Starting phenix.real_space_refine on Thu Mar 5 21:44:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7q_31778/03_2026/7v7q_31778.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7q_31778/03_2026/7v7q_31778.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v7q_31778/03_2026/7v7q_31778.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7q_31778/03_2026/7v7q_31778.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7q_31778/03_2026/7v7q_31778.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7q_31778/03_2026/7v7q_31778.map" } resolution = 2.8 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= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16114 2.51 5 N 4129 2.21 5 O 5020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25371 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.32, per 1000 atoms: 0.25 Number of scatterers: 25371 At special positions: 0 Unit cell: (141.9, 145.2, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5020 8.00 N 4129 7.00 C 16114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.02 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=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.02 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 601 " " NAG A2003 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 341 " " NAG J 1 " - " ASN A 614 " " NAG K 1 " - " ASN A 707 " " NAG L 1 " - " ASN A 715 " " NAG M 1 " - " ASN A 799 " " NAG N 1 " - " ASN A1072 " " NAG O 1 " - " ASN A1096 " " NAG P 1 " - " ASN A1132 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 163 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 2.73 Conformation dependent library (CDL) restraints added in 1.2 seconds 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5802 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 47 sheets defined 25.3% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.649A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 369 Processing helix chain 'A' and resid 381 through 385 Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.232A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 removed outlier: 3.591A pdb=" N GLY A 883 " --> pdb=" O THR A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.076A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 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: 3.690A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 3.597A pdb=" N ALA A 987 " --> pdb=" O ASP A 983 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 3.705A 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: 4.000A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.632A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.724A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 420 Processing helix chain 'B' and resid 436 through 441 removed outlier: 3.623A pdb=" N SER B 441 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.832A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.683A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.644A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.985A 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 917 removed outlier: 3.639A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 Processing helix chain 'B' and resid 943 through 963 removed outlier: 3.526A 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: 3.628A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.324A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.874A 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 347 through 351 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.831A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 388 removed outlier: 3.733A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 4.083A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.820A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.653A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.643A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 917 removed outlier: 4.048A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN C 917 " --> pdb=" O VAL C 913 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 917' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.265A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.631A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.995A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.359A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.265A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.922A 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: 6.548A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.165A 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: 4.129A 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: 7.082A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.352A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.110A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.159A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.625A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 