Starting phenix.real_space_refine on Thu Mar 5 21:44:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7r_31779/03_2026/7v7r_31779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7r_31779/03_2026/7v7r_31779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7r_31779/03_2026/7v7r_31779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7r_31779/03_2026/7v7r_31779.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7r_31779/03_2026/7v7r_31779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7r_31779/03_2026/7v7r_31779.cif" } resolution = 2.9 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= -0.002 sd= 0.039 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 16108 2.51 5 N 4127 2.21 5 O 5019 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 25362 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8074 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 54, 'TRANS': 978} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" 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 Time building chain proxies: 5.46, per 1000 atoms: 0.22 Number of scatterers: 25362 At special positions: 0 Unit cell: (139.7, 144.1, 196.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5019 8.00 N 4127 7.00 C 16108 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.05 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 341 " " NAG J 1 " - " ASN A 614 " " NAG K 1 " - " ASN A 707 " " NAG L 1 " - " ASN A 715 " " NAG M 1 " - " ASN A 799 " " NAG N 1 " - " ASN A1072 " " NAG O 1 " - " ASN A1096 " " NAG P 1 " - " ASN A1132 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 163 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 991.1 milliseconds 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5800 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 45 sheets defined 25.1% alpha, 26.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.542A pdb=" N GLU A 296 " --> pdb=" O ASP A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 383 through 387 removed outlier: 4.178A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.730A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.595A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 896 through 906 removed outlier: 3.787A pdb=" N TYR A 902 " --> pdb=" O MET A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.256A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.677A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.981A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.570A pdb=" N PHE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.139A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 388 removed outlier: 4.379A pdb=" N ASN B 386 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU B 388 " --> pdb=" O LEU B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.100A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.567A pdb=" N SER B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.806A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.536A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.530A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.054A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.569A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.589A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.363A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.957A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.666A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.640A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.983A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.593A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.557A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 4.106A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.154A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.856A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.731A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.091A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.229A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU A 132 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLN A 134 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ALA A 161 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.489A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.681A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.079A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.065A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.613A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.565A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 4.547A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.995A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.570A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.313A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.108A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.185A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.155A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.903A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.023A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.429A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.308A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.197A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 702 removed outlier: 3.576A pdb=" N LYS C 788 " --> pdb=" O ASN B 701 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 717 removed outlier: 6.043A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 712 through 717 removed