Starting phenix.real_space_refine on Thu Mar 5 21:21:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7s_31780/03_2026/7v7s_31780.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7s_31780/03_2026/7v7s_31780.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v7s_31780/03_2026/7v7s_31780.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7s_31780/03_2026/7v7s_31780.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7s_31780/03_2026/7v7s_31780.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7s_31780/03_2026/7v7s_31780.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16039 2.51 5 N 4113 2.21 5 O 4995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25255 Number of models: 1 Model: "" Number of chains: 39 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: 8028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1028, 8028 Classifications: {'peptide': 1028} Link IDs: {'PTRANS': 53, 'TRANS': 974} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.66, per 1000 atoms: 0.22 Number of scatterers: 25255 At special positions: 0 Unit cell: (140.8, 145.2, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 4995 8.00 N 4113 7.00 C 16039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 163 " " NAG A2004 " - " ASN A 232 " " NAG A2005 " - " ASN A 601 " " NAG A2006 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 280 " " NAG E 1 " - " ASN A 329 " " NAG F 1 " - " ASN A 341 " " NAG G 1 " - " ASN A 614 " " NAG H 1 " - " ASN A 707 " " NAG I 1 " - " ASN A 715 " " NAG J 1 " - " ASN A 799 " " NAG K 1 " - " ASN A1072 " " NAG L 1 " - " ASN A1096 " " NAG M 1 " - " ASN A1132 " " NAG N 1 " - " ASN B 122 " " NAG O 1 " - " ASN B 163 " " NAG P 1 " - " ASN B 280 " " NAG Q 1 " - " ASN B 341 " " NAG R 1 " - " ASN B 614 " " NAG S 1 " - " ASN B 707 " " NAG T 1 " - " ASN B 715 " " NAG U 1 " - " ASN B 799 " " NAG V 1 " - " ASN B1072 " " NAG W 1 " - " ASN B1096 " " NAG X 1 " - " ASN B1132 " " NAG Y 1 " - " ASN C 122 " " NAG Z 1 " - " ASN C 163 " " NAG a 1 " - " ASN C 232 " " NAG b 1 " - " ASN C 280 " " NAG c 1 " - " ASN C 341 " " NAG d 1 " - " ASN C 614 " " NAG e 1 " - " ASN C 707 " " NAG f 1 " - " ASN C 715 " " NAG g 1 " - " ASN C 799 " " NAG h 1 " - " ASN C1072 " " NAG i 1 " - " ASN C1096 " " NAG j 1 " - " ASN C1132 " Time building additional restraints: 1.78 Conformation dependent library (CDL) restraints added in 766.4 milliseconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5786 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 46 sheets defined 24.6% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.438A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 387 removed outlier: 4.277A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 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 753 removed outlier: 4.097A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 939 removed outlier: 4.290A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LYS A 919 " --> pdb=" O TYR A 915 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU A 920 " --> pdb=" O GLU A 916 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.644A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.531A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL A1031 " --> pdb=" O MET A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.019A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 removed outlier: 3.582A pdb=" N LEU B 385 " --> pdb=" O PRO B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.294A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.738A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.684A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.628A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.078A pdb=" N GLY B 889 " --> pdb=" O PHE B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 895 through 906 Processing helix chain 'B' and resid 911 through 916 removed outlier: 3.579A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 916 " --> pdb=" O ASN B 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 911 through 916' Processing helix chain 'B' and resid 917 through 939 Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 980 removed outlier: 3.552A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.351A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B1031 " --> pdb=" O MET B1027 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.811A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 368 Processing helix chain 'C' and resid 381 through 388 removed outlier: 4.549A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.818A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.627A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 757 through 781 removed outlier: 3.511A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.597A 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: 4.319A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS C 919 " --> pdb=" O TYR C 915 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU C 920 " --> pdb=" O GLU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.508A pdb=" N GLN C 947 " --> pdb=" O LEU C 943 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.715A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.434A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.606A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.863A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.130A