3.501A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.601A pdb=" N VAL A 574 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.795A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.948A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 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: 6.050A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.121A 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 701 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: 6.145A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 6.079A 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: 4.547A 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 26 through 30 removed outlier: 7.946A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ASN B 186 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.318A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.939A 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: 4.193A 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: 7.239A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.290A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.996A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.158A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.535A 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: 5.540A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.434A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N GLY B 564 " --> pdb=" O ASP B 572 " (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: 6.180A 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 452 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: 6.052A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD3, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.026A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.946A 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: 4.475A 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: 5.035A 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: 5.082A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.051A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.922A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.057A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.207A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.556A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE4, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.778A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE6, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.508A pdb=" N TYR C 487 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 652 through 653 removed outlier: 5.830A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.779A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.574A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AF2, first strand: chain 'C' and resid 1092 through 1095 989 hydrogen bonds defined for protein. 2703 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 3.55 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: 8002 1.34 - 1.46: 6372 1.46 - 1.58: 11416 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25922 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.98e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.58e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 NAG k 1 " pdb=" O5 NAG k 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 NAG B2003 " pdb=" O5 NAG B2003 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.49e+00 ... (remaining 25917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 34307 1.61 - 3.23: 873 3.23 - 4.84: 71 4.84 - 6.45: 15 6.45 - 8.07: 7 Bond angle restraints: 35273 Sorted by residual: angle pdb=" N PRO A 984 " pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 110.70 114.57 -3.87 1.22e+00 6.72e-01 1.01e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.48 -3.78 1.22e+00 6.72e-01 9.59e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.58 -6.11 2.06e+00 2.36e-01 8.81e+00 angle pdb=" C CYS C 660 " pdb=" N ASP C 661 " pdb=" CA ASP C 661 " ideal model delta sigma weight residual 121.54 127.09 -5.55 1.91e+00 2.74e-01 8.44e+00 angle pdb=" C VAL C 779 " pdb=" N PHE C 780 " pdb=" CA PHE C 780 " ideal model delta sigma weight residual 122.53 117.21 5.32 1.92e+00 2.71e-01 7.68e+00 ... (remaining 35268 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.50: 15333 21.50 - 43.00: 997 43.00 - 64.50: 163 64.50 - 86.01: 46 86.01 - 107.51: 7 Dihedral angle restraints: 16546 sinusoidal: 7534 harmonic: 9012 Sorted by residual: dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 -9.18 -76.82 1 1.00e+01 1.00e-02 7.41e+01 dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -9.92 -76.08 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS A 536 " pdb=" SG CYS A 536 " pdb=" SG CYS A 588 " pdb=" CB CYS A 588 " ideal model delta sinusoidal sigma weight residual -86.00 -10.02 -75.98 1 1.00e+01 