Starting phenix.real_space_refine on Thu Mar 5 21:27:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7u_31782/03_2026/7v7u_31782.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7u_31782/03_2026/7v7u_31782.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/7v7u_31782/03_2026/7v7u_31782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7u_31782/03_2026/7v7u_31782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7u_31782/03_2026/7v7u_31782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7u_31782/03_2026/7v7u_31782.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= 0.056 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 16055 2.51 5 N 4115 2.21 5 O 5005 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s 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: 25283 Number of models: 1 Model: "" Number of chains: 41 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: "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: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 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: 5.59, per 1000 atoms: 0.22 Number of scatterers: 25283 At special positions: 0 Unit cell: (139.7, 145.2, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5005 8.00 N 4115 7.00 C 16055 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=2.04 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.02 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.02 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.03 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 341 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 329 " " NAG f 1 " - " ASN C 614 " " NAG g 1 " - " ASN C 707 " " NAG h 1 " - " ASN C 715 " " NAG i 1 " - " ASN C 799 " " NAG j 1 " - " ASN C1072 " " NAG k 1 " - " ASN C1096 " " NAG l 1 " - " ASN C1132 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 62 helices and 43 sheets defined 24.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 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 363 through 369 Processing helix chain 'A' and resid 382 through 387 removed outlier: 3.892A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 removed outlier: 3.838A pdb=" N VAL A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.539A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 742 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.068A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 781 removed outlier: 3.928A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.265A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.598A pdb=" N LEU A 936 " --> pdb=" O ILE A 932 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER A 938 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.692A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.024A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (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: 4.109A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.902A 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: 3.716A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.557A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.556A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.005A 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: 3.593A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.791A 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: 3.732A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.408A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.680A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.641A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 420 Processing helix chain 'C' and resid 735 through 741 Processing helix chain 'C' and resid 744 through 752 Processing helix chain 'C' and resid 753 through 755 No H-bonds generated for 'chain 'C' and resid 753 through 755' Processing helix chain 'C' and resid 758 through 781 removed outlier: 3.514A pdb=" N ASN C 762 " --> pdb=" O CYS C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.531A pdb=" N VAL C 824 " --> pdb=" O LEU C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.635A 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 917 removed outlier: 4.265A pdb=" N LEU C 914 " --> pdb=" O THR C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.609A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU C 982 " --> pdb=" O ILE C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1031 removed outlier: 4.529A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C1031 " --> pdb=" O MET C1027 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.558A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 30 removed outlier: 7.847A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.209A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.985A pdb=" N PHE A 43 " --> pdb=" O ARG C 565 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.032A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.093A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.468A pdb=" N VAL A 126 " --> pdb=" O GLU A 167 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N GLU A 167 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.383A pdb=" N ILE A 128 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 8.855A pdb=" N THR A 165 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL A 130 " --> pdb=" O ASN A 163 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ASN A 163 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLU A 132 " --> pdb=" O ALA A 161 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ALA A 161 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN A 134 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 309 through 317 removed outlier: 3.548A pdb=" N THR A 313 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.754A pdb=" N ASN A 540 " --> pdb=" O ILE A 324 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AA9, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB1, first strand: chain 'A' and resid 571 through 574 removed outlier: 6.662A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.046A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 711 Processing sheet with id=AB4, first strand: chain 'A' and resid 715 through 726 removed outlier: 3.508A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.569A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB7, first strand: chain 'A' and resid 1092 through 1095 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.331A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.480A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.375A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.005A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.547A