pdb=" N LEU A 84 " --> pdb=" O PHE A 236 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 103 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL A 126 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 128 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLU A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL A 130 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU A 132 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ASN A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLN A 134 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ALA A 161 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 7.111A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.790A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA8, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AA9, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.165A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 699 through 700 removed outlier: 7.029A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 709 through 711 removed outlier: 3.511A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.548A 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: 6.151A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.484A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 785 through 787 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 26 through 30 removed outlier: 8.615A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.164A 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: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.181A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.128A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.506A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.345A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.440A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA B 573 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC5, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.258A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC7, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC8, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.007A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 699 through 701 removed outlier: 6.974A pdb=" N ALA B 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.089A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.535A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1118 through 1120 Processing sheet with id=AD4, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.081A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N GLU B1109 " --> pdb=" O GLN B1104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 26 through 30 removed outlier: 7.620A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.517A 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: 6.909A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.075A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.195A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N GLU C 132 " --> pdb=" O CYS C 164 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N CYS C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N GLN C 134 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 9.901A pdb=" N ASN C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 317 removed outlier: 7.130A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 323 through 324 Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.516A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.743A pdb=" N TYR C 471 " --> pdb=" O TYR C 487 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N TYR C 487 " --> pdb=" O TYR C 471 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 564 through 565 removed outlier: 6.741A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.022A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.522A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.570A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA C1076 " --> pdb=" O PHE C1093 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE C1093 " --> pdb=" O ALA C1076 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N GLN C1104 " --> pdb=" O GLU C1109 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N GLU C1109 " --> pdb=" O GLN C1104 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.540A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.516A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1118 through 1120 1006 hydrogen bonds defined for protein. 