1.00e-02 7.27e+01 ... (remaining 16543 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3259 0.050 - 0.099: 768 0.099 - 0.149: 206 0.149 - 0.199: 15 0.199 - 0.248: 2 Chirality restraints: 4250 Sorted by residual: chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.19 -0.21 2.00e-01 2.50e+01 1.08e+00 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 2.52 0.20 2.00e-01 2.50e+01 9.72e-01 ... (remaining 4247 not shown) Planarity restraints: 4504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1137 " -0.047 5.00e-02 4.00e+02 7.23e-02 8.35e+00 pdb=" N PRO A1138 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A1138 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1138 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO A 984 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 558 " -0.030 5.00e-02 4.00e+02 4.52e-02 3.27e+00 pdb=" N PRO A 559 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 559 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 559 " -0.025 5.00e-02 4.00e+02 ... (remaining 4501 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 691 2.70 - 3.25: 24245 3.25 - 3.80: 37902 3.80 - 4.35: 47221 4.35 - 4.90: 81838 Nonbonded interactions: 191897 Sorted by model distance: nonbonded pdb=" OH TYR C 754 " pdb=" OD1 ASP C 992 " model vdw 2.148 3.040 nonbonded pdb=" O ASP A 403 " pdb=" NH1 ARG A 406 " model vdw 2.156 3.120 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.164 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.193 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.196 3.040 ... (remaining 191892 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 633 through 825 or resid 853 throu \ gh 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: 3.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.880 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 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 0.049 26045 Z= 0.184 Angle : 0.614 10.820 35603 Z= 0.295 Chirality : 0.046 0.248 4250 Planarity : 0.004 0.072 4456 Dihedral : 13.999 107.507 10627 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3048 helix: 1.99 (0.21), residues: 663 sheet: 0.60 (0.19), residues: 721 loop : -1.10 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.016 0.001 TYR C1065 PHE 0.025 0.001 PHE A 904 TRP 0.011 0.001 TRP C 884 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00380 (25922) covalent geometry : angle 0.58488 (35273) SS BOND : bond 0.00340 ( 39) SS BOND : angle 1.64705 ( 78) hydrogen bonds : bond 0.11466 ( 989) hydrogen bonds : angle 5.61599 ( 2703) link_BETA1-4 : bond 0.00382 ( 36) link_BETA1-4 : angle 1.94488 ( 108) link_NAG-ASN : bond 0.00251 ( 48) link_NAG-ASN : angle 2.24425 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.914 Fit side-chains REVERT: A 367 TYR cc_start: 0.8201 (t80) cc_final: 0.7735 (t80) REVERT: B 454 PHE cc_start: 0.8801 (m-10) cc_final: 0.8552 (m-80) REVERT: C 133 PHE cc_start: 0.8596 (m-80) cc_final: 0.8259 (m-80) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.7043 time to fit residues: 55.7761 Evaluate side-chains 52 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 3.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 802 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.073059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.045558 restraints weight = 88892.981| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 4.12 r_work: 0.2703 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.0612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26045 Z= 0.166 Angle : 0.597 17.934 35603 Z= 0.295 Chirality : 0.045 0.216 4250 Planarity : 0.004 0.059 4456 Dihedral : 8.286 91.346 5084 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 0.30 % Allowed : 5.50 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.15), residues: 3048 helix: 2.12 (0.21), residues: 671 sheet: 0.64 (0.19), residues: 715 loop : -1.09 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 406 TYR 0.019 0.001 TYR A 493 PHE 0.022 0.001 PHE A 904 TRP 0.010 0.001 TRP C 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00390 (25922) covalent geometry : angle 0.57177 (35273) SS BOND : bond 0.00416 ( 39) SS BOND : angle 1.66837 ( 78) hydrogen bonds : bond 0.05805 ( 989) hydrogen bonds : angle 4.91396 ( 2703) link_BETA1-4 : bond 0.00335 ( 36) link_BETA1-4 : angle 1.83921 ( 108) link_NAG-ASN : bond 0.00230 ( 48) link_NAG-ASN : angle 2.01400 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8561 (t80) cc_final: 0.8075 (t80) REVERT: A 898 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.9036 (mtm) REVERT: B 454 PHE cc_start: 0.9227 (m-10) cc_final: 0.8763 (m-80) REVERT: B 1027 MET cc_start: 0.9128 (OUTLIER) cc_final: 0.8561 (tpp) outliers start: 8 outliers final: 3 residues processed: 59 average time/residue: 0.6449 time to fit residues: 44.7534 Evaluate side-chains 51 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain C residue 387 