outlier: 6.043A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.459A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1074 through 1076 removed outlier: 4.073A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.076A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 26 through 30 removed outlier: 8.045A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.340A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.007A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.994A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 308 through 317 removed outlier: 3.656A pdb=" N THR C 313 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE3, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.696A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.070A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.848A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C1057 " --> pdb=" O ALA C1054 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.848A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.573A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1120 1010 hydrogen bonds defined for protein. 2757 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: 5.17 Time building geometry restraints manager: 2.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 8001 1.35 - 1.48: 6833 1.48 - 1.60: 10947 1.60 - 1.73: 0 1.73 - 1.86: 132 Bond restraints: 25913 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.47e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.38e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 2.98e+00 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C1 NAG U 2 " pdb=" O5 NAG U 2 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 ... (remaining 25908 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 34321 1.70 - 3.39: 843 3.39 - 5.09: 75 5.09 - 6.79: 16 6.79 - 8.48: 7 Bond angle restraints: 35262 Sorted by residual: angle pdb=" C GLU B 482 " pdb=" CA GLU B 482 " pdb=" CB GLU B 482 " ideal model delta sigma weight residual 116.63 110.46 6.17 1.16e+00 7.43e-01 2.83e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 116.02 -5.32 1.22e+00 6.72e-01 1.90e+01 angle pdb=" CA CYS C 430 " pdb=" CB CYS C 430 " pdb=" SG CYS C 430 " ideal model delta sigma weight residual 114.40 122.84 -8.44 2.30e+00 1.89e-01 1.35e+01 angle pdb=" CB LYS A 384 " pdb=" CG LYS A 384 " pdb=" CD LYS A 384 " ideal model delta sigma weight residual 111.30 118.55 -7.25 2.30e+00 1.89e-01 9.95e+00 angle pdb=" CA PRO B 984 " pdb=" C PRO B 984 " pdb=" N PRO B 985 " ideal model delta sigma weight residual 117.93 121.69 -3.76 1.20e+00 6.94e-01 9.80e+00 ... (remaining 35257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 14963 17.79 - 35.58: 1221 35.58 - 53.38: 263 53.38 - 71.17: 68 71.17 - 88.96: 27 Dihedral angle restraints: 16542 sinusoidal: 7533 harmonic: 9009 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 -7.26 -78.74 1 1.00e+01 1.00e-02 7.73e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -159.94 73.94 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CB CYS C1080 " pdb=" SG CYS C1080 " pdb=" SG CYS C1124 " pdb=" CB CYS C1124 " ideal model delta sinusoidal sigma weight residual -86.00 -12.26 -73.74 1 1.00e+01 1.00e-02 6.91e+01 ... (remaining 16539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3571 0.065 - 0.130: 642 0.130 - 0.195: 31 0.195 - 0.260: 4 0.260 - 0.325: 1 Chirality restraints: 4249 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 1.35e+00 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C 707 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 4246 not shown) Planarity restraints: 4503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1137 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A1138 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A1138 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1138 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO C 984 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 518 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO C 519 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO C 519 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 519 " -0.022 5.00e-02 4.00e+02 ... (remaining 4500 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 880 2.71 - 3.26: 24575 3.26 - 3.81: 38501 3.81 - 4.35: 46674 4.35 - 4.90: 81575 Nonbonded interactions: 192205 Sorted by model distance: nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.163 3.040 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.168 3.040 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.170 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.185 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.210 3.040 ... (remaining 192200 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 633 through 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 4.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.120 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: 0.000 Load rotamer database and sin/cos tables:6.