Starting phenix.real_space_refine on Mon Jul 6 12:19:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.map" model { file = "/net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v88_31793/07_2026/7v88_31793.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.047 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 166 5.16 5 C 22330 2.51 5 N 5732 2.21 5 O 6870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35098 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 8016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8016 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 53, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8035 Classifications: {'peptide': 1029} Link IDs: {'PTRANS': 53, 'TRANS': 975} Chain breaks: 7 Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 chiralities: 5 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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 chiralities: 2 Time building chain proxies: 9.15, per 1000 atoms: 0.26 Number of scatterers: 35098 At special positions: 0 Unit cell: (139.7, 155.1, 245.3, 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 166 16.00 O 6870 8.00 N 5732 7.00 C 22330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, 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=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 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=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 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 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 n 1 " - " NAG n 2 " " NAG o 1 " - " NAG o 2 " " NAG p 1 " - " NAG p 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 601 " " NAG C2003 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 901 " - " ASN F 103 " " NAG F 902 " - " ASN F 322 " " NAG G 901 " - " ASN G 90 " " NAG G 902 " - " ASN G 322 " " NAG H 1 " - " ASN A 232 " " NAG I 1 " - " ASN A 280 " " NAG J 1 " - " ASN A 329 " " NAG K 1 " - " ASN A 341 " " NAG L 1 " - " ASN A 614 " " NAG M 1 " - " ASN A 707 " " NAG N 1 " - " ASN A 715 " " NAG O 1 " - " ASN A 799 " " NAG P 1 " - " ASN A1072 " " NAG Q 1 " - " ASN A1096 " " NAG R 1 " - " ASN A1132 " " NAG S 1 " - " ASN B 122 " " NAG T 1 " - " ASN B 163 " " NAG U 1 " - " ASN B 280 " " NAG V 1 " - " ASN B 341 " " NAG W 1 " - " ASN B 614 " " NAG X 1 " - " ASN B 707 " " NAG Y 1 " - " ASN B 715 " " NAG Z 1 " - " ASN B 799 " " NAG a 1 " - " ASN B1072 " " NAG b 1 " - " ASN B1096 " " NAG c 1 " - " ASN B1132 " " NAG d 1 " - " ASN C 122 " " NAG e 1 " - " ASN C 163 " " NAG f 1 " - " ASN C 232 " " NAG g 1 " - " ASN C 280 " " NAG h 1 " - " ASN C 329 " " NAG i 1 " - " ASN C 341 " " NAG j 1 " - " ASN C 614 " " NAG k 1 " - " ASN C 707 " " NAG l 1 " - " ASN C 715 " " NAG m 1 " - " ASN C 799 " " NAG n 1 " - " ASN C1072 " " NAG o 1 " - " ASN C1096 " " NAG p 1 " - " ASN C1132 " Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8044 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 48 sheets defined 36.5% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 removed outlier: 3.520A pdb=" N PHE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 351 Processing helix chain 'A' and resid 362 through 368 removed outlier: 4.197A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 3.993A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 408 removed outlier: 4.670A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) removed outlier: 3.525A 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 742 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 757 through 781 removed outlier: 3.917A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.622A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.506A pdb=" N ILE A 907 " --> pdb=" O ARG A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.505A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 removed outlier: 3.500A pdb=" N GLN A 947 " --> pdb=" O LEU A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 980 removed outlier: 3.525A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.889A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.707A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.190A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.363A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) removed outlier: 3.545A 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 Processing helix chain 'B' and resid 566 through 570 removed outlier: 3.692A pdb=" N THR B 570 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.782A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.672A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.723A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.724A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 938 removed outlier: 3.541A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.531A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 982 " --> pdb=" O ILE B 978 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.650A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU B 994 " --> pdb=" O GLN B 990 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.986A 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 removed outlier: 3.615A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 4.403A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 386 removed outlier: 4.029A pdb=" N ASN C 386 " --> pdb=" O PRO C 382 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.816A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 436 through 441 Processing helix chain 'C' and resid 500 through 503 Processing helix chain 'C' and resid 735 through 741 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 758 through 781 removed outlier: 3.505A pdb=" N ASN C 762 " --> pdb=" O CYS C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.540A 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 910 through 939 removed outlier: 4.335A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 Processing helix chain 'C' and resid 983 through 1032 removed outlier: 5.426A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU C 994 " --> pdb=" O GLN C 990 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.825A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 53 removed outlier: 3.623A pdb=" N GLN F 24 " --> pdb=" O THR F 20 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU F 39 " --> pdb=" O GLU F 35 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 79 removed outlier: 3.519A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LYS F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.536A pdb=" N ALA F 99 " --> pdb=" O LEU F 95 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU F 100 " --> pdb=" O GLN