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 53 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 221 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 132 optimal weight: 0.1980 chunk 256 optimal weight: 7.9990 chunk 137 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 150 optimal weight: 4.9990 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.071377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.043629 restraints weight = 89077.697| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 4.10 r_work: 0.2644 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 26045 Z= 0.271 Angle : 0.667 26.104 35603 Z= 0.328 Chirality : 0.047 0.255 4250 Planarity : 0.004 0.056 4456 Dihedral : 7.754 83.305 5084 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.79 % Favored : 95.11 % Rotamer: Outliers : 0.74 % Allowed : 8.97 % Favored : 90.29 % 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: 3048 helix: 2.02 (0.21), residues: 668 sheet: 0.42 (0.19), residues: 705 loop : -1.19 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1037 TYR 0.020 0.001 TYR C1065 PHE 0.034 0.002 PHE A 904 TRP 0.012 0.001 TRP C 884 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00648 (25922) covalent geometry : angle 0.63972 (35273) SS BOND : bond 0.00527 ( 39) SS BOND : angle 2.03047 ( 78) hydrogen bonds : bond 0.07001 ( 989) hydrogen bonds : angle 5.05412 ( 2703) link_BETA1-4 : bond 0.00274 ( 36) link_BETA1-4 : angle 1.91778 ( 108) link_NAG-ASN : bond 0.00356 ( 48) link_NAG-ASN : angle 2.15409 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.969 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8577 (t80) cc_final: 0.8115 (t80) REVERT: A 569 ASP cc_start: 0.9015 (m-30) cc_final: 0.8392 (p0) REVERT: A 898 MET cc_start: 0.9395 (OUTLIER) cc_final: 0.9047 (mtp) REVERT: B 1027 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8895 (tpp) REVERT: C 983 ASP cc_start: 0.7413 (OUTLIER) cc_final: 0.6986 (t0) outliers start: 20 outliers final: 5 residues processed: 68 average time/residue: 0.5723 time to fit residues: 46.5577 Evaluate side-chains 58 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1027 MET Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 387 ASP Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 272 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 28 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 243 optimal weight: 8.9990 chunk 282 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.072758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.045285 restraints weight = 88337.814| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.10 r_work: 0.2693 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26045 Z= 0.130 Angle : 0.581 26.734 35603 Z= 0.282 Chirality : 0.044 0.239 4250 Planarity : 0.004 0.057 4456 Dihedral : 7.099 76.531 5084 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.84 % Favored : 96.06 % Rotamer: Outliers : 1.03 % Allowed : 10.63 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3048 helix: 2.14 (0.21), residues: 672 sheet: 0.61 (0.19), residues: 705 loop : -1.10 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1089 TYR 0.016 0.001 TYR C1065 PHE 0.020 0.001 PHE A 390 TRP 0.009 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00293 (25922) covalent geometry : angle 0.55550 (35273) SS BOND : bond 0.00426 ( 39) SS BOND : angle 1.57420 ( 78) hydrogen bonds : bond 0.05692 ( 989) hydrogen bonds : angle 4.77444 ( 2703) link_BETA1-4 : bond 0.00357 ( 36) link_BETA1-4 : angle 1.88503 ( 108) link_NAG-ASN : bond 0.00230 ( 48) link_NAG-ASN : angle 1.96254 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 0.914 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8567 (t80) cc_final: 0.8107 (t80) REVERT: A 569 ASP cc_start: 0.8970 (m-30) cc_final: 0.8326 (p0) REVERT: A 898 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.9029 (mtm) REVERT: C 974 VAL cc_start: 0.9129 (OUTLIER) cc_final: 0.8875 (m) REVERT: C 983 ASP cc_start: 0.7332 (OUTLIER) cc_final: 0.6905 (t0) outliers start: 28 outliers final: 11 residues processed: 77 average time/residue: 0.5381 time to fit residues: 50.3354 Evaluate side-chains 63 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 778 GLU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 116 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 273 optimal weight: 3.9990 chunk 237 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.071574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.043948 restraints weight = 88707.778| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 4.08 r_work: 0.2653 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 26045 Z= 0.233 Angle : 0.636 28.861 35603 Z= 0.308 Chirality : 0.046 0.239 4250 Planarity : 0.004 0.061 4456 Dihedral : 6.949 71.687 5084 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.69 % Favored : 95.21 % Rotamer: Outliers : 1.44 % Allowed : 11.70 % Favored : 86.86 % 