2748 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.86 Time building geometry restraints manager: 2.23 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: 7977 1.34 - 1.46: 6421 1.46 - 1.58: 11272 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25802 Sorted by residual: bond pdb=" C PRO A 984 " pdb=" N PRO A 985 " ideal model delta sigma weight residual 1.333 1.376 -0.043 1.44e-02 4.82e+03 8.88e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.451 -0.045 2.00e-02 2.50e+03 5.05e+00 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.12e+00 bond pdb=" C1 NAG B2004 " pdb=" O5 NAG B2004 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.70e+00 ... (remaining 25797 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 34042 1.55 - 3.10: 945 3.10 - 4.64: 92 4.64 - 6.19: 19 6.19 - 7.74: 11 Bond angle restraints: 35109 Sorted by residual: angle pdb=" C SER B 170 " pdb=" N GLN B 171 " pdb=" CA GLN B 171 " ideal model delta sigma weight residual 120.49 125.03 -4.54 1.42e+00 4.96e-01 1.02e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.55 -3.85 1.22e+00 6.72e-01 9.98e+00 angle pdb=" C ASN A 329 " pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 121.97 127.51 -5.54 1.80e+00 3.09e-01 9.47e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.68 -6.21 2.06e+00 2.36e-01 9.09e+00 angle pdb=" N PRO C 559 " pdb=" CA PRO C 559 " pdb=" C PRO C 559 " ideal model delta sigma weight residual 112.47 118.26 -5.79 2.06e+00 2.36e-01 7.89e+00 ... (remaining 35104 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 14681 17.28 - 34.55: 1361 34.55 - 51.83: 299 51.83 - 69.10: 67 69.10 - 86.38: 34 Dihedral angle restraints: 16442 sinusoidal: 7455 harmonic: 8987 Sorted by residual: dihedral pdb=" CB CYS A 736 " pdb=" SG CYS A 736 " pdb=" SG CYS A 758 " pdb=" CB CYS A 758 " ideal model delta sinusoidal sigma weight residual -86.00 -0.91 -85.09 1 1.00e+01 1.00e-02 8.78e+01 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 -169.13 83.13 1 1.00e+01 1.00e-02 8.45e+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 -166.07 80.07 1 1.00e+01 1.00e-02 7.95e+01 ... (remaining 16439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 3661 0.073 - 0.146: 539 0.146 - 0.219: 20 0.219 - 0.291: 1 0.291 - 0.364: 3 Chirality restraints: 4224 Sorted by residual: chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" C1 NAG A2005 " pdb=" ND2 ASN A 601 " pdb=" C2 NAG A2005 " pdb=" O5 NAG A2005 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.02e+00 chirality pdb=" C1 NAG A2004 " pdb=" ND2 ASN A 232 " pdb=" C2 NAG A2004 " pdb=" O5 NAG A2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 4221 not shown) Planarity restraints: 4490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 329 " -0.025 2.00e-02 2.50e+03 2.31e-02 6.69e+00 pdb=" CG ASN A 329 " 0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 329 " 0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 329 " 0.027 2.00e-02 2.50e+03 pdb=" C1 NAG E 1 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 558 " 0.033 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO C 559 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO C 559 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 559 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 983 " -0.032 5.00e-02 4.00e+02 4.80e-02 3.69e+00 pdb=" N PRO A 984 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 984 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 984 " -0.026 5.00e-02 4.00e+02 ... (remaining 4487 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1862 2.74 - 3.28: 24679 3.28 - 3.82: 39948 3.82 - 4.36: 44918 4.36 - 4.90: 80399 Nonbonded interactions: 191806 Sorted by model distance: nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.197 3.040 nonbonded pdb=" OG1 THR B 109 " pdb=" OD1 ASP B 111 " model vdw 2.206 3.040 nonbonded pdb=" OG SER A 347 " pdb=" O ARG A 450 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR C 91 " pdb=" OE2 GLU C 189 " model vdw 2.226 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.231 3.040 ... (remaining 191801 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 14 through 2004) selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 635 through 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.330 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 25923 Z= 0.188 Angle : 0.624 11.453 35432 Z= 0.296 Chirality : 0.047 0.364 4224 Planarity : 0.004 0.050 4442 Dihedral : 13.700 86.376 10536 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3040 helix: 2.30 (0.22), residues: 656 sheet: 0.52 (0.19), residues: 719 loop : -1.07 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.016 0.001 TYR A 503 PHE 0.019 0.001 PHE B 904 TRP 0.023 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00393 (25802) covalent geometry : angle 0.59023 (35109) SS BOND : bond 0.00285 ( 40) SS BOND : angle 1.58207 ( 80) hydrogen bonds : bond 0.11920 ( 1003) hydrogen bonds : angle 5.58193 ( 2748) link_BETA1-4 : bond 0.00360 ( 33) link_BETA1-4 : angle 1.93685 ( 99) link_NAG-ASN : bond 0.00397 ( 48) link_NAG-ASN : angle 2.62068 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 569 ASP cc_start: 0.6995 (t0) cc_final: 0.6793 (OUTLIER) outliers start: 0 outliers final: 1 residues processed: 87 average time/residue: 0.5410 time to fit residues: 56.7108 Evaluate side-chains 59 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 899 GLN B1000 GLN C 269 GLN C 386 ASN C1003 GLN ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.085455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050560 restraints weight = 86583.088| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 4.32 r_work: 0.2691 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 25923 Z= 0.271 Angle : 0.664 13.579 35432 Z= 0.329 Chirality : 0.048 0.374 4224 Planarity : 0.004 0.054 4442 Dihedral : 7.587 59.673 5011 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.93 % Rotamer: Outliers : 0.44 % Allowed : 6.96 % Favored : 92.60 % 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: -0.01 (0.15), residues: 3040 helix: 2.22 (0.21), residues: 656 sheet: 0.37 (0.19), residues: 728 loop : -1.15 (0.15), residues: 1656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.025 0.002 PHE C 904 TRP 0.017 0.002 TRP C 351 HIS 0.004 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00643 (25802) covalent geometry : angle 0.63593 (35109) SS BOND : bond 0.00435 ( 40) SS BOND : angle 1.78068 ( 80) hydrogen bonds : bond 0.06655 ( 1003) hydrogen bonds : angle 5.24107 ( 2748) link_BETA1-4 : bond 0.00237 ( 33) link_BETA1-4 : angle 1.67702 ( 99) link_NAG-ASN : bond 0.00456 ( 48) link_NAG-ASN : angle 2.46237 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8304 (t0) cc_final: 0.8064 (t0) REVERT: A 898 MET cc_start: 0.9476 (OUTLIER) cc_final: 0.9227 (mtp) REVERT: B 867 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8986 (mtp) REVERT: C 988 GLU cc_start: 0.8506 (pp20) cc_final: 0.8158 (pm20) outliers start: 12 outliers final: 3 residues processed: 72 average time/residue: 0.5384 time to fit residues: 47.1491 Evaluate side-chains 67 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 62 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 867 MET Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 898 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 155 optimal weight: 5.9990 chunk 121 optimal weight: 0.9990 chunk 304 optimal weight: 0.7980 chunk 124 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 195 optimal weight: 0.9980 chunk 208 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.087205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.052690 restraints weight = 86298.660| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.18 r_work: 0.2767 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25923 Z= 0.114 Angle : 0.559 11.416 35432 Z= 0.275 Chirality : 0.045 0.362 4224 Planarity : 0.004 0.051 4442 Dihedral : 6.886 58.235 5011 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.49 % Favored : 96.48 % Rotamer: Outliers : 0.56 % Allowed : 9.44 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3040 helix: 2.46 (0.22), residues: 651 sheet: 0.54 (0.19), residues: 717 loop : -1.05 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.016 0.001 TYR A 449 PHE 0.014 0.001 PHE B1050 TRP 0.013 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00249 (25802) covalent geometry : angle 0.53033 (35109) SS BOND : bond 0.00297 ( 40) SS BOND : angle 1.33279 ( 80) hydrogen bonds : bond 0.05337 ( 1003) hydrogen bonds : angle 4.88922 ( 2748) link_BETA1-4 : bond 0.00380 ( 33) link_BETA1-4 : angle 1.61764 ( 99) link_NAG-ASN : bond 0.00426 ( 48) link_NAG-ASN : angle 2.32260 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8083 (t0) cc_final: 0.7756 (t0) REVERT: A 898 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.9046 (mtp) REVERT: B 867 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8888 (mtp) REVERT: B 988 GLU cc_start: 0.8787 (pp20) cc_final: 0.8389 (pm20) outliers start: 15 outliers final: 5 residues processed: 74 average time/residue: 0.5315 time to fit residues: 47.5865 Evaluate side-chains 70 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 63 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 867 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 147 optimal weight: 0.7980 chunk 161 optimal weight: 1.9990 chunk 243 optimal weight: 0.4980 chunk 299 optimal weight: 2.9990 chunk 178 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 160 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 214 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.087226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.052619 restraints weight = 85907.660| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 4.28 r_work: 0.2771 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.0944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25923 Z= 0.119 Angle : 0.547 11.302 35432 Z= 0.269 Chirality : 0.045 0.358 4224 Planarity : 0.004 0.050 4442 Dihedral : 6.500 56.796 5011 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 0.93 % Allowed : 10.96 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3040 helix: 2.50 (0.22), residues: 651 sheet: 0.58 (0.19), residues: 718 loop : -1.02 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 235 TYR 0.016 0.001 TYR A1065 PHE 0.012 0.001 PHE C1119 TRP 0.031 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00269 (25802) covalent geometry : angle 0.51927 (35109) SS BOND : bond 0.00280 ( 40) SS BOND : angle 1.26562 ( 80) hydrogen bonds : bond 0.05168 ( 1003) hydrogen bonds : angle 4.79980 ( 2748) link_BETA1-4 : bond 0.00325 ( 33) link_BETA1-4 : angle 1.60389 ( 99) link_NAG-ASN : bond 0.00409 ( 48) link_NAG-ASN : angle 2.31314 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 66 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8064 (t0) cc_final: 0.7729 (t0) REVERT: A 898 MET cc_start: 0.9298 (OUTLIER) cc_final: 0.8987 (mtp) REVERT: B 1000 GLN cc_start: 0.9002 (tt0) cc_final: 0.8740 (tm-30) outliers start: 25 outliers final: 9 residues processed: 82 average time/residue: 0.5001 time to fit residues: 50.6083 Evaluate side-chains 69 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 517 HIS Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 298 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 27 