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 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 0.051 26037 Z= 0.190 Angle : 0.639 9.458 35594 Z= 0.308 Chirality : 0.047 0.325 4249 Planarity : 0.003 0.047 4455 Dihedral : 13.573 88.960 10622 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.53 % Favored : 95.37 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 0.06 (0.15), residues: 3047 helix: 2.08 (0.21), residues: 675 sheet: 0.60 (0.19), residues: 731 loop : -1.16 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 981 TYR 0.014 0.001 TYR A1065 PHE 0.015 0.001 PHE C 140 TRP 0.012 0.001 TRP B 884 HIS 0.002 0.000 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00399 (25913) covalent geometry : angle 0.61132 (35262) SS BOND : bond 0.00398 ( 40) SS BOND : angle 1.67209 ( 80) hydrogen bonds : bond 0.11912 ( 994) hydrogen bonds : angle 5.65829 ( 2757) link_BETA1-4 : bond 0.00409 ( 36) link_BETA1-4 : angle 2.20889 ( 108) link_NAG-ASN : bond 0.00235 ( 48) link_NAG-ASN : angle 2.02909 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.908 Fit side-chains REVERT: A 345 PHE cc_start: 0.7842 (m-10) cc_final: 0.7561 (m-10) REVERT: B 400 ILE cc_start: 0.8975 (mm) cc_final: 0.8764 (pp) REVERT: B 1027 MET cc_start: 0.8959 (tpp) cc_final: 0.8204 (tpp) outliers start: 0 outliers final: 2 residues processed: 83 average time/residue: 0.5367 time to fit residues: 53.7727 Evaluate side-chains 58 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 56 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN C 237 GLN ** C1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.076892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045528 restraints weight = 86796.898| |-----------------------------------------------------------------------------| r_work (start): 0.2767 rms_B_bonded: 4.20 r_work: 0.2617 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.0948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 26037 Z= 0.317 Angle : 0.713 9.547 35594 Z= 0.357 Chirality : 0.049 0.234 4249 Planarity : 0.004 0.047 4455 Dihedral : 7.910 59.982 5087 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.61 % Favored : 94.29 % Rotamer: Outliers : 0.70 % Allowed : 6.13 % Favored : 93.17 % 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: -0.17 (0.15), residues: 3047 helix: 1.86 (0.21), residues: 675 sheet: 0.36 (0.19), residues: 712 loop : -1.22 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1037 TYR 0.018 0.001 TYR B1065 PHE 0.030 0.002 PHE C 904 TRP 0.016 0.002 TRP A 434 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00756 (25913) covalent geometry : angle 0.68853 (35262) SS BOND : bond 0.00563 ( 40) SS BOND : angle 2.08315 ( 80) hydrogen bonds : bond 0.07609 ( 994) hydrogen bonds : angle 5.33513 ( 2757) link_BETA1-4 : bond 0.00265 ( 36) link_BETA1-4 : angle 1.95863 ( 108) link_NAG-ASN : bond 0.00434 ( 48) link_NAG-ASN : angle 2.03167 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.897 Fit side-chains REVERT: B 400 ILE cc_start: 0.9071 (mm) cc_final: 0.8692 (pp) REVERT: C 1000 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8202 (tm-30) outliers start: 19 outliers final: 10 residues processed: 69 average time/residue: 0.5452 time to fit residues: 45.6446 Evaluate side-chains 61 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 105 optimal weight: 0.5980 chunk 127 optimal weight: 1.9990 chunk 227 optimal weight: 0.7980 chunk 56 optimal weight: 6.9990 chunk 286 optimal weight: 0.9990 chunk 307 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 221 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.078853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.047814 restraints weight = 85782.839| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.18 r_work: 0.2689 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26037 Z= 0.122 Angle : 0.581 9.313 35594 Z= 0.291 Chirality : 0.045 0.239 4249 Planarity : 0.004 0.051 4455 Dihedral : 7.070 59.093 5083 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 0.92 % Allowed : 8.53 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3047 helix: 2.19 (0.21), residues: 668 sheet: 0.64 (0.19), residues: 717 loop : -1.10 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.014 0.001 TYR C1065 PHE 0.017 0.001 PHE C 140 TRP 0.011 0.001 TRP A 434 HIS 0.002 0.000 HIS C1062 Details of bonding type rmsd covalent geometry : bond 0.00264 (25913) covalent geometry : angle 0.55870 (35262) SS BOND : bond 0.00411 ( 40) SS BOND : angle 1.54562 ( 80) hydrogen bonds : bond 0.05822 ( 994) hydrogen bonds : angle 4.94097 ( 2757) link_BETA1-4 : bond 0.00432 ( 36) link_BETA1-4 : angle 1.93114 ( 108) link_NAG-ASN : bond 0.00276 ( 48) link_NAG-ASN : angle 1.71232 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 0.835 Fit side-chains REVERT: B 400 ILE cc_start: 0.9005 (mm) cc_final: 0.8644 (pp) REVERT: B 516 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7034 (tm) REVERT: C 1000 GLN cc_start: 0.8408 (tm-30) cc_final: 0.7949 (tm-30) outliers start: 25 outliers final: 11 residues processed: 81 average time/residue: 0.4853 time to fit residues: 48.4257 Evaluate side-chains 67 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 516 LEU Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 154 optimal weight: 3.9990 chunk 237 optimal weight: 3.9990 chunk 57 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 10.0000 chunk 199 optimal weight: 2.9990 chunk 159 optimal weight: 0.6980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 ASN ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.078134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.047059 restraints weight = 85593.737| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 4.15 r_work: 0.2660 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.0962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26037 Z= 0.167 Angle : 0.593 9.582 35594 Z= 0.295 Chirality : 0.045 0.241 4249 Planarity : 0.004 0.054 4455 Dihedral : 6.835 59.952 