F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 129 Processing helix chain 'F' and resid 147 through 154 Processing helix chain 'F' and resid 158 through 172 removed outlier: 3.667A pdb=" N LEU F 162 " --> pdb=" O TYR F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 194 Processing helix chain 'F' and resid 198 through 205 removed outlier: 3.656A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.963A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 252 removed outlier: 3.656A pdb=" N HIS F 239 " --> pdb=" O PRO F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 300 Processing helix chain 'F' and resid 303 through 319 Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 removed outlier: 3.520A pdb=" N TYR F 385 " --> pdb=" O TYR F 381 " (cutoff:3.500A) Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.720A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 412 removed outlier: 4.120A pdb=" N HIS F 401 " --> pdb=" O ASN F 397 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLU F 402 " --> pdb=" O GLU F 398 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 449 through 466 Processing helix chain 'F' and resid 473 through 484 removed outlier: 3.858A pdb=" N GLU F 483 " --> pdb=" O GLU F 479 " (cutoff:3.500A) Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.738A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) Processing helix chain 'F' and resid 512 through 532 removed outlier: 3.813A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 538 through 542 Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.506A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) Processing helix chain 'F' and resid 560 through 564 removed outlier: 3.532A pdb=" N SER F 563 " --> pdb=" O LEU F 560 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU F 564 " --> pdb=" O GLY F 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 560 through 564' Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 581 through 588 removed outlier: 3.669A pdb=" N PHE F 588 " --> pdb=" O LEU F 584 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.786A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 53 removed outlier: 4.018A pdb=" N HIS G 34 " --> pdb=" O ASP G 30 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU G 35 " --> pdb=" O LYS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 80 removed outlier: 3.519A pdb=" N VAL G 59 " --> pdb=" O THR G 55 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLU G 75 " --> pdb=" O ALA G 71 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 101 Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 147 through 154 Processing helix chain 'G' and resid 158 through 194 removed outlier: 3.793A pdb=" N LYS G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 5.550A pdb=" N GLN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) Proline residue: G 178 - end of helix Processing helix chain 'G' and resid 198 through 204 Processing helix chain 'G' and resid 218 through 231 removed outlier: 3.567A pdb=" N LEU G 222 " --> pdb=" O SER G 218 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLU G 227 " --> pdb=" O ILE G 223 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS G 228 " --> pdb=" O GLU G 224 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 252 Processing helix chain 'G' and resid 275 through 279 Processing helix chain 'G' and resid 293 through 300 Processing helix chain 'G' and resid 303 through 319 Processing helix chain 'G' and resid 326 through 331 Processing helix chain 'G' and resid 365 through 386 Processing helix chain 'G' and resid 387 through 388 No H-bonds generated for 'chain 'G' and resid 387 through 388' Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 399 through 412 removed outlier: 3.798A pdb=" N MET G 408 " --> pdb=" O VAL G 404 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N SER G 409 " --> pdb=" O GLY G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 removed outlier: 3.784A pdb=" N ILE G 421 " --> pdb=" O HIS G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 447 removed outlier: 4.237A pdb=" N THR G 445 " --> pdb=" O LYS G 441 " (cutoff:3.500A) Processing helix chain 'G' and resid 449 through 465 Processing helix chain 'G' and resid 473 through 485 removed outlier: 3.885A pdb=" N GLU G 483 " --> pdb=" O GLU G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 502 removed outlier: 3.508A pdb=" N SER G 502 " --> pdb=" O ASP G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 503 through 507 removed outlier: 3.526A pdb=" N VAL G 506 " --> pdb=" O LEU G 503 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER G 507 " --> pdb=" O PHE G 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 503 through 507' Processing helix chain 'G' and resid 513 through 532 removed outlier: 3.680A pdb=" N THR G 517 " --> pdb=" O ILE G 513 " (cutoff:3.500A) Processing helix chain 'G' and resid 538 through 542 Processing helix chain 'G' and resid 547 through 559 removed outlier: 3.680A pdb=" N GLY G 551 " --> pdb=" O SER G 547 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG G 559 " --> pdb=" O PHE G 555 " (cutoff:3.500A) Processing helix chain 'G' and resid 560 through 564 removed outlier: 3.721A pdb=" N GLU G 564 " --> pdb=" O GLY G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 570 Processing helix chain 'G' and resid 581 through 588 Processing helix chain 'G' and resid 588 through 599 removed outlier: 3.585A pdb=" N PHE G 592 " --> pdb=" O PHE G 588 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP G 597 " --> pdb=" O THR G 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.993A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.677A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.357A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.960A 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: 6.619A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL C 574 " --> pdb=" O LEU C 583 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.018A 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: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.573A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 6.970A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.529A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 658 removed outlier: 5.873A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 8.735A pdb=" N VAL A 654 " --> pdb=" O THR A 694 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.670A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.586A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.474A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.391A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.430A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.099A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.518A