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: 3048 helix: 2.13 (0.21), residues: 669 sheet: 0.48 (0.19), residues: 707 loop : -1.19 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1037 TYR 0.021 0.001 TYR C1065 PHE 0.021 0.001 PHE A 904 TRP 0.008 0.001 TRP C 884 HIS 0.004 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00557 (25922) covalent geometry : angle 0.60977 (35273) SS BOND : bond 0.00473 ( 39) SS BOND : angle 1.81600 ( 78) hydrogen bonds : bond 0.06538 ( 989) hydrogen bonds : angle 4.89967 ( 2703) link_BETA1-4 : bond 0.00274 ( 36) link_BETA1-4 : angle 1.91690 ( 108) link_NAG-ASN : bond 0.00305 ( 48) link_NAG-ASN : angle 2.06139 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 50 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8577 (t80) cc_final: 0.8125 (t80) REVERT: A 668 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8731 (pp) REVERT: A 898 MET cc_start: 0.9392 (OUTLIER) cc_final: 0.8991 (mtm) REVERT: A 982 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8826 (pp) REVERT: C 974 VAL cc_start: 0.9146 (OUTLIER) cc_final: 0.8825 (m) REVERT: C 983 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6936 (t0) outliers start: 39 outliers final: 14 residues processed: 85 average time/residue: 0.4633 time to fit residues: 48.6883 Evaluate side-chains 67 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 21 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 300 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 245 optimal weight: 0.9990 chunk 218 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 173 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.072758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.045283 restraints weight = 89017.410| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 4.12 r_work: 0.2694 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26045 Z= 0.125 Angle : 0.576 28.049 35603 Z= 0.277 Chirality : 0.044 0.232 4250 Planarity : 0.004 0.060 4456 Dihedral : 6.510 64.498 5084 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.67 % Favored : 96.23 % Rotamer: Outliers : 1.37 % Allowed : 12.51 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3048 helix: 2.26 (0.21), residues: 672 sheet: 0.63 (0.19), residues: 707 loop : -1.08 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.016 0.001 TYR C1065 PHE 0.016 0.001 PHE A 390 TRP 0.008 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00284 (25922) covalent geometry : angle 0.55096 (35273) SS BOND : bond 0.00354 ( 39) SS BOND : angle 1.49035 ( 78) hydrogen bonds : bond 0.05524 ( 989) hydrogen bonds : angle 4.69103 ( 2703) link_BETA1-4 : bond 0.00391 ( 36) link_BETA1-4 : angle 1.89779 ( 108) link_NAG-ASN : bond 0.00229 ( 48) link_NAG-ASN : angle 1.92321 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 52 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8544 (t80) cc_final: 0.8087 (t80) REVERT: A 569 ASP cc_start: 0.8946 (m-30) cc_final: 0.8308 (p0) REVERT: A 898 MET cc_start: 0.9335 (OUTLIER) cc_final: 0.9015 (mtm) REVERT: A 982 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8783 (pp) REVERT: C 974 VAL cc_start: 0.9148 (OUTLIER) cc_final: 0.8933 (m) REVERT: C 983 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6913 (t0) outliers start: 37 outliers final: 17 residues processed: 85 average time/residue: 0.4727 time to fit residues: 49.9112 Evaluate side-chains 71 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 183 optimal weight: 1.9990 chunk 304 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 241 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 198 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 279 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.071373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.043673 restraints weight = 88800.128| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 4.08 r_work: 0.2644 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 26045 Z= 0.245 Angle : 0.646 29.648 35603 Z= 0.313 Chirality : 0.046 0.238 4250 Planarity : 0.004 0.062 4456 Dihedral : 6.527 59.673 5084 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.86 % Favored : 95.05 % Rotamer: Outliers : 1.59 % Allowed : 13.18 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3048 helix: 2.20 (0.21), residues: 669 sheet: 0.45 (0.19), residues: 715 loop : -1.16 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1037 TYR 0.021 0.001 TYR C1065 PHE 0.016 0.001 PHE B1119 TRP 0.007 0.001 TRP C 884 HIS 0.004 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00584 (25922) covalent geometry : angle 0.62042 (35273) SS BOND : bond 0.00491 ( 39) SS BOND : angle 1.87493 ( 78) hydrogen bonds : bond 0.06615 ( 989) hydrogen bonds : angle 4.87589 ( 2703) link_BETA1-4 : bond 0.00291 ( 36) link_BETA1-4 : angle 1.94401 ( 108) link_NAG-ASN : bond 0.00326 ( 48) link_NAG-ASN : angle 2.06009 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 49 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 