi-restraints excluded: chain A residue 1101 VAL Chi-restraints excluded: chain A residue 1119 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 567 ASP Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 912 VAL Chi-restraints excluded: chain B residue 913 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 970 ILE Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1104 ARG Chi-restraints excluded: chain B residue 1135 TYR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 93 THR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 333 CYS Chi-restraints excluded: chain C residue 424 ASP Chi-restraints excluded: chain C residue 480 VAL Chi-restraints excluded: chain C residue 521 VAL Chi-restraints excluded: chain C residue 522 CYS Chi-restraints excluded: chain C residue 560 GLN Chi-restraints excluded: chain C residue 581 ILE Chi-restraints excluded: chain C residue 660 ASP Chi-restraints excluded: chain C residue 670 SER Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 777 GLU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 974 LEU Chi-restraints excluded: chain C residue 1079 CYS Chi-restraints excluded: chain C residue 1119 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 244 optimal weight: 0.0070 chunk 255 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 45 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 236 optimal weight: 0.0170 chunk 69 optimal weight: 0.7980 chunk 294 optimal weight: 0.3980 chunk 179 optimal weight: 3.9990 overall best weight: 0.3436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 910 GLN B 999 GLN C 85 ASN C 759 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.166661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.117925 restraints weight = 39958.854| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 3.47 r_work: 0.3550 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 25363 Z= 0.100 Angle : 0.570 11.726 34653 Z= 0.275 Chirality : 0.044 0.363 4135 Planarity : 0.004 0.120 4336 Dihedral : 5.864 58.451 4887 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.52 % Favored : 94.31 % Rotamer: Outliers : 1.82 % Allowed : 13.84 % Favored : 84.34 % 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 (0.16), residues: 2971 helix: 1.70 (0.22), residues: 677 sheet: 0.21 (0.20), residues: 672 loop : -1.64 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 454 TYR 0.015 0.001 TYR B1064 PHE 0.012 0.001 PHE A 165 TRP 0.009 0.001 TRP B 433 HIS 0.002 0.000 HIS C1085 Details of bonding type rmsd covalent geometry : bond 0.00222 (25249) covalent geometry : angle 0.53615 (34346) SS BOND : bond 0.00345 ( 35) SS BOND : angle 1.12408 ( 70) hydrogen bonds : bond 0.04321 ( 837) hydrogen bonds : angle 4.39140 ( 2307) link_BETA1-4 : bond 0.00615 ( 31) link_BETA1-4 : angle 2.07757 ( 93) link_NAG-ASN : bond 0.00415 ( 48) link_NAG-ASN : angle 2.49240 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6036.96 seconds wall clock time: 103 minutes 54.51 seconds (6234.51 seconds total)