Starting phenix.real_space_refine on Thu Mar 5 21:37:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7v_31783/03_2026/7v7v_31783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7v_31783/03_2026/7v7v_31783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v7v_31783/03_2026/7v7v_31783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7v_31783/03_2026/7v7v_31783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7v_31783/03_2026/7v7v_31783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7v_31783/03_2026/7v7v_31783.map" } resolution = 3.1 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= 0.055 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 16068 2.51 5 N 4117 2.21 5 O 5011 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s 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: 25304 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} 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: 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: "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: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 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: 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 Time building chain proxies: 6.15, per 1000 atoms: 0.24 Number of scatterers: 25304 At special positions: 0 Unit cell: (139.7, 148.5, 200.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5011 8.00 N 4117 7.00 C 16068 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=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 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=2.03 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 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " 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 601 " " NAG C2003 " - " 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 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 329 " " 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 seconds 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5788 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 46 sheets defined 24.4% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 removed outlier: 3.686A 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 362 through 369 removed outlier: 4.324A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.860A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 742 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 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.313A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (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: 3.670A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.149A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.843A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.112A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.151A 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 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 753 removed outlier: 4.141A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.677A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.529A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.568A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.937A 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: 3.509A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.705A 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 removed outlier: 3.528A pdb=" N GLN B 947 " --> pdb=" O LEU B 943 " (cutoff:3.500A) 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: 3.550A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.383A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.767A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.568A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.884A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 4.462A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 882 Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 910 through 939 removed outlier: 4.306A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) 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 982 removed outlier: 3.565A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.834A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.756A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.319A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.907A 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: 6.837A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.634A 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: 4.040A 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: 7.238A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.533A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 3.539A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 removed outlier: 5.505A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.181A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.797A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB5, 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: 