pdb=" N LEU B 239 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N VAL B 126 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N VAL B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ILE B 128 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N GLU B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 130 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLU B 132 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N GLN B 134 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ALA B 161 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.256A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 326 Processing sheet with id=AC3, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC4, first strand: chain 'B' and resid 450 through 451 Processing sheet with id=AC5, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC6, first strand: chain 'B' and resid 563 through 564 removed outlier: 6.931A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.287A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.866A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 699 through 701 removed outlier: 7.007A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 715 through 726 removed outlier: 6.026A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.492A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.155A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.496A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.521A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.078A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.407A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL C 126 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE C 128 " --> pdb=" O GLU C 167 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLU C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N VAL C 130 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLU C 132 " --> pdb=" O ASN C 163 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N ASN C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN C 134 " --> pdb=" O ALA C 161 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ALA C 161 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.963A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AD9, first strand: chain 'C' and resid 359 through 360 removed outlier: 6.871A pdb=" N CYS C 359 " --> pdb=" O CYS C 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.201A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 709 through 711 Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.547A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.606A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE8, first strand: chain 'C' and resid 1092 through 1095 removed outlier: 4.837A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 262 through 263 removed outlier: 6.892A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE9 Processing sheet with id=AF1, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.247A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 131 through 133 Processing sheet with id=AF3, first strand: chain 'G' and resid 347 through 350 1491 hydrogen bonds defined for protein. 4158 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: 8.91 Time building geometry restraints manager: 4.57 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: 11134 1.34 - 1.46: 8944 1.46 - 1.58: 15609 1.58 - 1.70: 0 1.70 - 1.82: 232 Bond restraints: 35919 Sorted by residual: bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C1 NAG n 1 " pdb=" O5 NAG n 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.30e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.14e+00 bond pdb=" C1 NAG Z 2 " pdb=" O5 NAG Z 2 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.53e+00 ... (remaining 35914 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 47732 1.89 - 3.79: 1009 3.79 - 5.68: 89 5.68 - 7.57: 18 7.57 - 9.47: 7 Bond angle restraints: 48855 Sorted by residual: angle pdb=" N VAL G 506 " pdb=" CA VAL G 506 " pdb=" C VAL G 506 " ideal model delta sigma weight residual 113.71 108.12 5.59 9.50e-01 1.11e+00 3.46e+01 angle pdb=" N VAL F 172 " pdb=" CA VAL F 172 " pdb=" C VAL F 172 " ideal model delta sigma weight residual 112.96 108.33 4.63 1.00e+00 1.00e+00 2.15e+01 angle pdb=" CB ARG F 192 " pdb=" CG ARG F 192 " pdb=" CD ARG F 192 " ideal model delta sigma weight residual 111.30 120.23 -8.93 2.30e+00 1.89e-01 1.51e+01 angle pdb=" C GLN C 23 " pdb=" N LEU C 24 " pdb=" CA LEU C 24 " ideal model delta sigma weight residual 121.80 131.27 -9.47 2.44e+00 1.68e-01 1.51e+01 angle pdb=" C TRP G 461 " pdb=" N MET G 462 " pdb=" CA MET G 462 " ideal model delta sigma weight residual 122.38 115.51 6.87 1.81e+00 3.05e-01 1.44e+01 ... (remaining 48850 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 18540 17.94 - 35.89: 1739 35.89 - 53.83: 279 53.83 - 71.77: 52 71.77 - 89.72: 43 Dihedral angle restraints: 20653 sinusoidal: 8161 harmonic: 12492 Sorted by residual: dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -171.39 85.39 1 1.00e+01 1.00e-02 8.83e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -170.06 84.06 1 1.00e+01 1.00e-02 8.61e+01 dihedral pdb=" CB CYS A 289 " pdb=" SG CYS A 289 " pdb=" SG CYS A 299 " pdb=" CB CYS A 299 " ideal model delta sinusoidal sigma weight residual -86.00 -169.15 83.15 1 1.00e+01 1.00e-02 8.45e+01 ... (remaining 20650 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 5104 0.080 - 0.160: 562 0.160 - 0.240: 16 0.240 - 0.320: 1 0.320 - 0.400: 1 Chirality restraints: 5684 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 4.00e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN A 329 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5681 not shown) Planarity restraints: 6261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.032 2.00e-02 2.50e+03 2.96e-02 1.10e+01 pdb=" CG ASN B1072 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.033 2.00e-02 2.50e+03 pdb=" C1 NAG a 1 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 232 " -0.024 2.00e-02 2.50e+03 2.23e-02 6.19e+00 pdb=" CG ASN A 232 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 232 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 232 " 0.025 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 234 " 0.034 5.00e-02 4.00e+02 5.07e-02 4.11e+00 pdb=" N PRO F 235 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO F 235 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO F 235 " 0.029 5.00e-02 4.00e+02 ... (remaining 6258 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 742 2.66 - 3.22: 34513 