367 TYR cc_start: 0.8586 (t80) cc_final: 0.8132 (t80) REVERT: A 668 ILE cc_start: 0.9082 (OUTLIER) cc_final: 0.8775 (pp) REVERT: A 898 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.9001 (mtp) REVERT: A 982 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8779 (pp) REVERT: C 387 ASP cc_start: 0.9421 (m-30) cc_final: 0.9210 (m-30) REVERT: C 974 VAL cc_start: 0.9123 (OUTLIER) cc_final: 0.8920 (m) REVERT: C 983 ASP cc_start: 0.7376 (OUTLIER) cc_final: 0.6935 (t0) outliers start: 43 outliers final: 21 residues processed: 90 average time/residue: 0.4468 time to fit residues: 50.1441 Evaluate side-chains 74 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 277 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 210 optimal weight: 10.0000 chunk 186 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 192 optimal weight: 0.7980 chunk 266 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.071820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.044192 restraints weight = 88568.250| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 4.09 r_work: 0.2660 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 26045 Z= 0.184 Angle : 0.616 29.715 35603 Z= 0.296 Chirality : 0.045 0.238 4250 Planarity : 0.004 0.061 4456 Dihedral : 6.354 59.354 5084 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.59 % Allowed : 13.77 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.15), residues: 3048 helix: 2.21 (0.21), residues: 670 sheet: 0.48 (0.19), residues: 708 loop : -1.14 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1037 TYR 0.018 0.001 TYR C1065 PHE 0.015 0.001 PHE B1119 TRP 0.008 0.001 TRP C 884 HIS 0.003 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00435 (25922) covalent geometry : angle 0.59084 (35273) SS BOND : bond 0.00428 ( 39) SS BOND : angle 1.71831 ( 78) hydrogen bonds : bond 0.06173 ( 989) hydrogen bonds : angle 4.79301 ( 2703) link_BETA1-4 : bond 0.00340 ( 36) link_BETA1-4 : angle 1.93697 ( 108) link_NAG-ASN : bond 0.00237 ( 48) link_NAG-ASN : angle 1.99775 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 49 time to evaluate : 0.786 Fit side-chains revert: symmetry clash REVERT: A 668 ILE cc_start: 0.9055 (OUTLIER) cc_final: 0.8715 (pp) REVERT: A 898 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.9042 (mtm) REVERT: A 982 LEU cc_start: 0.9136 (OUTLIER) cc_final: 0.8770 (pp) REVERT: B 738 MET cc_start: 0.9608 (mmm) cc_final: 0.9367 (ttm) REVERT: C 387 ASP cc_start: 0.9413 (m-30) cc_final: 0.9202 (m-30) REVERT: C 983 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6950 (t0) outliers start: 43 outliers final: 24 residues processed: 90 average time/residue: 0.4304 time to fit residues: 48.5336 Evaluate side-chains 75 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 47 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 662 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Chi-restraints excluded: chain C residue 1134 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 240 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 17 optimal weight: 6.9990 chunk 210 optimal weight: 9.9990 chunk 276 optimal weight: 0.8980 chunk 37 optimal weight: 20.0000 chunk 159 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.072815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.045355 restraints weight = 88930.164| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 4.11 r_work: 0.2694 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26045 Z= 0.124 Angle : 0.587 28.648 35603 Z= 0.281 Chirality : 0.044 0.264 4250 Planarity : 0.004 0.059 4456 Dihedral : 6.032 57.704 5084 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.64 % Rotamer: Outliers : 1.22 % Allowed : 14.29 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3048 helix: 2.30 (0.21), residues: 673 sheet: 0.62 (0.19), residues: 716 loop : -1.08 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 981 TYR 0.016 0.001 TYR C1065 PHE 0.013 0.001 PHE C1119 TRP 0.009 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00284 (25922) covalent geometry : angle 0.56306 (35273) SS BOND : bond 0.00341 ( 39) SS BOND : angle 1.47870 ( 78) hydrogen bonds : bond 0.05417 ( 989) hydrogen bonds : angle 4.64833 ( 2703) link_BETA1-4 : bond 0.00388 ( 36) link_BETA1-4 : angle 1.91467 ( 108) link_NAG-ASN : bond 0.00230 ( 48) link_NAG-ASN : angle 1.90802 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 51 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8938 (m-30) cc_final: 0.8322 (p0) REVERT: A 668 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8684 (pp) REVERT: A 898 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.9012 (mtm) REVERT: A 982 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8789 (pp) REVERT: B 454 PHE cc_start: 0.9274 (m-10) cc_final: 0.8809 (m-80) REVERT: B 738 MET cc_start: 0.9490 (mmm) cc_final: 0.9268 (ttm) REVERT: C 983 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6924 (t0) outliers