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 275 optimal weight: 0.0170 chunk 245 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 154 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 overall best weight: 1.9624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.086283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.051395 restraints weight = 86004.557| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 4.31 r_work: 0.2716 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25923 Z= 0.177 Angle : 0.584 11.135 35432 Z= 0.288 Chirality : 0.045 0.358 4224 Planarity : 0.004 0.051 4442 Dihedral : 6.345 57.052 5011 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 0.89 % Allowed : 12.81 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3040 helix: 2.54 (0.21), residues: 642 sheet: 0.49 (0.19), residues: 721 loop : -1.04 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.014 0.001 PHE B1119 TRP 0.019 0.001 TRP C 434 HIS 0.003 0.001 HIS C1086 Details of bonding type rmsd covalent geometry : bond 0.00419 (25802) covalent geometry : angle 0.55656 (35109) SS BOND : bond 0.00329 ( 40) SS BOND : angle 1.41601 ( 80) hydrogen bonds : bond 0.05807 ( 1003) hydrogen bonds : angle 4.89224 ( 2748) link_BETA1-4 : bond 0.00262 ( 33) link_BETA1-4 : angle 1.65274 ( 99) link_NAG-ASN : bond 0.00407 ( 48) link_NAG-ASN : angle 2.33497 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 569 ASP cc_start: 0.8321 (t0) cc_final: 0.8014 (t0) REVERT: A 898 MET cc_start: 0.9470 (OUTLIER) cc_final: 0.9192 (mtp) REVERT: B 1000 GLN cc_start: 0.9112 (tt0) cc_final: 0.8663 (tm-30) REVERT: C 108 THR cc_start: 0.8818 (OUTLIER) cc_final: 0.8479 (m) REVERT: C 242 LEU cc_start: 0.8216 (pp) cc_final: 0.7793 (tm) outliers start: 24 outliers final: 10 residues processed: 78 average time/residue: 0.4993 time to fit residues: 47.9076 Evaluate side-chains 70 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 58 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 898 MET Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 98 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 112 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 253 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 302 optimal weight: 0.0670 chunk 144 optimal weight: 0.0370 chunk 203 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 20.0000 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 237 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** 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 = 0.3775 r_free = 0.3775 target = 0.087698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.053292 restraints weight = 86702.243| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.31 r_work: 0.2788 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25923 Z= 0.101 Angle : 0.547 11.539 35432 Z= 0.267 Chirality : 0.044 0.353 4224 Planarity : 0.003 0.049 4442 Dihedral : 5.979 57.358 5011 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 0.96 % Allowed : 13.77 % Favored : 85.26 % 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: 0.35 (0.15), residues: 3040 helix: 2.64 (0.22), residues: 646 sheet: 0.63 (0.19), residues: 712 loop : -0.96 (0.15), residues: 1682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1017 TYR 0.016 0.001 TYR B1065 PHE 0.015 0.001 PHE B 454 TRP 0.013 0.001 TRP C 434 HIS 0.001 0.000 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00216 (25802) covalent geometry : angle 0.52008 (35109) SS BOND : bond 0.00283 ( 40) SS BOND : angle 1.15824 ( 80) hydrogen bonds : bond 0.04781 ( 1003) hydrogen bonds : angle 4.65982 ( 2748) link_BETA1-4 : bond 0.00397 ( 33) link_BETA1-4 : angle 1.58370 ( 99) link_NAG-ASN : bond 0.00437 ( 48) link_NAG-ASN : angle 2.25533 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 CYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7287 (p) REVERT: A 569 ASP cc_start: 0.8054 (t0) cc_final: 0.7735 (t0) REVERT: B 1000 GLN cc_start: 0.9042 (tt0) cc_final: 0.8740 (tm-30) REVERT: C 108 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8741 (m) REVERT: C 242 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7751 (tm) REVERT: C 876 LEU cc_start: 0.9361 (OUTLIER) cc_final: 0.9154 (tt) outliers start: 26 outliers final: 8 residues processed: 82 average time/residue: 0.4753 time to fit residues: 47.8756 Evaluate side-chains 72 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 255 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 45 optimal weight: 20.0000 chunk 186 optimal weight: 3.9990 chunk 272 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN C 392 ASN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.086060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.050986 restraints weight = 86211.285| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.36 r_work: 0.2706 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25923 Z= 0.206 Angle : 0.603 13.205 35432 Z= 0.295 Chirality : 0.046 0.358 4224 Planarity : 0.004 0.049 4442 Dihedral : 6.091 57.126 5011 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 1.22 % Allowed : 13.92 % Favored : 84.