6.138A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.544A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.886A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.501A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.449A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.021A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.255A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.261A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.316A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 321 through 326 removed outlier: 5.032A pdb=" N ASN B 538 " --> pdb=" O GLU B 322 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC7, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.369A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC9, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD1, first strand: chain 'B' and resid 652 through 653 removed outlier: 5.933A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.581A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.988A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.057A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.737A 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: 4.412A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.976A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.045A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.769A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.541A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.387A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.975A 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: 4.099A 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: 7.196A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.276A pdb=" N VAL C 126 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 9.961A pdb=" N GLU C 167 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.122A pdb=" N ILE C 128 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 8.597A pdb=" N THR C 165 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL C 130 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 7.279A pdb=" N ASN C 163 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N GLU C 132 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ALA C 161 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLN C 134 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.100A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.636A 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 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.198A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.648A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.013A 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 711 Processing sheet with id=AE7, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.565A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.513A 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 1123 removed outlier: 4.552A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1092 through 1095 1001 hydrogen bonds defined for protein. 2751 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: 6.58 Time building geometry restraints manager: 3.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7983 1.34 - 1.46: 6432 1.46 - 1.58: 11304 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25851 Sorted by residual: bond pdb=" C1 NAG A2002 " pdb=" O5 NAG A2002 " ideal model delta sigma weight residual 1.406 1.486 -0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.91e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.84e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.02e+00 ... (remaining 25846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 34167 1.58 - 3.15: 903 3.15 - 4.73: 69 4.73 - 6.31: 26 6.31 - 7.89: 11 Bond angle restraints: 35176 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 116.63 110.28 6.35 1.16e+00 7.43e-01 3.00e+01 angle pdb=" N VAL A 157 " pdb=" CA VAL A 157 " pdb=" C VAL A 157 " ideal model delta sigma weight residual 113.39 108.70 4.69 1.47e+00 4.63e-01 1.02e+01 angle pdb=" CA GLU B 482 " pdb=" C GLU B 482 " pdb=" N GLY B 483 " ideal model delta sigma weight residual 119.63 117.05 2.58 8.10e-01 1.52e+00 1.02e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.52 -3.82 1.22e+00 6.72e-01 9.79e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.08 -5.61 2.06e+00 2.36e-01 7.42e+00 ... (remaining 35171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.43: 15484 23.43 - 46.87: 862 46.87 - 70.30: 118 70.30 - 93.74: 29 93.74 - 117.17: 16 Dihedral angle restraints: 16509 sinusoidal: 7519 harmonic: 8990 Sorted by residual: dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -173.03 87.03 1 1.00e+01 1.00e-02 9.10e+01 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 -6.10 -79.90 1 1.00e+01 1.00e-02 7.92e+01 dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 -7.14 -78.86 1 1.00e+01 1.00e-02 7.74e+01 ... (remaining 16506 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4218 0.136 - 0.272: 22 0.272 - 0.409: 0 0.409 - 0.545: 0 0.545 - 0.681: 1 Chirality restraints: 4241 Sorted by residual: chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.72 -0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA PRO C 559 " pdb=" N PRO C 559 " pdb=" C PRO C 559 " pdb=" CB PRO C 559 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.18 2.00e-01 2.50e+01 8.51e-01 chirality pdb=" CA PRO A 559 " pdb=" N PRO A 559 " pdb=" C PRO A 559 " pdb=" CB PRO A 559 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 4238 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.032 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 984 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 983 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO C 984 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 984 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO C 985 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO C 985 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 985 " -0.026 5.00e-02 4.00e+02 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 655 2.70 - 3.25: 24049 3.25 - 3.80: 38256 3.80 - 4.35: 47620 4.35 - 4.90: 82054 Nonbonded interactions: 192634 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.145 3.040 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.154 3.040 nonbonded pdb=" OG1 THR C 124 " pdb=" OD1 ASN C 125 " model vdw 2.170 3.040 nonbonded pdb=" O ASN A 437 " pdb=" OG SER A 441 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.212 3.040 ... (remaining 192629 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 2003) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 635 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: 4.840 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: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.860 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 0.080 25975 Z= 0.181 Angle : 0.608 16.060 35508 Z= 0.287 Chirality : 0.047 0.681 4241 Planarity : 0.003 0.048 4446 Dihedral : 14.230 117.173 10601 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.04 % Favored : 95.86 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 3041 helix: 2.40 (0.22), residues: 668 sheet: 0.82 (0.19), residues: 716 loop : -0.94 (0.15), residues: 1657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1037 TYR 0.016 0.001 TYR B1065 PHE 0.016 0.001 PHE B 904 TRP 0.012 0.001 TRP B 884 HIS 0.001 0.000 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00372 (25851) covalent geometry : angle 0.58199 (35176) SS BOND : bond 0.00258 ( 40) SS BOND : angle 1.22045 ( 80) hydrogen bonds : bond 0.11267 ( 1001) hydrogen bonds : angle 5.47611 ( 2751) link_BETA1-4 : bond 0.00388 ( 36) link_BETA1-4 : angle 1.82263 ( 108) link_NAG-ASN : bond 0.00321 ( 48) link_NAG-ASN : angle 2.28508 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TYR cc_start: 0.7196 (t80) cc_final: 0.6880 (t80) REVERT: A 644 ARG cc_start: 0.7396 (tpp-160) cc_final: 0.7144 (tpm170) REVERT: A 757 PHE cc_start: 0.7975 (p90) cc_final: 0.7160 (p90) REVERT: A 771 GLU cc_start: 0.8243 (tt0) cc_final: 0.7955 (tt0) REVERT: B 52 GLN cc_start: 0.8536 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 129 LYS cc_start: 0.6971 (mmmm) cc_final: 0.6751 (mttt) REVERT: B 133 PHE cc_start: 0.7998 (m-80) cc_final: 0.7652 (m-80) REVERT: B 140 PHE cc_start: 0.7371 (p90) cc_final: 0.7114 (p90) REVERT: B 240 LEU cc_start: 0.7653 (mm) cc_final: 0.7439 (mp) REVERT: B 243 HIS cc_start: 0.4393 (p-80) cc_final: 0.3916 (p-80) REVERT: B 416 ILE cc_start: 0.8892 (pt) cc_final: 0.8592 (pt) REVERT: B 451 TYR cc_start: 0.7849 (p90) cc_final: 0.6971 (p90) REVERT: B 659 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6962 (tm-30) REVERT: B 876 LEU cc_start: 0.8997 (tp) cc_final: 0.8598 (mt) REVERT: B 955 GLN cc_start: 0.8523 (tt0) cc_final: 0.8308 (tt0) REVERT: C 363 TYR cc_start: 0.9060 (m-80) cc_final: 0.8779 (m-80) REVERT: C 372 PHE cc_start: 0.7823 (m-80) cc_final: 0.7561 (m-80) REVERT: C 572 ASP cc_start: 0.7309 (m-30) cc_final: 0.6847 (m-30) REVERT: C 979 LEU cc_start: 0.9193 (mt) cc_final: 0.8988 (mt) REVERT: C 1140 GLN cc_start: 0.8729 (mm-40) cc_final: 0.8489 (mm-40) outliers start: 0 outliers final: 0 residues processed: 212 average time/residue: 0.1604 time to fit residues: 53.9280 Evaluate side-chains 119 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B 899 GLN B 976 ASN C 125 ASN C 802 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.138823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.079836 restraints weight = 46707.920| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.24 r_work: 0.2960 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25975 Z= 0.187 Angle : 0.635 10.876 35508 Z= 0.312 Chirality : 0.047 0.265 4241 Planarity : 0.004 0.066 4446 Dihedral : 9.006 111.339 5075 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.31 % Favored : 95.59 % Rotamer: Outliers : 0.48 % Allowed : 6.11 % Favored : 93.41 % 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: 0.24 (0.15), residues: 3041 helix: 2.16 (0.21), residues: 686 sheet: 0.78 (0.19), residues: 689 loop : -1.02 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1037 TYR 0.024 0.001 TYR A1065 PHE 0.025 0.002 PHE C 904 TRP 0.011 0.001 TRP C 884 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00457 (25851) covalent geometry : angle 0.61351 (35176) SS BOND : bond 0.00517 ( 40) SS BOND : angle 1.68223 ( 80) hydrogen bonds : bond 0.06036 ( 1001) hydrogen bonds : angle 4.97739 ( 2751) link_BETA1-4 : bond 0.00393 ( 36) link_BETA1-4 : angle 1.78093 ( 108) link_NAG-ASN : bond 0.00266 ( 48) link_NAG-ASN : angle 1.89340 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7830 (m-80) cc_final: 0.6657 (m-80) REVERT: A 168 TYR cc_start: 0.7369 (t80) cc_final: 0.7131 (t80) REVERT: A 235 ARG cc_start: 0.8627 (mtm110) cc_final: 0.8295 (ttp-110) REVERT: A 757 PHE cc_start: 0.8254 (p90) cc_final: 0.7889 (p90) REVERT: A 771 GLU cc_start: 0.8649 (tt0) cc_final: 0.8345 (tt0) REVERT: B 52 GLN cc_start: 0.8754 (tm-30) cc_final: 0.8490 (tm-30) REVERT: B 140 PHE cc_start: 0.7509 (p90) cc_final: 0.7251 (p90) REVERT: B 243 HIS cc_start: 0.4450 (p-80) cc_final: 0.3968 (p-80) REVERT: B 451 TYR cc_start: 0.7843 (p90) cc_final: 0.6885 (p90) REVERT: B 955 GLN cc_start: 0.9023 (tt0) cc_final: 0.8816 (tt0) REVERT: C 140 PHE cc_start: 0.7678 (p90) cc_final: 0.7449 (p90) REVERT: C 363 TYR cc_start: 0.9088 (m-80) cc_final: 0.8797 (m-80) REVERT: C 372 PHE cc_start: 0.7920 (m-80) cc_final: 0.7672 (m-80) REVERT: C 572 ASP cc_start: 0.7812 (m-30) cc_final: 0.7486 (m-30) outliers start: 13 outliers final: 10 residues processed: 133 average time/residue: 0.1739 time to fit residues: 36.6414 Evaluate side-chains 117 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 107 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 1140 GLN Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 192 optimal weight: 0.9980 chunk 207 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 246 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 228 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.147439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.087825 restraints weight = 46724.093| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.25 r_work: 0.2896 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25975 Z= 0.225 Angle : 0.648 15.504 35508 Z= 0.319 Chirality : 0.048 0.257 4241 Planarity : 0.004 0.051 4446 Dihedral : 8.574 111.623 5075 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.41 % Favored : 95.49 % Rotamer: Outliers : 1.26 % Allowed : 9.77 % Favored : 88.97 % 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: 0.07 (0.15), residues: 3041 helix: 2.04 (0.21), residues: 684 sheet: 0.67 (0.19), residues: 691 loop : -1.14 (0.14), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 401 TYR 0.024 0.001 TYR A1065 PHE 0.026 0.002 PHE C 904 TRP 0.016 0.001 TRP C 884 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00553 (25851) covalent geometry : angle 0.62630 (35176) SS BOND : bond 0.00485 ( 40) SS BOND : angle 1.69873 ( 80) hydrogen bonds : bond 0.06748 ( 1001) hydrogen bonds : angle 5.06504 ( 2751) link_BETA1-4 : bond 0.00371 ( 36) link_BETA1-4 : angle 1.80748 ( 108) link_NAG-ASN : bond 0.00231 ( 48) link_NAG-ASN : angle 1.87981 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7797 (m-80) cc_final: 0.6696 (m-80) REVERT: A 235 ARG cc_start: 0.8732 (mtm110) cc_final: 0.8147 (mtm-85) REVERT: A 757 PHE cc_start: 0.8250 (p90) cc_final: 0.7872 (p90) REVERT: B 52 GLN cc_start: 0.8798 (tm-30) cc_final: 0.8529 (tm-30) REVERT: B 140 PHE cc_start: 0.7525 (p90) cc_final: 0.7229 (p90) REVERT: B 451 TYR cc_start: 0.7909 (p90) cc_final: 0.6986 (p90) REVERT: B 955 GLN cc_start: 0.9028 (tt0) cc_final: 0.8814 (tt0) REVERT: C 140 PHE cc_start: 0.7829 (p90) cc_final: 0.7552 (p90) REVERT: C 171 GLN cc_start: 0.7370 (tm-30) cc_final: 0.7134 (tm-30) REVERT: C 363 TYR cc_start: 0.9136 (m-80) cc_final: 0.8816 (m-80) REVERT: C 372 PHE cc_start: 0.8054 (m-80) cc_final: 0.7793 (m-80) REVERT: C 572 ASP cc_start: 0.7840 (m-30) cc_final: 0.7557 (m-30) outliers start: 34 outliers final: 18 residues processed: 142 average time/residue: 0.1425 time to fit residues: 33.7607 Evaluate side-chains 118 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 133 optimal weight: 3.9990 chunk 283 optimal weight: 0.6980 chunk 194 optimal weight: 0.9980 chunk 101 optimal weight: 0.0770 chunk 16 optimal weight: 5.9990 chunk 226 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 245 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 227 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.136604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.079286 restraints weight = 46130.227| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.16 r_work: 0.2951 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 25975 Z= 0.127 Angle : 0.579 12.998 35508 Z= 0.280 Chirality : 0.045 0.261 4241 Planarity : 0.004 0.049 4446 Dihedral : 7.973 108.361 5075 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 1.33 % Allowed : 11.21 % Favored : 87.45 % 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: 3041 helix: 2.15 (0.21), residues: 690 sheet: 0.73 (0.19), residues: 696 loop : -1.06 (0.14), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 401 TYR 0.018 0.001 TYR B1065 PHE 0.021 0.001 PHE B 166 TRP 0.012 0.001 TRP C 884 HIS 0.002 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00293 (25851) covalent geometry : angle 0.55795 (35176) SS BOND : bond 0.00341 ( 40) SS BOND : angle 1.24629 ( 80) hydrogen bonds : bond 0.05591 ( 1001) hydrogen bonds : angle 4.84907 ( 2751) link_BETA1-4 : bond 0.00409 ( 36) link_BETA1-4 : angle 1.82527 ( 108) link_NAG-ASN : bond 0.00198 ( 48) link_NAG-ASN : angle 1.78013 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 110 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7803 (m-80) cc_final: 0.6684 (m-80) REVERT: A 235 ARG cc_start: 0.8722 (mtm110) cc_final: 0.8203 (mtm-85) REVERT: A 757 PHE cc_start: 0.8392 (p90) cc_final: 0.7941 (p90) REVERT: B 52 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8557 (tm-30) REVERT: B 133 PHE cc_start: 0.7958 (m-10) cc_final: 0.7606 (m-10) REVERT: B 140 PHE cc_start: 0.7429 (p90) cc_final: 0.7066 (p90) REVERT: B 158 TYR cc_start: 0.7867 (p90) cc_final: 0.7262 (p90) REVERT: B 451 TYR cc_start: 0.7864 (p90) cc_final: 0.7021 (p90) REVERT: B 738 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8740 (tpt) REVERT: B 1037 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8530 (mtp180) REVERT: C 140 PHE cc_start: 0.7815 (p90) cc_final: 0.7611 (p90) REVERT: C 171 GLN cc_start: 0.7456 (tm-30) cc_final: 0.7067 (tm-30) REVERT: C 363 TYR cc_start: 0.9114 (m-80) cc_final: 0.8819 (m-80) REVERT: C 372 PHE cc_start: 0.8058 (m-80) cc_final: 0.7776 (m-80) REVERT: C 572 ASP cc_start: 0.8054 (m-30) cc_final: 0.7647 (m-30) outliers start: 36 outliers final: 23 residues processed: 141 average time/residue: 0.1482 time to fit residues: 34.3543 Evaluate side-chains 127 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 102 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 115 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 53 optimal weight: 3.9990 chunk 197 optimal weight: 2.9990 chunk 212 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 72 optimal weight: 0.0070 chunk 133 optimal weight: 4.9990 overall best weight: 1.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.135440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.077751 restraints weight = 46210.166| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 3.16 r_work: 0.2922 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25975 Z= 0.174 Angle : 0.603 12.785 35508 Z= 0.293 Chirality : 0.046 0.261 4241 Planarity : 0.004 0.049 4446 Dihedral : 7.752 107.223 5075 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.21 % Favored : 95.69 % Rotamer: Outliers : 1.85 % Allowed : 11.88 % Favored : 86.27 % 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: 0.08 (0.15), residues: 3041 helix: 2.17 (0.21), residues: 680 sheet: 0.64 (0.20), residues: 669 loop : -1.13 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1037 TYR 0.021 0.001 TYR A1065 PHE 0.022 0.001 PHE B1119 TRP 0.013 0.001 TRP C 884 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00424 (25851) covalent geometry : angle 0.58188 (35176) SS BOND : bond 0.00399 ( 40) SS BOND : angle 1.34908 ( 80) hydrogen bonds : bond 0.06094 ( 1001) hydrogen bonds : angle 4.87961 ( 2751) link_BETA1-4 : bond 0.00364 ( 36) link_BETA1-4 : angle 1.84445 ( 108) link_NAG-ASN : bond 0.00198 ( 48) link_NAG-ASN : angle 1.84764 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 101 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8740 (mtm110) cc_final: 0.8251 (mtm-85) REVERT: A 757 PHE cc_start: 0.8439 (p90) cc_final: 0.8073 (p90) REVERT: B 52 GLN cc_start: 0.8848 (tm-30) cc_final: 0.8572 (tm-30) REVERT: B 133 PHE cc_start: 0.7963 (m-10) cc_final: 0.7555 (m-10) REVERT: B 140 PHE cc_start: 0.7480 (p90) cc_final: 0.7104 (p90) REVERT: B 158 TYR cc_start: 0.7866 (p90) cc_final: 0.7251 (p90) REVERT: B 233 ILE cc_start: 0.7825 (mm) cc_final: 0.7581 (mm) REVERT: B 321 THR cc_start: 0.7218 (OUTLIER) cc_final: 0.7014 (p) REVERT: B 738 MET cc_start: 0.9156 (OUTLIER) cc_final: 0.8810 (tpt) REVERT: C 140 PHE cc_start: 0.7913 (p90) cc_final: 0.7668 (p90) REVERT: C 363 TYR cc_start: 0.9117 (m-80) cc_final: 0.8826 (m-80) REVERT: C 372 PHE cc_start: 0.8125 (m-80) cc_final: 0.7807 (m-80) REVERT: C 572 ASP cc_start: 0.8024 (m-30) cc_final: 0.7637 (m-30) REVERT: C 876 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8750 (tt) REVERT: C 982 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8754 (pt) outliers start: 50 outliers final: 33 residues processed: 147 average time/residue: 0.1441 time to fit residues: 35.1352 Evaluate side-chains 136 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 99 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 2.9990 chunk 193 optimal weight: 0.7980 chunk 79 optimal weight: 0.5980 chunk 196 optimal weight: 0.6980 chunk 102 optimal weight: 30.0000 chunk 176 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 46 optimal weight: 30.0000 chunk 269 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.136596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079471 restraints weight = 46256.122| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.16 r_work: 0.2947 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25975 Z= 0.129 Angle : 0.577 12.822 35508 Z= 0.278 Chirality : 0.045 0.260 4241 Planarity : 0.004 0.049 4446 Dihedral : 7.248 101.426 5075 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.81 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 12.44 % Favored : 85.75 % 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: 0.22 (0.15), residues: 3041 helix: 2.23 (0.21), residues: 683 sheet: 0.75 (0.19), residues: 697 loop : -1.08 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.018 0.001 TYR B1065 PHE 0.020 0.001 PHE B1119 TRP 0.012 0.001 TRP C 884 HIS 0.002 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00299 (25851) covalent