start: 33 outliers final: 21 residues processed: 81 average time/residue: 0.4720 time to fit residues: 47.2910 Evaluate side-chains 73 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 260 optimal weight: 0.9980 chunk 145 optimal weight: 8.9990 chunk 190 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** C 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.073129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.045781 restraints weight = 88889.350| |-----------------------------------------------------------------------------| r_work (start): 0.2849 rms_B_bonded: 4.10 r_work: 0.2707 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26045 Z= 0.118 Angle : 0.584 28.248 35603 Z= 0.278 Chirality : 0.044 0.277 4250 Planarity : 0.004 0.059 4456 Dihedral : 5.808 57.002 5084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.97 % Favored : 95.93 % Rotamer: Outliers : 1.11 % Allowed : 14.51 % Favored : 84.39 % 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: 3048 helix: 2.34 (0.21), residues: 667 sheet: 0.66 (0.19), residues: 732 loop : -1.05 (0.15), residues: 1649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 188 TYR 0.017 0.001 TYR C1065 PHE 0.012 0.001 PHE A 390 TRP 0.008 0.001 TRP C 434 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00268 (25922) covalent geometry : angle 0.56044 (35273) SS BOND : bond 0.00327 ( 39) SS BOND : angle 1.45962 ( 78) hydrogen bonds : bond 0.05180 ( 989) hydrogen bonds : angle 4.57417 ( 2703) link_BETA1-4 : bond 0.00390 ( 36) link_BETA1-4 : angle 1.88735 ( 108) link_NAG-ASN : bond 0.00217 ( 48) link_NAG-ASN : angle 1.87361 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6096 Ramachandran restraints generated. 3048 Oldfield, 0 Emsley, 3048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 53 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 51 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8936 (p) REVERT: A 367 TYR cc_start: 0.8166 (t80) cc_final: 0.7965 (t80) REVERT: A 569 ASP cc_start: 0.8903 (m-30) cc_final: 0.8283 (p0) REVERT: A 668 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8663 (pp) REVERT: A 982 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8769 (pp) REVERT: B 454 PHE cc_start: 0.9273 (m-10) cc_final: 0.8803 (m-80) REVERT: B 738 MET cc_start: 0.9481 (mmm) cc_final: 0.9240 (ttm) REVERT: C 387 ASP cc_start: 0.9382 (m-30) cc_final: 0.9119 (m-30) REVERT: C 983 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.6902 (t0) outliers start: 30 outliers final: 22 residues processed: 81 average time/residue: 0.4558 time to fit residues: 45.8131 Evaluate side-chains 72 residues out of total 2709 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 46 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 588 CYS Chi-restraints excluded: chain A residue 668 ILE Chi-restraints excluded: chain A residue 757 PHE Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 992 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 428 THR Chi-restraints excluded: chain B residue 551 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 586 THR Chi-restraints excluded: chain C residue 669 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 983 ASP Chi-restraints excluded: chain C residue 1120 VAL Chi-restraints excluded: chain C residue 1128 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 227 optimal weight: 0.5980 chunk 269 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 152 optimal weight: 8.9990 chunk 136 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 214 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 270 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.072485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.045117 restraints weight = 88177.796| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 4.07 r_work: 0.2691 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26045 Z= 0.148 Angle : 0.594 28.738 35603 Z= 0.284 Chirality : 0.044 0.283 4250 Planarity : 0.004 0.060 4456 Dihedral : 5.786 57.046 5084 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.18 % Allowed : 14.65 % Favored : 84.16 % 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: 0.19 (0.15), residues: 3048 helix: 2.33 (0.21), residues: 672 sheet: 0.63 (0.19), residues: 704 loop : -1.09 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1037 TYR 0.018 0.001 TYR C1065 PHE 0.015 0.001 PHE B1119 TRP 0.007 0.001 TRP C 884 HIS 0.003 0.001 HIS A1062 Details of bonding type rmsd covalent geometry : bond 0.00347 (25922) covalent geometry : angle 0.57040 (35273) SS BOND : bond 0.00369 ( 39) SS BOND : angle 1.55435 ( 78) hydrogen bonds : bond 0.05531 ( 989) hydrogen bonds : angle 4.62118 ( 2703) link_BETA1-4 : bond 0.00360 ( 36) link_BETA1-4 : angle 1.87188 ( 108) link_NAG-ASN : bond 0.00221 ( 48) link_NAG-ASN : angle 1.89416 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7518.86 seconds wall clock time: 128 minutes 47.49 seconds (7727.49 seconds total)