5083 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.66 % Favored : 95.24 % Rotamer: Outliers : 1.18 % Allowed : 10.49 % Favored : 88.33 % 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: 0.15 (0.15), residues: 3047 helix: 2.26 (0.21), residues: 667 sheet: 0.63 (0.19), residues: 705 loop : -1.09 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.015 0.001 TYR B1065 PHE 0.018 0.001 PHE A 390 TRP 0.008 0.001 TRP B 884 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00393 (25913) covalent geometry : angle 0.56944 (35262) SS BOND : bond 0.00433 ( 40) SS BOND : angle 1.62276 ( 80) hydrogen bonds : bond 0.06117 ( 994) hydrogen bonds : angle 4.90960 ( 2757) link_BETA1-4 : bond 0.00352 ( 36) link_BETA1-4 : angle 1.91687 ( 108) link_NAG-ASN : bond 0.00239 ( 48) link_NAG-ASN : angle 1.79290 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 57 time to evaluate : 1.001 Fit side-chains REVERT: A 982 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8693 (pt) REVERT: B 400 ILE cc_start: 0.8980 (mm) cc_final: 0.8599 (pp) REVERT: C 1000 GLN cc_start: 0.8432 (tm-30) cc_final: 0.7968 (tm-30) outliers start: 32 outliers final: 19 residues processed: 79 average time/residue: 0.4873 time to fit residues: 47.5862 Evaluate side-chains 72 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 957 LEU Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 204 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 159 optimal weight: 0.5980 chunk 42 optimal weight: 20.0000 chunk 137 optimal weight: 4.9990 chunk 224 optimal weight: 7.9990 chunk 140 optimal weight: 2.9990 chunk 143 optimal weight: 10.0000 chunk 227 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.076658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.045439 restraints weight = 85872.127| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 4.10 r_work: 0.2611 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 26037 Z= 0.296 Angle : 0.684 10.157 35594 Z= 0.342 Chirality : 0.048 0.248 4249 Planarity : 0.004 0.055 4455 Dihedral : 6.994 59.434 5083 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.35 % Favored : 94.55 % Rotamer: Outliers : 1.96 % Allowed : 11.12 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3047 helix: 2.01 (0.21), residues: 676 sheet: 0.48 (0.20), residues: 658 loop : -1.15 (0.14), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1037 TYR 0.017 0.001 TYR B1065 PHE 0.017 0.002 PHE C 904 TRP 0.009 0.001 TRP B 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00705 (25913) covalent geometry : angle 0.65935 (35262) SS BOND : bond 0.00537 ( 40) SS BOND : angle 1.98915 ( 80) hydrogen bonds : bond 0.07429 ( 994) hydrogen bonds : angle 5.15772 ( 2757) link_BETA1-4 : bond 0.00296 ( 36) link_BETA1-4 : angle 1.97553 ( 108) link_NAG-ASN : bond 0.00401 ( 48) link_NAG-ASN : angle 2.01625 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 54 time to evaluate : 0.954 Fit side-chains REVERT: A 114 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 400 ILE cc_start: 0.8980 (mm) cc_final: 0.8585 (pp) REVERT: B 985 PRO cc_start: 0.8660 (OUTLIER) cc_final: 0.8411 (Cg_endo) REVERT: C 1000 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8337 (tm-30) outliers start: 53 outliers final: 23 residues processed: 98 average time/residue: 0.4254 time to fit residues: 52.5056 Evaluate side-chains 73 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 971 ILE Chi-restraints excluded: chain B residue 985 PRO Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 0.9980 chunk 289 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 42 optimal weight: 30.0000 chunk 292 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 223 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.0060 chunk 249 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.078537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047699 restraints weight = 85403.053| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 4.16 r_work: 0.2678 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26037 Z= 0.118 Angle : 0.581 9.716 35594 Z= 0.287 Chirality : 0.045 0.246 4249 Planarity : 0.004 0.052 4455 Dihedral : 6.531 57.580 5083 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 1.33 % Allowed : 12.15 % Favored : 86.52 % 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: 0.17 (0.15), residues: 3047 helix: 2.20 (0.21), residues: 673 sheet: 0.68 (0.19), residues: 699 loop : -1.07 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 507 TYR 0.015 0.001 TYR C1065 PHE 0.017 0.001 PHE C 140 TRP 0.008 0.001 TRP A 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00255 (25913) covalent geometry : angle 0.55875 (35262) SS BOND : bond 0.00381 ( 40) SS BOND : angle 1.50693 ( 80) hydrogen bonds : bond 0.05794 ( 994) hydrogen bonds : angle 4.83779 ( 2757) link_BETA1-4 : bond 0.00433 ( 36) link_BETA1-4 : angle 1.91993 ( 108) link_NAG-ASN : bond 0.00256 ( 48) link_NAG-ASN : angle 1.73050 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 60 time to evaluate : 0.987 Fit side-chains REVERT: A 114 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (p) REVERT: A 390 PHE cc_start: 0.7896 (OUTLIER) cc_final: 0.7495 (p90) REVERT: B 400 ILE cc_start: 0.8962 (mm) cc_final: 0.8573 (pp) REVERT: C 1000 GLN cc_start: 0.8535 (tm-30) cc_final: 0.7986 (tm-30) outliers start: 36 outliers final: 15 residues processed: 89 average time/residue: 0.4511 time to fit residues: 49.6966 Evaluate side-chains 72 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 