geometry : angle 0.55578 (35176) SS BOND : bond 0.00345 ( 40) SS BOND : angle 1.17603 ( 80) hydrogen bonds : bond 0.05446 ( 1001) hydrogen bonds : angle 4.76368 ( 2751) link_BETA1-4 : bond 0.00394 ( 36) link_BETA1-4 : angle 1.86457 ( 108) link_NAG-ASN : bond 0.00184 ( 48) link_NAG-ASN : angle 1.84450 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 105 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 235 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8285 (mtm-85) REVERT: A 757 PHE cc_start: 0.8378 (p90) cc_final: 0.7864 (p90) REVERT: B 52 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8537 (tm-30) REVERT: B 133 PHE cc_start: 0.7876 (m-10) cc_final: 0.7365 (m-10) REVERT: B 140 PHE cc_start: 0.7443 (p90) cc_final: 0.7053 (p90) REVERT: B 158 TYR cc_start: 0.7777 (p90) cc_final: 0.7185 (p90) REVERT: B 321 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.7009 (p) REVERT: B 404 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8133 (mp0) REVERT: B 738 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8801 (tpt) REVERT: B 1037 ARG cc_start: 0.9170 (OUTLIER) cc_final: 0.8584 (mtp180) REVERT: C 363 TYR cc_start: 0.9090 (m-80) cc_final: 0.8767 (m-80) REVERT: C 372 PHE cc_start: 0.8146 (m-80) cc_final: 0.7834 (m-80) REVERT: C 572 ASP cc_start: 0.8059 (m-30) cc_final: 0.7652 (m-30) REVERT: C 803 ILE cc_start: 0.9156 (OUTLIER) cc_final: 0.8881 (mt) outliers start: 49 outliers final: 35 residues processed: 149 average time/residue: 0.1439 time to fit residues: 35.6929 Evaluate side-chains 137 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 97 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 404 GLU Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 177 optimal weight: 2.9990 chunk 142 optimal weight: 0.2980 chunk 154 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 105 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 222 optimal weight: 3.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.135270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.077753 restraints weight = 46252.062| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 3.15 r_work: 0.2913 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25975 Z= 0.192 Angle : 0.616 13.162 35508 Z= 0.299 Chirality : 0.046 0.264 4241 Planarity : 0.004 0.050 4446 Dihedral : 7.055 95.029 5075 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.56 % Rotamer: Outliers : 2.00 % Allowed : 13.03 % Favored : 84.97 % 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: 0.09 (0.15), residues: 3041 helix: 2.20 (0.21), residues: 673 sheet: 0.64 (0.20), residues: 665 loop : -1.13 (0.14), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1037 TYR 0.021 0.001 TYR A1065 PHE 0.021 0.001 PHE B1119 TRP 0.013 0.001 TRP C 884 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00470 (25851) covalent geometry : angle 0.59249 (35176) SS BOND : bond 0.00430 ( 40) SS BOND : angle 1.44590 ( 80) hydrogen bonds : bond 0.06229 ( 1001) hydrogen bonds : angle 4.86892 ( 2751) link_BETA1-4 : bond 0.00367 ( 36) link_BETA1-4 : angle 1.85971 ( 108) link_NAG-ASN : bond 0.00201 ( 48) link_NAG-ASN : angle 1.98396 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 99 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7943 (m-80) cc_final: 0.6756 (m-80) REVERT: A 235 ARG cc_start: 0.8766 (mtm110) cc_final: 0.8300 (mtm-85) REVERT: A 738 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8715 (tpp) REVERT: A 757 PHE cc_start: 0.8310 (p90) cc_final: 0.7736 (p90) REVERT: B 52 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 133 PHE cc_start: 0.7860 (m-10) cc_final: 0.7374 (m-10) REVERT: B 140 PHE cc_start: 0.7495 (p90) cc_final: 0.7071 (p90) REVERT: B 158 TYR cc_start: 0.7862 (p90) cc_final: 0.7248 (p90) REVERT: B 321 THR cc_start: 0.7283 (OUTLIER) cc_final: 0.7070 (p) REVERT: B 738 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8846 (tpt) REVERT: C 363 TYR cc_start: 0.9113 (m-80) cc_final: 0.8791 (m-80) REVERT: C 372 PHE cc_start: 0.8147 (m-80) cc_final: 0.7845 (m-80) REVERT: C 572 ASP cc_start: 0.8040 (m-30) cc_final: 0.7659 (m-30) REVERT: C 803 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8927 (mt) REVERT: C 876 LEU cc_start: 0.9183 (OUTLIER) cc_final: 0.8724 (tt) REVERT: C 982 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8780 (pt) outliers start: 54 outliers final: 42 residues processed: 148 average time/residue: 0.1446 time to fit residues: 35.9440 Evaluate side-chains 145 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 97 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 13 optimal weight: 2.9990 chunk 274 optimal weight: 1.9990 chunk 279 optimal weight: 0.0050 chunk 0 optimal weight: 20.0000 chunk 241 optimal weight: 20.0000 chunk 240 optimal weight: 6.9990 chunk 301 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 chunk 259 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.134997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077587 restraints weight = 46216.012| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.13 r_work: 0.2910 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25975 Z= 0.187 Angle : 0.622 13.557 35508 Z= 0.301 Chirality : 0.046 0.264 4241 Planarity : 0.004 0.050 4446 Dihedral : 6.831 86.764 5075 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.08 % Favored : 95.82 % Rotamer: Outliers : 2.04 % Allowed : 13.73 % Favored : 84.23 % 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: 0.05 (0.15), residues: 3041 helix: 2.15 (0.21), residues: 679 sheet: 0.63 (0.20), residues: 670 loop : -1.17 (0.14), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 212 TYR 0.021 0.001 TYR A1065 PHE 0.022 0.001 PHE B1119 TRP 0.016 0.001 TRP C 884 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00456 (25851) covalent geometry : angle 0.59737 (35176) SS BOND : bond 0.00430 ( 40) SS BOND : angle 1.45224 ( 80) hydrogen bonds : bond 0.06276 ( 1001) hydrogen bonds : angle 4.88209 ( 2751) link_BETA1-4 : bond 0.00377 ( 36) link_BETA1-4 : angle 1.84844 ( 108) link_NAG-ASN : bond 0.00198 ( 48) link_NAG-ASN : angle 2.12514 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 103 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7895 (m-80) cc_final: 0.6763 (m-80) REVERT: A 235 ARG cc_start: 0.8786 (mtm110) cc_final: 0.8420 (mtm-85) REVERT: A 757 PHE cc_start: 0.8330 (p90) cc_final: 0.7680 (p90) REVERT: B 52 GLN cc_start: 0.8839 (tm-30) cc_final: 0.8550 (tm-30) REVERT: B 133 PHE cc_start: 0.7720 (m-10) cc_final: 0.7308 (m-10) REVERT: B 140 PHE cc_start: 0.7502 (p90) cc_final: 0.7069 (p90) REVERT: B 158 TYR cc_start: 0.7760 (p90) cc_final: 0.7186 (p90) REVERT: B 321 THR cc_start: 0.7417 (OUTLIER) cc_final: 0.7196 (p) REVERT: B 738 MET cc_start: 0.9214 (OUTLIER) cc_final: 0.8945 (tpt) REVERT: B 1037 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8888 (ptm160) REVERT: C 363 TYR cc_start: 0.9108 (m-80) cc_final: 0.8816 (m-80) REVERT: C 372 PHE cc_start: 0.8179 (m-80) cc_final: 0.7883 (m-80) REVERT: C 572 ASP cc_start: 0.8035 (m-30) cc_final: 0.7649 (m-30) REVERT: C 803 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8909 (mt) REVERT: C 876 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8720 (tt) REVERT: C 982 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8719 (pt) outliers start: 55 outliers final: 43 residues processed: 154 average time/residue: 0.1450 time to fit residues: 37.2868 Evaluate side-chains 143 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 94 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 7 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 206 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 chunk 164 optimal weight: 0.8980 chunk 133 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 144 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 287 optimal weight: 0.0010 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.134326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.076714 restraints weight = 46380.560| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 3.12 r_work: 0.2893 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25975 Z= 0.221 Angle : 0.648 13.507 35508 Z= 0.316 Chirality : 0.047 0.267 4241 Planarity : 0.004 0.050 4446 Dihedral : 6.840 84.938 5075 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 2.07 % Allowed : 14.14 % Favored : 83.79 % 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: 3041 helix: 2.08 (0.21), residues: 679 sheet: 0.57 (0.20), residues: 669 loop : -1.22 (0.14), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B1037 TYR 0.023 0.001 TYR A1065 PHE 0.023 0.002 PHE B1119 TRP 0.014 0.001 TRP C 884 HIS 0.004 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00544 (25851) covalent geometry : angle 0.62241 (35176) SS BOND : bond 0.00450 ( 40) SS BOND : angle 1.52128 ( 80) hydrogen bonds : bond 0.06694 ( 1001) hydrogen bonds : angle 4.96038 ( 2751) link_BETA1-4 : bond 0.00360 ( 36) link_BETA1-4 : angle 1.85510 ( 108) link_NAG-ASN : bond 0.00228 ( 48) link_NAG-ASN : angle 2.21426 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 96 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7921 (m-80) cc_final: 0.6773 (m-80) REVERT: A 235 ARG cc_start: 0.8779 (mtm110) cc_final: 0.8420 (mtm-85) REVERT: A 757 PHE cc_start: 0.8369 (p90) cc_final: 0.7748 (p90) REVERT: B 52 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8573 (tm-30) REVERT: B 133 PHE cc_start: 0.7813 (m-10) cc_final: 0.7449 (m-10) REVERT: B 140 PHE cc_start: 0.7454 (p90) cc_final: 0.7054 (p90) REVERT: B 158 TYR cc_start: 0.7768 (p90) cc_final: 0.7113 (p90) REVERT: B 321 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.7265 (p) REVERT: B 738 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8983 (tpt) REVERT: B 1037 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8910 (ptm160) REVERT: C 363 TYR cc_start: 0.9116 (m-80) cc_final: 0.8823 (m-80) REVERT: C 372 PHE cc_start: 0.8210 (m-80) cc_final: 0.7919 (m-80) REVERT: C 572 ASP cc_start: 0.8007 (m-30) cc_final: 0.7669 (m-30) REVERT: C 803 ILE cc_start: 0.9212 (OUTLIER) cc_final: 0.8938 (mt) REVERT: C 876 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8728 (tt) REVERT: C 982 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8774 (pt) outliers start: 56 outliers final: 45 residues processed: 146 average time/residue: 0.1491 time to fit residues: 36.1086 Evaluate side-chains 145 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 94 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 