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.15), residues: 3040 helix: 2.51 (0.22), residues: 648 sheet: 0.46 (0.19), residues: 726 loop : -1.00 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.017 0.001 PHE B1119 TRP 0.016 0.001 TRP C 884 HIS 0.003 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00485 (25802) covalent geometry : angle 0.57596 (35109) SS BOND : bond 0.00381 ( 40) SS BOND : angle 1.49412 ( 80) hydrogen bonds : bond 0.05938 ( 1003) hydrogen bonds : angle 4.87341 ( 2748) link_BETA1-4 : bond 0.00256 ( 33) link_BETA1-4 : angle 1.66497 ( 99) link_NAG-ASN : bond 0.00420 ( 48) link_NAG-ASN : angle 2.32148 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 389 CYS cc_start: 0.7679 (OUTLIER) cc_final: 0.7315 (p) REVERT: A 558 LEU cc_start: 0.9527 (OUTLIER) cc_final: 0.9231 (mp) REVERT: A 569 ASP cc_start: 0.8352 (t0) cc_final: 0.8052 (t0) REVERT: B 1000 GLN cc_start: 0.9130 (tt0) cc_final: 0.8715 (tm-30) REVERT: C 108 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8480 (m) REVERT: C 242 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7834 (tm) REVERT: C 876 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8946 (tt) outliers start: 33 outliers final: 14 residues processed: 84 average time/residue: 0.4719 time to fit residues: 48.9963 Evaluate side-chains 76 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 389 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 736 CYS Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 231 optimal weight: 2.9990 chunk 218 optimal weight: 6.9990 chunk 158 optimal weight: 10.0000 chunk 281 optimal weight: 3.9990 chunk 123 optimal weight: 4.9990 chunk 196 optimal weight: 0.4980 chunk 109 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 271 optimal weight: 2.9990 chunk 289 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** C1104 GLN ** 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 = 0.3721 r_free = 0.3721 target = 0.085520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.050095 restraints weight = 86364.807| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 4.45 r_work: 0.2682 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 25923 Z= 0.231 Angle : 0.627 12.026 35432 Z= 0.309 Chirality : 0.046 0.361 4224 Planarity : 0.004 0.050 4442 Dihedral : 6.232 57.435 5011 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.84 % Favored : 95.13 % Rotamer: Outliers : 1.48 % Allowed : 14.03 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.15), residues: 3040 helix: 2.37 (0.21), residues: 653 sheet: 0.36 (0.19), residues: 726 loop : -1.06 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.017 0.001 TYR A1065 PHE 0.019 0.001 PHE C 375 TRP 0.021 0.002 TRP C 884 HIS 0.003 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00546 (25802) covalent geometry : angle 0.59970 (35109) SS BOND : bond 0.00402 ( 40) SS BOND : angle 1.58036 ( 80) hydrogen bonds : bond 0.06414 ( 1003) hydrogen bonds : angle 4.99892 ( 2748) link_BETA1-4 : bond 0.00249 ( 33) link_BETA1-4 : angle 1.69716 ( 99) link_NAG-ASN : bond 0.00429 ( 48) link_NAG-ASN : angle 2.35446 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 64 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.6993 (OUTLIER) cc_final: 0.6510 (p) REVERT: A 352 ASN cc_start: 0.9136 (t0) cc_final: 0.8740 (m110) REVERT: A 558 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9205 (mp) REVERT: A 569 ASP cc_start: 0.8377 (t0) cc_final: 0.8125 (t0) REVERT: B 988 GLU cc_start: 0.8770 (pp20) cc_final: 0.8435 (pm20) REVERT: B 1000 GLN cc_start: 0.9157 (tt0) cc_final: 0.8730 (tm-30) REVERT: C 108 THR cc_start: 0.8745 (OUTLIER) cc_final: 0.8358 (m) REVERT: C 242 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7912 (tm) REVERT: C 876 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8960 (tt) outliers start: 40 outliers final: 21 residues processed: 94 average time/residue: 0.4480 time to fit residues: 52.3890 Evaluate side-chains 85 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1000 GLN Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 453 LEU 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 900 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 39 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 75 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 152 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 84 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** C1104 GLN ** 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 = 0.3735 r_free = 0.3735 target = 0.086214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.051065 restraints weight = 85919.243| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.30 r_work: 0.2713 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25923 Z= 0.160 Angle : 0.591 11.850 35432 Z= 0.289 Chirality : 0.045 0.359 4224 Planarity : 0.004 0.050 4442 Dihedral : 6.110 56.910 5011 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Rotamer: Outliers : 0.93 % Allowed : 14.74 % 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: 0.16 (0.15), residues: 3040 helix: 2.53 (0.21), residues: 642 sheet: 0.40 (0.19), residues: 725 loop : -1.04 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.018 0.001 TYR B 447 PHE 0.022 0.001 PHE C 375 TRP 0.029 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00373 (25802) covalent geometry : angle 0.56291 (35109) SS BOND : bond 0.00326 ( 40) SS BOND : angle 1.60837 ( 80) hydrogen bonds : bond 0.05830 ( 1003) hydrogen bonds : angle 4.85812 ( 2748) link_BETA1-4 : bond 0.00289 ( 33) link_BETA1-4 : angle 1.66967 ( 99) link_NAG-ASN : bond 0.00398 ( 48) link_NAG-ASN : angle 2.29783 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 59 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 VAL cc_start: 0.7009 (OUTLIER) cc_final: 0.6547 (p) REVERT: A 352 ASN cc_start: 0.9136 (t0) cc_final: 0.8737 (m110) REVERT: A 558 LEU cc_start: 0.9505 (OUTLIER) cc_final: 0.9204 (mp) REVERT: A 569 ASP cc_start: 0.8339 (t0) cc_final: 0.8069 (t0) REVERT: B 1000 GLN cc_start: 0.9128 (tt0) cc_final: 0.8703 (tm-30) REVERT: C 108 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8413 (m) REVERT: C 242 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7881 (tm) REVERT: C 876 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8933 (tt) outliers start: 25 outliers final: 17 residues processed: 79 average time/residue: 0.4797 time to fit residues: 46.7463 Evaluate side-chains 79 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU 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 738 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 224 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 278 optimal weight: 0.0020 chunk 133 optimal weight: 8.9990 chunk 266 optimal weight: 4.9990 chunk 174 optimal weight: 0.4980 overall best weight: 1.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** 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 = 0.3741 r_free = 0.3741 target = 0.086498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.051414 restraints weight = 86260.019| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 4.37 r_work: 0.2722 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 25923 Z= 0.144 Angle : 0.579 11.713 35432 Z= 0.284 Chirality : 0.045 0.360 4224 Planarity : 0.004 0.050 4442 Dihedral : 5.992 56.868 5011 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 0.85 % Allowed : 14.92 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3040 helix: 2.46 (0.21), residues: 655 sheet: 0.41 (0.19), residues: 725 loop : -1.00 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1037 TYR 0.016 0.001 TYR A1065 PHE 0.022 0.001 PHE C 375 TRP 0.023 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00334 (25802) covalent geometry : angle 0.55206 (35109) SS BOND : bond 0.00301 ( 40) SS BOND : angle 1.47166 ( 80) hydrogen bonds : bond 0.05532 ( 1003) hydrogen bonds : angle 4.79489 ( 2748) link_BETA1-4 : bond 0.00311 ( 33) link_BETA1-4 : angle 1.64994 ( 99) link_NAG-ASN : bond 0.00395 ( 48) link_NAG-ASN : angle 2.26724 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 58 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 352 ASN cc_start: 0.9205 (t0) cc_final: 0.8812 (m110) REVERT: A 569 ASP cc_start: 0.8344 (t0) cc_final: 0.8073 (t0) REVERT: B 988 GLU cc_start: 0.8684 (pp20) cc_final: 0.8377 (pm20) REVERT: B 1000 GLN cc_start: 0.9132 (tt0) cc_final: 0.8697 (tm-30) REVERT: C 108 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8490 (m) REVERT: C 242 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7922 (tm) REVERT: C 876 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8927 (tt) outliers start: 23 outliers final: 16 residues processed: 78 average time/residue: 0.4892 time to fit residues: 46.8978 Evaluate side-chains 76 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 643 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 453 LEU 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 C residue 62 VAL Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 643 THR Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 212 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 chunk 234 optimal weight: 5.9990 chunk 161 optimal weight: 0.0970 chunk 195 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 242 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 297 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 GLN ** C 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1104 GLN ** 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 = 0.3731 r_free = 0.3731 target = 0.085990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.050750 restraints weight = 85960.557| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 4.48 r_work: 0.2701 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25923 Z= 0.183 Angle : 0.600 11.541 35432 Z= 0.294 Chirality : 0.046 0.360 4224 Planarity : 0.004 0.050 4442 Dihedral : 6.046 57.071 5011 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.38 % Favored : 95.59 % Rotamer: Outliers : 0.96 % Allowed : 14.96 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3040 helix: 2.44 (0.21), residues: 654 sheet: 0.38 (0.19), residues: 725 loop : -1.03 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1037 TYR 0.018 0.001 TYR B 447 PHE 0.023 0.001 PHE C 375 TRP 0.022 0.002 TRP C 351 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00431 (25802) covalent geometry : angle 0.57259 (35109) SS BOND : bond 0.00343 ( 40) SS BOND : angle 1.56031 ( 80) hydrogen bonds : bond 0.05916 ( 1003) hydrogen bonds : angle 4.86989 ( 2748) link_BETA1-4 : bond 0.00267 ( 33) link_BETA1-4 : angle 1.68241 ( 99) link_NAG-ASN : bond 0.00406 ( 48) link_NAG-ASN : angle 2.28899 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8081.41 seconds wall clock time: 138 minutes 14.81 seconds (8294.81 seconds total)