250 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 203 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 229 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.076969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.045719 restraints weight = 86991.438| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 4.09 r_work: 0.2638 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 26037 Z= 0.303 Angle : 0.691 10.313 35594 Z= 0.343 Chirality : 0.048 0.259 4249 Planarity : 0.004 0.053 4455 Dihedral : 6.802 59.468 5083 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.58 % Favored : 94.32 % Rotamer: Outliers : 1.81 % Allowed : 12.30 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.15), residues: 3047 helix: 2.07 (0.21), residues: 674 sheet: 0.45 (0.20), residues: 665 loop : -1.13 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B1037 TYR 0.017 0.001 TYR B1065 PHE 0.015 0.002 PHE C 140 TRP 0.009 0.001 TRP B 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00725 (25913) covalent geometry : angle 0.66609 (35262) SS BOND : bond 0.00533 ( 40) SS BOND : angle 2.01961 ( 80) hydrogen bonds : bond 0.07322 ( 994) hydrogen bonds : angle 5.13531 ( 2757) link_BETA1-4 : bond 0.00303 ( 36) link_BETA1-4 : angle 1.98940 ( 108) link_NAG-ASN : bond 0.00400 ( 48) link_NAG-ASN : angle 2.00582 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 49 time to evaluate : 0.923 Fit side-chains REVERT: A 114 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 390 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7561 (p90) REVERT: B 400 ILE cc_start: 0.9010 (mm) cc_final: 0.8628 (pp) REVERT: B 757 PHE cc_start: 0.8223 (p90) cc_final: 0.8010 (p90) REVERT: B 856 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9139 (pp) REVERT: B 1104 GLN cc_start: 0.9326 (OUTLIER) cc_final: 0.8691 (pt0) REVERT: C 1000 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8288 (tm-30) outliers start: 49 outliers final: 25 residues processed: 91 average time/residue: 0.4318 time to fit residues: 49.3130 Evaluate side-chains 78 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 49 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 727 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1104 GLN Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 961 VAL Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 136 optimal weight: 9.9990 chunk 43 optimal weight: 0.2980 chunk 208 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 109 optimal weight: 6.9990 chunk 197 optimal weight: 0.8980 chunk 191 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 223 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.078887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.048146 restraints weight = 86040.624| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 4.04 r_work: 0.2711 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 26037 Z= 0.116 Angle : 0.586 9.834 35594 Z= 0.289 Chirality : 0.045 0.246 4249 Planarity : 0.004 0.057 4455 Dihedral : 6.372 57.969 5083 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.74 % Favored : 96.16 % Rotamer: Outliers : 1.29 % Allowed : 13.04 % Favored : 85.67 % 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: 0.23 (0.15), residues: 3047 helix: 2.30 (0.21), residues: 666 sheet: 0.73 (0.19), residues: 691 loop : -1.04 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 212 TYR 0.014 0.001 TYR C1065 PHE 0.018 0.001 PHE A 390 TRP 0.008 0.001 TRP A 434 HIS 0.002 0.000 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00247 (25913) covalent geometry : angle 0.56294 (35262) SS BOND : bond 0.00382 ( 40) SS BOND : angle 1.60428 ( 80) hydrogen bonds : bond 0.05633 ( 994) hydrogen bonds : angle 4.80506 ( 2757) link_BETA1-4 : bond 0.00449 ( 36) link_BETA1-4 : angle 1.92265 ( 108) link_NAG-ASN : bond 0.00263 ( 48) link_NAG-ASN : angle 1.73389 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 57 time to evaluate : 0.959 Fit side-chains REVERT: A 114 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8684 (p) REVERT: B 400 ILE cc_start: 0.8993 (mm) cc_final: 0.8626 (pp) REVERT: B 856 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8984 (pp) REVERT: C 322 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8440 (pm20) REVERT: C 867 MET cc_start: 0.9254 (mtt) cc_final: 0.9000 (mtt) REVERT: C 1000 GLN cc_start: 0.8590 (tm-30) cc_final: 0.8086 (tm-30) outliers start: 35 outliers final: 22 residues processed: 87 average time/residue: 0.4764 time to fit residues: 50.9613 Evaluate side-chains 79 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 60 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 298 optimal weight: 4.9990 chunk 21 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 188 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.077072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.045850 restraints weight = 87253.577| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 4.08 r_work: 0.2644 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 26037 Z= 0.282 Angle : 0.682 10.570 35594 Z= 0.337 Chirality : 0.047 0.241 4249 Planarity : 0.004 0.059 4455 Dihedral : 6.654 59.644 5083 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.51 % Favored : 94.39 % Rotamer: Outliers : 1.48 % Allowed : 13.15 % Favored : 85.38 % 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: 0.04 (0.15), residues: 3047 helix: 2.18 (0.21), residues: 668 sheet: 0.45 (0.20), residues: 671 loop : -1.08 (0.14), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1037 