325 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 157 optimal weight: 0.9980 chunk 233 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 276 optimal weight: 0.9980 chunk 211 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 282 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.135828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.078685 restraints weight = 46035.090| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.10 r_work: 0.2932 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25975 Z= 0.143 Angle : 0.596 13.598 35508 Z= 0.288 Chirality : 0.045 0.265 4241 Planarity : 0.004 0.050 4446 Dihedral : 6.620 82.073 5075 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.75 % Favored : 96.15 % Rotamer: Outliers : 1.89 % Allowed : 14.36 % Favored : 83.75 % 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: 0.10 (0.15), residues: 3041 helix: 2.21 (0.21), residues: 677 sheet: 0.66 (0.20), residues: 674 loop : -1.15 (0.14), residues: 1690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 344 TYR 0.020 0.001 TYR C 493 PHE 0.021 0.001 PHE B1119 TRP 0.012 0.001 TRP C 884 HIS 0.002 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00338 (25851) covalent geometry : angle 0.57060 (35176) SS BOND : bond 0.00351 ( 40) SS BOND : angle 1.26604 ( 80) hydrogen bonds : bond 0.05750 ( 1001) hydrogen bonds : angle 4.81208 ( 2751) link_BETA1-4 : bond 0.00398 ( 36) link_BETA1-4 : angle 1.83247 ( 108) link_NAG-ASN : bond 0.00185 ( 48) link_NAG-ASN : angle 2.14658 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6082 Ramachandran restraints generated. 3041 Oldfield, 0 Emsley, 3041 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 102 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 PHE cc_start: 0.7863 (m-80) cc_final: 0.6720 (m-80) REVERT: A 235 ARG cc_start: 0.8772 (mtm110) cc_final: 0.8416 (mtm-85) REVERT: B 52 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8556 (tm-30) REVERT: B 133 PHE cc_start: 0.7847 (m-10) cc_final: 0.7448 (m-10) REVERT: B 158 TYR cc_start: 0.7582 (p90) cc_final: 0.6938 (p90) REVERT: B 321 THR cc_start: 0.7486 (OUTLIER) cc_final: 0.7265 (p) REVERT: B 738 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8931 (tpt) REVERT: B 1037 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.8601 (mtp180) REVERT: C 363 TYR cc_start: 0.9087 (m-80) cc_final: 0.8795 (m-80) REVERT: C 372 PHE cc_start: 0.8222 (m-80) cc_final: 0.7931 (m-80) REVERT: C 572 ASP cc_start: 0.8076 (m-30) cc_final: 0.7686 (m-30) REVERT: C 803 ILE cc_start: 0.9186 (OUTLIER) cc_final: 0.8902 (mt) REVERT: C 876 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8724 (tt) REVERT: C 982 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8705 (pt) outliers start: 51 outliers final: 44 residues processed: 149 average time/residue: 0.1381 time to fit residues: 34.7301 Evaluate side-chains 146 residues out of total 2702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 551 THR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 316 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1079 ILE Chi-restraints excluded: chain B residue 1103 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 126 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 722 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 757 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 853 PHE Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 36 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 255 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 294 optimal weight: 1.9990 chunk 205 optimal weight: 20.0000 chunk 250 optimal weight: 0.0270 chunk 247 optimal weight: 8.9990 chunk 102 optimal weight: 30.0000 chunk 265 optimal weight: 3.9990 chunk 223 optimal weight: 7.9990 overall best weight: 1.6844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 976 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.134959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077236 restraints weight = 46116.681| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.15 r_work: 0.2909 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25975 Z= 0.181 Angle : 0.618 13.601 35508 Z= 0.302 Chirality : 0.046 0.266 4241 Planarity : 0.004 0.051 4446 Dihedral : 6.595 82.120 5075 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.24 % Favored : 95.66 % Rotamer: Outliers : 1.89 % Allowed : 14.54 % Favored : 83.57 % 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: 0.02 (0.15), residues: 3041 helix: 2.18 (0.21), residues: 673 sheet: 0.62 (0.20), residues: 666 loop : -1.20 (0.14), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1037 TYR 0.020 0.001 TYR A1065 PHE 0.022 0.001 PHE B1119 TRP 0.013 0.001 TRP C 884 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00440 (25851) covalent geometry : angle 0.59434 (35176) SS BOND : bond 0.00398 ( 40) SS BOND : angle 1.38532 ( 80) hydrogen bonds : bond 0.06184 ( 1001) hydrogen bonds : angle 4.86042 ( 2751) link_BETA1-4 : bond 0.00363 ( 36) link_BETA1-4 : angle 1.82982 ( 108) link_NAG-ASN : bond 0.00204 ( 48) link_NAG-ASN : angle 2.07989 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8227.41 seconds wall clock time: 140 minutes 39.21 seconds (8439.21 seconds total)