3.22 - 3.78: 54832 3.78 - 4.34: 70687 4.34 - 4.90: 116840 Nonbonded interactions: 277614 Sorted by model distance: nonbonded pdb=" OG SER C 814 " pdb=" OE1 GLU C 817 " model vdw 2.106 3.040 nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.147 3.040 nonbonded pdb=" OG SER C 347 " pdb=" O ARG C 450 " model vdw 2.151 3.040 nonbonded pdb=" OH TYR G 237 " pdb=" O VAL G 485 " model vdw 2.154 3.040 nonbonded pdb=" O PHE A 345 " pdb=" OH TYR A 449 " model vdw 2.154 3.040 ... (remaining 277609 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 635 through 825 or resid 853 throu \ gh 2003)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 2003)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain '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' selection = chain 'n' selection = chain 'o' selection = chain 'p' } ncs_group { reference = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 36.190 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 36054 Z= 0.213 Angle : 0.650 9.469 49214 Z= 0.325 Chirality : 0.046 0.400 5684 Planarity : 0.004 0.056 6209 Dihedral : 14.175 89.719 12471 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: -0.29 (0.13), residues: 4229 helix: 1.52 (0.14), residues: 1357 sheet: 0.09 (0.18), residues: 775 loop : -1.52 (0.13), residues: 2097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 192 TYR 0.020 0.001 TYR G 385 PHE 0.031 0.001 PHE B 904 TRP 0.019 0.001 TRP A 884 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (35919) covalent geometry : angle 0.63209 / 0.32 (48855) SS BOND : bond 0.00296 / 0.20 ( 46) SS BOND : angle 1.41460 / 0.90 ( 92) hydrogen bonds : bond 0.12763 / 8.09 ( 1488) hydrogen bonds : angle 5.98769 / 4.16 ( 4158) link_BETA1-4 : bond 0.00357 / 0.23 ( 37) link_BETA1-4 : angle 1.91260 / 1.23 ( 111) link_NAG-ASN : bond 0.00264 / 0.17 ( 52) link_NAG-ASN : angle 2.10295 / 1.36 ( 156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 513 PHE cc_start: 0.8614 (m-10) cc_final: 0.8138 (m-80) REVERT: C 363 TYR cc_start: 0.9291 (m-80) cc_final: 0.8982 (m-80) REVERT: F 82 MET cc_start: 0.6586 (pmm) cc_final: 0.6168 (pmm) REVERT: F 462 MET cc_start: 0.3424 (mmt) cc_final: 0.3064 (ptt) REVERT: F 557 MET cc_start: 0.7578 (tpt) cc_final: 0.6929 (ttm) REVERT: F 579 MET cc_start: -0.0641 (mmt) cc_final: -0.3153 (tpt) REVERT: F 600 LYS cc_start: 0.3925 (tttt) cc_final: 0.3704 (tptp) REVERT: G 190 MET cc_start: 0.7884 (mpp) cc_final: 0.7665 (mpp) REVERT: G 249 MET cc_start: 0.3159 (mmt) cc_final: 0.1310 (ttp) REVERT: G 360 MET cc_start: 0.6524 (ppp) cc_final: 0.6233 (ppp) REVERT: G 455 MET cc_start: 0.8141 (tmm) cc_final: 0.7903 (tmm) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2114 time to fit residues: 51.0991 Evaluate side-chains 113 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 1.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 40.0000 chunk 155 optimal weight: 4.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 472 GLN A 802 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 899 GLN B 905 ASN B 917 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 358 ASN C 924 GLN C 955 GLN ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 531 GLN G 524 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.109346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.062207 restraints weight = 119006.531| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 4.74 r_work: 0.2847 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 36054 Z= 0.212 Angle : 0.621 9.324 49214 Z= 0.313 Chirality : 0.045 0.262 5684 Planarity : 0.004 0.063 6209 Dihedral : 4.518 23.140 4593 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.03 % Favored : 93.90 % Rotamer: Outliers : 0.11 % Allowed : 6.63 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4229 helix: 1.61 (0.14), residues: 1380 sheet: 0.07 (0.18), residues: 738 loop : -1.49 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 192 TYR 0.028 0.001 TYR C1065 PHE 0.028 0.002 PHE B 904 TRP 0.013 0.001 TRP G 477 HIS 0.006 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.21 (35919) covalent geometry : angle 0.60797 / 0.31 (48855) SS BOND : bond 0.00359 / 0.26 ( 46) SS BOND : angle 1.44028 / 0.88 ( 92) hydrogen bonds : bond 0.05623 / 3.61 ( 1488) hydrogen bonds : angle 5.10746 / 3.52 ( 4158) link_BETA1-4 : bond 0.00414 / 0.26 ( 37) link_BETA1-4 : angle 1.53931 / 0.98 ( 111) link_NAG-ASN : bond 0.00228 / 0.15 ( 52) link_NAG-ASN : angle 1.74499 / 1.18 ( 156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 116 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8347 (m-80) cc_final: 0.7816 (m-80) REVERT: A 777 GLN cc_start: 0.9362 (tm-30) cc_final: 0.9112 (tm-30) REVERT: B 513 PHE cc_start: 0.8604 (m-10) cc_final: 0.7965 (m-80) REVERT: C 344 ARG cc_start: 0.8986 (ttp80) cc_final: 0.8657 (tmm160) REVERT: C 363 TYR cc_start: 0.9443 (m-80) cc_final: 0.9031 (m-80) REVERT: C 738 MET cc_start: 0.9073 (mmm) cc_final: 0.8812 (tmm) REVERT: F 82 MET cc_start: 0.6769 (pmm) cc_final: 0.6461 (pmm) REVERT: F 557 MET cc_start: 0.8180 (tpt) cc_final: 0.7413 (ptm) REVERT: G 249 MET cc_start: 0.3795 (mmt) cc_final: 0.2283 (ttp) REVERT: G 557 MET cc_start: 0.8604 (mpp) cc_final: 0.8390 (mpp) outliers start: 4 outliers final: 1 residues processed: 119 average time/residue: 0.1981 time to fit residues: 40.8086 Evaluate side-chains 109 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 108 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 413 optimal weight: 0.4980 chunk 424 optimal weight: 50.0000 chunk 93 optimal weight: 0.0770 chunk 305 optimal weight: 0.6980 chunk 373 optimal weight: 9.9990 chunk 159 optimal weight: 0.9990 chunk 60 optimal weight: 5.9990 chunk 206 optimal weight: 0.9980 chunk 129 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 112 optimal weight: 9.9990 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 392 ASN B 899 GLN B 905 ASN ** B1000 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1003 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.111010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.064811 restraints weight = 118694.057| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 4.76 r_work: 0.2895 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 36054 Z= 0.105 Angle : 0.545 9.642 49214 Z= 0.272 Chirality : 0.043 0.260 5684 Planarity : 0.004 0.060 6209 Dihedral : 4.176 20.933 4593 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.45 % Favored : 95.51 % Rotamer: Outliers : 0.59 % Allowed : 8.63 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4229 helix: 1.78 (0.14), residues: 1370 sheet: 0.35 (0.19), residues: 743 loop : -1.43 (0.13), residues: 2116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.022 