TYR 0.017 0.001 TYR B1065 PHE 0.026 0.002 PHE B 757 TRP 0.008 0.001 TRP B 884 HIS 0.004 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00671 (25913) covalent geometry : angle 0.65708 (35262) SS BOND : bond 0.00524 ( 40) SS BOND : angle 2.02952 ( 80) hydrogen bonds : bond 0.07189 ( 994) hydrogen bonds : angle 5.07494 ( 2757) link_BETA1-4 : bond 0.00302 ( 36) link_BETA1-4 : angle 1.98819 ( 108) link_NAG-ASN : bond 0.00373 ( 48) link_NAG-ASN : angle 1.98553 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 52 time to evaluate : 0.874 Fit side-chains REVERT: A 114 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 400 ILE cc_start: 0.9023 (mm) cc_final: 0.8650 (pp) REVERT: B 856 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9105 (pp) REVERT: B 1104 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8713 (pt0) REVERT: C 166 PHE cc_start: 0.8026 (t80) cc_final: 0.7808 (t80) REVERT: C 322 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8380 (pm20) REVERT: C 1000 GLN cc_start: 0.8721 (tm-30) cc_final: 0.8331 (tm-30) outliers start: 40 outliers final: 26 residues processed: 88 average time/residue: 0.4625 time to fit residues: 50.5546 Evaluate side-chains 80 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1134 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1104 GLN Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 142 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 217 optimal weight: 9.9990 chunk 61 optimal weight: 4.9990 chunk 269 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 276 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.078062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.047270 restraints weight = 85668.925| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 4.01 r_work: 0.2685 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26037 Z= 0.155 Angle : 0.611 10.736 35594 Z= 0.301 Chirality : 0.045 0.242 4249 Planarity : 0.004 0.063 4455 Dihedral : 6.414 58.218 5083 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.29 % Allowed : 13.37 % Favored : 85.34 % 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: 0.18 (0.15), residues: 3047 helix: 2.31 (0.21), residues: 665 sheet: 0.65 (0.19), residues: 708 loop : -1.07 (0.14), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1037 TYR 0.014 0.001 TYR C1065 PHE 0.017 0.001 PHE C 140 TRP 0.008 0.001 TRP B 884 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00362 (25913) covalent geometry : angle 0.58806 (35262) SS BOND : bond 0.00414 ( 40) SS BOND : angle 1.70459 ( 80) hydrogen bonds : bond 0.06207 ( 994) hydrogen bonds : angle 4.89717 ( 2757) link_BETA1-4 : bond 0.00387 ( 36) link_BETA1-4 : angle 1.94299 ( 108) link_NAG-ASN : bond 0.00219 ( 48) link_NAG-ASN : angle 1.80993 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6094 Ramachandran restraints generated. 3047 Oldfield, 0 Emsley, 3047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 55 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 114 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8686 (p) REVERT: A 390 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7761 (p90) REVERT: A 876 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9231 (mt) REVERT: B 400 ILE cc_start: 0.9016 (mm) cc_final: 0.8647 (pp) REVERT: B 856 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9087 (pp) REVERT: C 658 TYR cc_start: 0.8747 (OUTLIER) cc_final: 0.8259 (p90) REVERT: C 1000 GLN cc_start: 0.8630 (tm-30) cc_final: 0.8111 (tm-30) outliers start: 35 outliers final: 25 residues processed: 85 average time/residue: 0.4586 time to fit residues: 48.4176 Evaluate side-chains 84 residues out of total 2708 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 54 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 503 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 880 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 22 THR Chi-restraints excluded: chain C residue 140 PHE Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 2 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 128 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 231 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.077955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.047157 restraints weight = 85653.828| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 4.03 r_work: 0.2676 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 26037 Z= 0.172 Angle : 0.618 10.441 35594 Z= 0.304 Chirality : 0.045 0.241 4249 Planarity : 0.004 0.063 4455 Dihedral : 6.376 59.318 5083 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.63 % Favored : 95.27 % Rotamer: Outliers : 1.33 % Allowed : 13.44 % Favored : 85.23 % 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: 0.20 (0.15), residues: 3047 helix: 2.32 (0.21), residues: 665 sheet: 0.66 (0.19), residues: 708 loop : -1.07 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.017 0.001 TYR B 447 PHE 0.018 0.001 PHE B 757 TRP 0.007 0.001 TRP B 884 HIS 0.002 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00405 (25913) covalent geometry : angle 0.59411 (35262) SS BOND : bond 0.00430 ( 40) SS BOND : angle 1.72283 ( 80) hydrogen bonds : bond 0.06264 ( 994) hydrogen bonds : angle 4.89252 ( 2757) link_BETA1-4 : bond 0.00350 ( 36) link_BETA1-4 : angle 1.94643 ( 108) link_NAG-ASN : bond 0.00231 ( 48) link_NAG-ASN : angle 1.83046 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8010.20 seconds wall clock time: 137 minutes 5.25 seconds (8225.25 seconds total)