0.001 TYR G 385 PHE 0.019 0.001 PHE A 375 TRP 0.016 0.001 TRP G 477 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (35919) covalent geometry : angle 0.53398 / 0.27 (48855) SS BOND : bond 0.00243 / 0.16 ( 46) SS BOND : angle 1.12192 / 0.73 ( 92) hydrogen bonds : bond 0.04378 / 2.81 ( 1488) hydrogen bonds : angle 4.71680 / 3.25 ( 4158) link_BETA1-4 : bond 0.00399 / 0.26 ( 37) link_BETA1-4 : angle 1.43627 / 0.92 ( 111) link_NAG-ASN : bond 0.00215 / 0.14 ( 52) link_NAG-ASN : angle 1.50672 / 1.04 ( 156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 447 TYR cc_start: 0.8983 (m-80) cc_final: 0.8660 (m-10) REVERT: A 449 TYR cc_start: 0.8304 (m-80) cc_final: 0.7708 (m-80) REVERT: A 955 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8839 (tm-30) REVERT: B 513 PHE cc_start: 0.8542 (m-10) cc_final: 0.7908 (m-80) REVERT: C 363 TYR cc_start: 0.9425 (m-80) cc_final: 0.9031 (m-80) REVERT: C 738 MET cc_start: 0.9001 (mmm) cc_final: 0.8759 (tmm) REVERT: C 898 MET cc_start: 0.9082 (mtt) cc_final: 0.8785 (mtt) REVERT: F 557 MET cc_start: 0.8130 (tpt) cc_final: 0.7303 (ptm) REVERT: G 249 MET cc_start: 0.3768 (mmt) cc_final: 0.2461 (ttp) REVERT: G 332 MET cc_start: 0.5335 (ppp) cc_final: 0.5115 (ppp) REVERT: G 366 MET cc_start: 0.6938 (tpp) cc_final: 0.6655 (mmm) outliers start: 22 outliers final: 3 residues processed: 139 average time/residue: 0.1881 time to fit residues: 45.2057 Evaluate side-chains 115 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 112 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 703 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 155 optimal weight: 1.9990 chunk 309 optimal weight: 10.0000 chunk 154 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 424 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 chunk 193 optimal weight: 2.9990 chunk 121 optimal weight: 7.9990 chunk 376 optimal weight: 0.9980 chunk 227 optimal weight: 10.0000 chunk 282 optimal weight: 3.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 990 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B1104 GLN C 762 ASN C1003 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.109907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.062975 restraints weight = 118955.213| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 4.74 r_work: 0.2860 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 36054 Z= 0.156 Angle : 0.563 9.446 49214 Z= 0.281 Chirality : 0.043 0.258 5684 Planarity : 0.004 0.056 6209 Dihedral : 4.175 19.390 4593 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.39 % Favored : 94.56 % Rotamer: Outliers : 0.83 % Allowed : 10.28 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 4229 helix: 1.83 (0.14), residues: 1367 sheet: 0.30 (0.19), residues: 709 loop : -1.42 (0.13), residues: 2153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 317 TYR 0.023 0.001 TYR C1065 PHE 0.020 0.001 PHE A1119 TRP 0.015 0.001 TRP G 477 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (35919) covalent geometry : angle 0.55061 / 0.28 (48855) SS BOND : bond 0.00288 / 0.21 ( 46) SS BOND : angle 1.23781 / 0.79 ( 92) hydrogen bonds : bond 0.04778 / 3.06 ( 1488) hydrogen bonds : angle 4.71972 / 3.25 ( 4158) link_BETA1-4 : bond 0.00309 / 0.20 ( 37) link_BETA1-4 : angle 1.47624 / 0.94 ( 111) link_NAG-ASN : bond 0.00190 / 0.13 ( 52) link_NAG-ASN : angle 1.57484 / 1.05 ( 156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 1.336 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8371 (m-80) cc_final: 0.6506 (m-80) REVERT: A 729 MET cc_start: 0.9404 (ptt) cc_final: 0.9146 (ptt) REVERT: A 955 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8693 (tm-30) REVERT: B 1000 GLN cc_start: 0.9155 (tt0) cc_final: 0.8872 (tm-30) REVERT: C 363 TYR cc_start: 0.9458 (m-80) cc_final: 0.9017 (m-80) REVERT: F 557 MET cc_start: 0.8200 (tpt) cc_final: 0.7328 (ptm) REVERT: G 190 MET cc_start: 0.7278 (mpp) cc_final: 0.7051 (mpp) REVERT: G 249 MET cc_start: 0.3722 (mmt) cc_final: 0.2403 (ttp) REVERT: G 332 MET cc_start: 0.5747 (ppp) cc_final: 0.5472 (ppp) REVERT: G 366 MET cc_start: 0.6799 (tpp) cc_final: 0.6509 (mmm) outliers start: 31 outliers final: 13 residues processed: 143 average time/residue: 0.1908 time to fit residues: 47.4591 Evaluate side-chains 126 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain F residue 159 ASN Chi-restraints excluded: chain F residue 600 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 313 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 235 optimal weight: 9.9990 chunk 193 optimal weight: 5.9990 chunk 380 optimal weight: 20.0000 chunk 367 optimal weight: 20.0000 chunk 389 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 411 optimal weight: 0.2980 chunk 67 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN B1104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.109330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.064443 restraints weight = 118166.165| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 5.46 r_work: 0.2825 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 : 0.005 0.060 36054 Z= 0.205 Angle : 0.597 11.531 49214 Z= 0.297 Chirality : 0.044 0.258 5684 Planarity : 0.004 0.058 6209 Dihedral : 4.283 19.403 4593 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.77 % Favored : 94.18 % Rotamer: Outliers : 1.09 % Allowed : 12.17 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.13), residues: 4229 helix: 1.79 (0.14), residues: 1370 sheet: 0.15 (0.19), residues: 686 loop : -1.47 (0.13), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 344 TYR 0.025 0.001 TYR C1065 PHE 0.022 0.001 PHE C1119 TRP 0.014 0.001 TRP G 477 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 (35919) covalent geometry : angle 0.58511 / 0.29 (48855) SS BOND : bond 0.00320 / 0.24 ( 46) SS BOND : angle 1.33906 / 0.85 ( 92) hydrogen bonds : bond 0.05159 / 3.30 ( 1488) hydrogen bonds : angle 4.76207 / 3.28 ( 4158) link_BETA1-4 : bond 0.00310 / 0.19 ( 37) link_BETA1-4 : angle 1.52040 / 0.98 ( 111) link_NAG-ASN : bond 0.00214 / 0.14 ( 52) link_NAG-ASN : angle 1.61793 / 1.08 ( 156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.483 Fit side-chains revert: symmetry clash REVERT: A 506 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7920 (m-80) REVERT: A 729 MET cc_start: 0.9390 (ptt) cc_final: 0.9154 (ptt) REVERT: A 955 GLN cc_start: 0.9045 (tm-30) cc_final: 0.8755 (tm-30) REVERT: B 513 PHE cc_start: 0.7900 (m-80) cc_final: 0.7529 (m-80) REVERT: B 1000 GLN cc_start: 0.9134 (tt0) cc_final: 0.8847 (tm-30) REVERT: B 1037 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8106 (ptm160) REVERT: C 114 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8049 (p) REVERT: C 363 TYR cc_start: 0.9448 (m-80) cc_final: 0.9033 (m-80) REVERT: C 898 MET cc_start: 0.9260 (mtt) cc_final: 0.9008 (mtp) REVERT: F 557 MET cc_start: 0.8128 (tpt) cc_final: 0.7324 (ptm) REVERT: F 579 MET cc_start: 0.0226 (mmt) cc_final: -0.2852 (tpt) REVERT: G 249 MET cc_start: 0.3864 (mmt) cc_final: 0.2347 (ttp) REVERT: G 332 MET cc_start: 0.6008 (ppp) cc_final: 0.5712 (ppp) REVERT: G 366 MET cc_start: 0.6881 (tpp) cc_final: 0.6595 (mmm) REVERT: G 579 MET cc_start: 0.4441 (OUTLIER) cc_final: 0.3515 (tmm) outliers start: 41 outliers final: 23 residues processed: 149 average time/residue: 0.2109 time to fit residues: 54.8574 Evaluate side-chains 133 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 168 optimal weight: 4.9990 chunk 218 optimal weight: 8.9990 chunk 370 optimal weight: 10.0000 chunk 363 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 418 optimal weight: 40.0000 chunk 388 optimal weight: 30.0000 chunk 275 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN A 673 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN G 572 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.107813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.063625 restraints weight = 118534.887| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 5.96 r_work: 0.2760 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.099 36054 Z= 0.331 Angle : 0.714 11.260 49214 Z= 0.356 Chirality : 0.047 0.262 5684 Planarity : 0.004 0.062 6209 Dihedral : 4.666 21.054 4593 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.79 % Favored : 93.17 % Rotamer: Outliers : 1.49 % Allowed : 13.48 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.13), residues: 4229 helix: 1.55 (0.14), residues: 1375 sheet: -0.17 (0.19), residues: 707 loop : -1.66 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 317 TYR 0.032 0.002 TYR C1065 PHE 0.033 0.002 PHE C1119 TRP 0.015 0.001 TRP F 477 HIS 0.009 0.001 HIS A1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00785 / 0.33 (35919) covalent geometry : angle 0.69981 / 0.35 (48855) SS BOND : bond 0.00457 / 0.34 ( 46) SS BOND : angle 1.60996 / 1.00 ( 92) hydrogen bonds : bond 0.06261 / 4.00 ( 1488) hydrogen bonds : angle 5.06381 / 3.49 ( 4158) link_BETA1-4 : bond 0.00295 / 0.19 ( 37) link_BETA1-4 : angle 1.70963 / 1.11 ( 111) link_NAG-ASN : bond 0.00414 / 0.28 ( 52) link_NAG-ASN : angle 1.91147 / 1.26 ( 156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 105 time to evaluate : 1.380 Fit side-chains revert: symmetry clash REVERT: A 227 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9024 (mm) REVERT: A 237 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8423 (tp40) REVERT: A 289 CYS cc_start: 0.8913 (OUTLIER) cc_final: 0.8686 (m) REVERT: A 449 TYR cc_start: 0.7861 (m-80) cc_final: 0.7557 (m-80) REVERT: A 506 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 729 MET cc_start: 0.9399 (ptt) cc_final: 0.9171 (ptt) REVERT: A 986 GLU cc_start: 0.9081 (mp0) cc_final: 0.8787 (tp30) REVERT: B 513 PHE cc_start: 0.7981 (m-80) cc_final: 0.7637 (m-80) REVERT: B 894 ILE cc_start: 0.9209 (OUTLIER) cc_final: 0.8987 (tp) REVERT: B 1037 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8192 (ptm160) REVERT: C 114 THR cc_start: 0.8173 (OUTLIER) cc_final: 0.7952 (p) REVERT: C 142 ASP cc_start: 0.4953 (OUTLIER) cc_final: 0.4620 (m-30) REVERT: C 363 TYR cc_start: 0.9454 (m-80) cc_final: 0.8987 (m-80) REVERT: C 738 MET cc_start: 0.9300 (mmm) cc_final: 0.9080 (mmm) REVERT: C 898 MET cc_start: 0.9337 (mtt) cc_final: 0.9098 (mtt) REVERT: F 557 MET cc_start: 0.8257 (tpt) cc_final: 0.7447 (ptm) REVERT: G 249 MET cc_start: 0.3959 (mmt) cc_final: 0.2466 (ttp) REVERT: G 332 MET cc_start: 0.6106 (ppp) cc_final: 0.5870 (ppp) REVERT: G 366 MET cc_start: 0.6895 (tpp) cc_final: 0.6631 (mmm) REVERT: G 557 MET cc_start: 0.8587 (mpp) cc_final: 0.8208 (mpp) REVERT: G 579 MET cc_start: 0.4645 (OUTLIER) cc_final: 0.3833 (tmm) outliers start: 56 outliers final: 33 residues processed: 158 average time/residue: 0.2071 time to fit residues: 56.8652 Evaluate side-chains 146 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 104 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 237 GLN Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 501 VAL Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 727 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 1131 VAL Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 29 optimal weight: 30.0000 chunk 273 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 226 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 133 optimal weight: 9.9990 chunk 407 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN G 417 HIS ** G 540 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.114824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.067939 restraints weight = 118131.637| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 4.78 r_work: 0.2864 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 36054 Z= 0.111 Angle : 0.574 13.575 49214 Z= 0.283 Chirality : 0.043 0.259 5684 Planarity : 0.004 0.060 6209 Dihedral : 4.197 20.266 4593 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.47 % Favored : 95.48 % Rotamer: Outliers : 1.15 % Allowed : 14.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4229 helix: 1.83 (0.14), residues: 1368 sheet: 0.22 (0.19), residues: 737 loop : -1.48 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 317 TYR 0.022 0.001 TYR G 385 PHE 0.019 0.001 PHE A 375 TRP 0.013 0.001 TRP G 163 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (35919) covalent geometry : angle 0.56280 / 0.28 (48855) SS BOND : bond 0.00251 / 0.18 ( 46) SS BOND : angle 1.14285 / 0.74 ( 92) hydrogen bonds : bond 0.04519 / 2.90 ( 1488) hydrogen bonds : angle 4.64984 / 3.20 ( 4158) link_BETA1-4 : bond 0.00424 / 0.28 ( 37) link_BETA1-4 : angle 1.49829 / 0.96 ( 111) link_NAG-ASN : bond 0.00221 / 0.15 ( 52) link_NAG-ASN : angle 1.49143 / 1.01 ( 156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 114 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 CYS cc_start: 0.8758 (OUTLIER) cc_final: 0.8514 (m) REVERT: A 449 TYR cc_start: 0.7995 (m-80) cc_final: 0.7603 (m-80) REVERT: A 506 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7818 (m-80) REVERT: A 729 MET cc_start: 0.9405 (ptt) cc_final: 0.9156 (ptt) REVERT: A 955 GLN cc_start: 0.9021 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 983 ASP cc_start: 0.7930 (p0) cc_final: 0.6227 (p0) REVERT: A 986 GLU cc_start: 0.9075 (mp0) cc_final: 0.8834 (mp0) REVERT: B 513 PHE cc_start: 0.7907 (m-80) cc_final: 0.7523 (m-80) REVERT: B 964 LEU cc_start: 0.9487 (OUTLIER) cc_final: 0.9263 (mm) REVERT: C 114 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7888 (p) REVERT: C 142 ASP cc_start: 0.4976 (OUTLIER) cc_final: 0.4613 (m-30) REVERT: C 363 TYR cc_start: 0.9441 (m-80) cc_final: 0.8966 (m-80) REVERT: C 738 MET cc_start: 0.9119 (mmm) cc_final: 0.8713 (tpp) REVERT: F 557 MET cc_start: 0.8179 (tpt) cc_final: 0.7344 (ptm) REVERT: G 249 MET cc_start: 0.3750 (mmt) cc_final: 0.2470 (ttp) REVERT: G 408 MET cc_start: 0.8416 (mpp) cc_final: 0.8156 (pmm) REVERT: G 462 MET cc_start: 0.7202 (pmm) cc_final: 0.6979 (pmm) REVERT: G 579 MET cc_start: 0.4396 (OUTLIER) cc_final: 0.3523 (tmm) outliers start: 43 outliers final: 25 residues processed: 154 average time/residue: 0.1955 time to fit residues: 52.7114 Evaluate side-chains 141 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 905 ASN Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 98 optimal weight: 0.0980 chunk 133 optimal weight: 0.5980 chunk 40 optimal weight: 30.0000 chunk 326 optimal weight: 0.0010 chunk 159 optimal weight: 2.9990 chunk 355 optimal weight: 0.0010 chunk 387 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN G 540 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.111055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.066205 restraints weight = 118109.926| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 5.33 r_work: 0.2885 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 36054 Z= 0.103 Angle : 0.565 12.528 49214 Z= 0.276 Chirality : 0.043 0.262 5684 Planarity : 0.004 0.056 6209 Dihedral : 3.990 20.671 4593 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.92 % Favored : 95.03 % Rotamer: Outliers : 1.07 % Allowed : 14.49 % Favored : 84.44 % 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 (0.13), residues: 4229 helix: 1.87 (0.14), residues: 1375 sheet: 0.36 (0.19), residues: 713 loop : -1.39 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 317 TYR 0.021 0.001 TYR G 385 PHE 0.021 0.001 PHE A 375 TRP 0.012 0.001 TRP G 477 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (35919) covalent geometry : angle 0.55476 / 0.27 (48855) SS BOND : bond 0.00268 / 0.16 ( 46) SS BOND : angle 1.00658 / 0.65 ( 92) hydrogen bonds : bond 0.04061 / 2.62 ( 1488) hydrogen bonds : angle 4.52437 / 3.11 ( 4158) link_BETA1-4 : bond 0.00369 / 0.24 ( 37) link_BETA1-4 : angle 1.46128 / 0.94 ( 111) link_NAG-ASN : bond 0.00176 / 0.12 ( 52) link_NAG-ASN : angle 1.49585 / 1.01 ( 156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 119 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 CYS cc_start: 0.8900 (OUTLIER) cc_final: 0.8645 (m) REVERT: A 447 TYR cc_start: 0.9007 (m-80) cc_final: 0.8718 (m-10) REVERT: A 449 TYR cc_start: 0.8071 (m-80) cc_final: 0.7691 (m-80) REVERT: A 506 TYR cc_start: 0.8422 (OUTLIER) cc_final: 0.7889 (m-80) REVERT: A 729 MET cc_start: 0.9411 (ptt) cc_final: 0.9149 (ptt) REVERT: A 955 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8790 (tm-30) REVERT: B 513 PHE cc_start: 0.7953 (m-80) cc_final: 0.7654 (m-80) REVERT: B 964 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9217 (mm) REVERT: B 1037 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8090 (ptm160) REVERT: C 114 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7922 (p) REVERT: C 142 ASP cc_start: 0.5060 (OUTLIER) cc_final: 0.4717 (m-30) REVERT: C 363 TYR cc_start: 0.9428 (m-80) cc_final: 0.8972 (m-80) REVERT: C 738 MET cc_start: 0.8874 (mmm) cc_final: 0.8544 (tmm) REVERT: F 227 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7544 (tp30) REVERT: F 557 MET cc_start: 0.8155 (tpt) cc_final: 0.7274 (ptm) REVERT: F 579 MET cc_start: 0.0698 (mmt) cc_final: -0.2418 (tpt) REVERT: G 249 MET cc_start: 0.3709 (mmt) cc_final: 0.2410 (ttp) REVERT: G 366 MET cc_start: 0.5948 (mmm) cc_final: 0.5695 (mmm) REVERT: G 408 MET cc_start: 0.8356 (mpp) cc_final: 0.8123 (pmm) REVERT: G 462 MET cc_start: 0.7168 (pmm) cc_final: 0.6966 (pmm) REVERT: G 579 MET cc_start: 0.4425 (OUTLIER) cc_final: 0.3425 (tmm) outliers start: 40 outliers final: 24 residues processed: 156 average time/residue: 0.2044 time to fit residues: 54.8068 Evaluate side-chains 144 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 112 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 1027 MET Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 69 optimal weight: 2.9990 chunk 336 optimal weight: 20.0000 chunk 55 optimal weight: 0.0870 chunk 59 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 146 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 338 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 overall best weight: 2.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 905 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.109409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.063954 restraints weight = 117954.177| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.51 r_work: 0.2811 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 36054 Z= 0.200 Angle : 0.612 12.305 49214 Z= 0.302 Chirality : 0.044 0.254 5684 Planarity : 0.004 0.055 6209 Dihedral : 4.160 20.483 4593 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.60 % Favored : 94.35 % Rotamer: Outliers : 1.09 % Allowed : 14.62 % Favored : 84.28 % 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: -0.01 (0.13), residues: 4229 helix: 1.92 (0.14), residues: 1357 sheet: 0.26 (0.20), residues: 684 loop : -1.42 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 981 TYR 0.027 0.001 TYR C1065 PHE 0.024 0.001 PHE A1119 TRP 0.011 0.001 TRP G 163 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.20 (35919) covalent geometry : angle 0.60096 / 0.30 (48855) SS BOND : bond 0.00308 / 0.23 ( 46) SS BOND : angle 1.29765 / 0.82 ( 92) hydrogen bonds : bond 0.04966 / 3.18 ( 1488) hydrogen bonds : angle 4.65513 / 3.20 ( 4158) link_BETA1-4 : bond 0.00312 / 0.20 ( 37) link_BETA1-4 : angle 1.54107 / 0.99 ( 111) link_NAG-ASN : bond 0.00215 / 0.15 ( 52) link_NAG-ASN : angle 1.58136 / 1.05 ( 156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 110 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 CYS cc_start: 0.8897 (OUTLIER) cc_final: 0.8667 (m) REVERT: A 449 TYR cc_start: 0.8053 (m-80) cc_final: 0.7712 (m-80) REVERT: A 506 TYR cc_start: 0.8479 (OUTLIER) cc_final: 0.7862 (m-80) REVERT: A 729 MET cc_start: 0.9418 (ptt) cc_final: 0.9168 (ptt) REVERT: A 955 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8727 (tm-30) REVERT: B 513 PHE cc_start: 0.7971 (m-80) cc_final: 0.7728 (m-80) REVERT: B 964 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9251 (mm) REVERT: B 1037 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8074 (ptm160) REVERT: C 114 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 142 ASP cc_start: 0.4618 (OUTLIER) cc_final: 0.4300 (m-30) REVERT: C 363 TYR cc_start: 0.9468 (m-80) cc_final: 0.8988 (m-80) REVERT: C 738 MET cc_start: 0.9104 (mmm) cc_final: 0.8727 (tmm) REVERT: F 227 GLU cc_start: 0.8200 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: F 557 MET cc_start: 0.8302 (tpt) cc_final: 0.7417 (ptm) REVERT: G 249 MET cc_start: 0.3899 (mmt) cc_final: 0.2514 (ttp) REVERT: G 408 MET cc_start: 0.8309 (mpp) cc_final: 0.8108 (pmm) REVERT: G 579 MET cc_start: 0.4321 (OUTLIER) cc_final: 0.3422 (tmm) outliers start: 41 outliers final: 26 residues processed: 148 average time/residue: 0.1971 time to fit residues: 50.2229 Evaluate side-chains 143 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 570 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 569 ASP Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 81 GLN Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 277 optimal weight: 0.5980 chunk 297 optimal weight: 3.9990 chunk 198 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 416 optimal weight: 20.0000 chunk 270 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 312 optimal weight: 20.0000 chunk 117 optimal weight: 0.9980 chunk 182 optimal weight: 0.7980 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4177 r_free = 0.4177 target = 0.110553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.064790 restraints weight = 117709.689| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 4.95 r_work: 0.2870 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 36054 Z= 0.116 Angle : 0.583 12.834 49214 Z= 0.286 Chirality : 0.043 0.258 5684 Planarity : 0.004 0.056 6209 Dihedral : 4.030 21.302 4593 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.75 % Favored : 95.20 % Rotamer: Outliers : 0.96 % Allowed : 14.70 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.13), residues: 4229 helix: 1.91 (0.14), residues: 1372 sheet: 0.34 (0.19), residues: 709 loop : -1.37 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 317 TYR 0.021 0.001 TYR G 385 PHE 0.036 0.001 PHE B 390 TRP 0.013 0.001 TRP G 477 HIS 0.004 0.001 HIS G 374 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (35919) covalent geometry : angle 0.57296 / 0.28 (48855) SS BOND : bond 0.00243 / 0.17 ( 46) SS BOND : angle 1.12335 / 0.73 ( 92) hydrogen bonds : bond 0.04325 / 2.77 ( 1488) hydrogen bonds : angle 4.54074 / 3.12 ( 4158) link_BETA1-4 : bond 0.00369 / 0.24 ( 37) link_BETA1-4 : angle 1.46558 / 0.94 ( 111) link_NAG-ASN : bond 0.00165 / 0.11 ( 52) link_NAG-ASN : angle 1.45015 / 0.97 ( 156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8458 Ramachandran restraints generated. 4229 Oldfield, 0 Emsley, 4229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 289 CYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8553 (m) REVERT: A 449 TYR cc_start: 0.8065 (m-80) cc_final: 0.7704 (m-80) REVERT: A 506 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.7852 (m-80) REVERT: A 729 MET cc_start: 0.9400 (ptt) cc_final: 0.9135 (ptt) REVERT: A 955 GLN cc_start: 0.9010 (tm-30) cc_final: 0.8671 (tm-30) REVERT: B 1037 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8044 (ptm160) REVERT: C 114 THR cc_start: 0.8120 (OUTLIER) cc_final: 0.7879 (p) REVERT: C 142 ASP cc_start: 0.5038 (OUTLIER) cc_final: 0.4661 (m-30) REVERT: C 363 TYR cc_start: 0.9397 (m-80) cc_final: 0.8938 (m-80) REVERT: C 738 MET cc_start: 0.8949 (mmm) cc_final: 0.8615 (tmm) REVERT: F 227 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7482 (tp30) REVERT: F 557 MET cc_start: 0.8160 (tpt) cc_final: 0.7275 (ptm) REVERT: F 579 MET cc_start: -0.0298 (mmt) cc_final: -0.3109 (tpt) REVERT: G 249 MET cc_start: 0.3591 (mmt) cc_final: 0.2237 (ttp) REVERT: G 366 MET cc_start: 0.5776 (mmm) cc_final: 0.5513 (mmm) REVERT: G 408 MET cc_start: 0.8293 (mpp) cc_final: 0.8087 (pmm) REVERT: G 579 MET cc_start: 0.4367 (OUTLIER) cc_final: 0.3310 (tmm) outliers start: 36 outliers final: 23 residues processed: 146 average time/residue: 0.1943 time to fit residues: 48.8738 Evaluate side-chains 142 residues out of total 3754 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 112 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 289 CYS Chi-restraints excluded: chain A residue 310 ILE Chi-restraints excluded: chain A residue 506 TYR Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 579 THR Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain B residue 367 TYR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 142 ASP Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 322 GLU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain F residue 81 GLN Chi-restraints excluded: chain F residue 227 GLU Chi-restraints excluded: chain F residue 600 LYS Chi-restraints excluded: chain G residue 141 CYS Chi-restraints excluded: chain G residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 425 random chunks: chunk 94 optimal weight: 4.9990 chunk 380 optimal weight: 20.0000 chunk 236 optimal weight: 2.9990 chunk 208 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 chunk 420 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 387 optimal weight: 20.0000 chunk 151 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 304 optimal weight: 3.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** B 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 = 0.4151 r_free = 0.4151 target = 0.109064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064164 restraints weight = 117678.606| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 5.26 r_work: 0.2818 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 36054 Z= 0.228 Angle : 0.639 12.954 49214 Z= 0.315 Chirality : 0.045 0.254 5684 Planarity : 0.004 0.055 6209 Dihedral : 4.230 20.456 4593 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.89 % Favored : 94.06 % Rotamer: Outliers : 1.01 % Allowed : 14.70 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.13), residues: 4229 helix: 1.85 (0.14), residues: 1373 sheet: 0.19 (0.19), residues: 695 loop : -1.45 (0.13), residues: 2161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 317 TYR 0.028 0.001 TYR C1065 PHE 0.025 0.001 PHE C1119 TRP 0.011 0.001 TRP G 477 HIS 0.005 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (35919) covalent geometry : angle 0.62791 / 0.31 (48855) SS BOND : bond 0.00330 / 0.25 ( 46) SS BOND : angle 1.36968 / 0.86 ( 92) hydrogen bonds : bond 0.05197 / 3.33 ( 1488) hydrogen bonds : angle 4.73244 / 3.26 ( 4158) link_BETA1-4 : bond 0.00291 / 0.18 ( 37) link_BETA1-4 : angle 1.57184 / 1.01 ( 111) link_NAG-ASN : bond 0.00258 / 0.17 ( 52) link_NAG-ASN : angle 1.61856 / 1.07 ( 156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11581.37 seconds wall clock time: 198 minutes 5.97 seconds (11885.97 seconds total)