pdb=" N LEU B 84 " --> pdb=" O PHE B 236 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.442A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 309 through 317 removed outlier: 6.951A pdb=" N VAL B 593 " --> pdb=" O THR B 313 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ASN B 315 " --> pdb=" O GLY B 591 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N GLY B 591 " --> pdb=" O ASN B 315 " (cutoff:3.500A) removed outlier: 4.633A 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: 5.408A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 6.885A 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: 6.378A 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 450 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: 5.846A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.464A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 5.717A 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: 7.110A 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 715 through 726 removed outlier: 5.999A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.846A 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: 4.540A 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 1123 removed outlier: 4.991A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1092 through 1095 removed outlier: 5.106A pdb=" N GLN B1104 " --> pdb=" O GLU B1109 " (cutoff:3.500A) removed outlier: 5.684A 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: 7.908A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.641A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.870A 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: 4.018A 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: 7.229A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 309 through 317 removed outlier: 6.967A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE1, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE2, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.181A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 709 through 711 removed outlier: 3.669A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 715 through 726 removed outlier: 3.564A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 731 through 733 removed outlier: 4.545A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1118 through 1120 1000 hydrogen bonds defined for protein. 2730 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.47 Time building geometry restraints manager: 3.05 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: 7964 1.34 - 1.46: 6252 1.46 - 1.58: 11482 1.58 - 1.70: 0 1.70 - 1.83: 132 Bond restraints: 25830 Sorted by residual: bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C1 NAG j 1 " pdb=" O5 NAG j 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.38e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C1 NAG a 1 " pdb=" O5 NAG a 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.01e+00 ... (remaining 25825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 35065 3.67 - 7.35: 78 7.35 - 11.02: 3 11.02 - 14.70: 0 14.70 - 18.37: 1 Bond angle restraints: 35147 Sorted by residual: angle pdb=" C LEU A 982 " pdb=" N ASP A 983 " pdb=" CA ASP A 983 " ideal model delta sigma weight residual 120.67 139.04 -18.37 1.34e+00 5.57e-01 1.88e+02 angle pdb=" N ILE A 466 " pdb=" CA ILE A 466 " pdb=" C ILE A 466 " ideal model delta sigma weight residual 112.43 109.12 3.31 9.20e-01 1.18e+00 1.30e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.63 -3.93 1.22e+00 6.72e-01 1.04e+01 angle pdb=" N PRO A 984 " pdb=" CA PRO A 984 " pdb=" C PRO A 984 " ideal model delta sigma weight residual 110.70 114.24 -3.54 1.22e+00 6.72e-01 8.40e+00 angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 121.75 117.44 4.31 1.73e+00 3.34e-01 6.19e+00 ... (remaining 35142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.04: 15219 21.04 - 42.07: 1023 42.07 - 63.11: 188 63.11 - 84.15: 37 84.15 - 105.19: 17 Dihedral angle restraints: 16484 sinusoidal: 7497 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 93.00 3.62 89.38 1 1.00e+01 1.00e-02 9.50e+01 dihedral pdb=" CB CYS A 389 " pdb=" SG CYS A 389 " pdb=" SG CYS A 523 " pdb=" CB CYS A 523 " ideal model delta sinusoidal sigma weight residual -86.00 2.95 -88.95 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS C 389 " pdb=" SG CYS C 389 " pdb=" SG CYS C 523 " pdb=" CB CYS C 523 " ideal model delta sinusoidal sigma weight residual 93.00 9.21 83.79 1 1.00e+01 1.00e-02 8.56e+01 ... (remaining 16481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3558 0.065 - 0.131: 628 0.131 - 0.196: 45 0.196 - 0.262: 2 0.262 - 0.327: 1 Chirality restraints: 4234 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 -2.07 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN B 707 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB THR A 95 " pdb=" CA THR A 95 " pdb=" OG1 THR A 95 " pdb=" CG2 THR A 95 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 4231 not shown) Planarity restraints: 4492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.032 2.00e-02 2.50e+03 2.98e-02 1.11e+01 pdb=" CG ASN B1072 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 904 " 0.019 2.00e-02 2.50e+03 1.81e-02 5.72e+00 pdb=" CG PHE B 904 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE B 904 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE B 904 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 904 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 904 " 0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 904 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 984 " 0.034 5.00e-02 4.00e+02 5.03e-02 4.06e+00 pdb=" N PRO A 985 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 985 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 985 " 0.028 5.00e-02 4.00e+02 ... (remaining 4489 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 2021 2.74 - 3.28: 24777 3.28 - 3.82: 39888 3.82 - 4.36: 45242 4.36 - 4.90: 80554 Nonbonded interactions: 192482 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.194 3.040 nonbonded pdb=" OG SER A 638 " pdb=" OD1 ASN A 639 " model vdw 2.203 3.040 nonbonded pdb=" OG1 THR B 616 " pdb=" OE1 GLU B 617 " model vdw 2.212 3.040 nonbonded pdb=" O ASN C 437 " pdb=" OG SER C 441 " model vdw 2.241 3.040 nonbonded pdb=" O SER C 965 " pdb=" OG SER C 965 " model vdw 2.248 3.040 ... (remaining 192477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 635 through 825 or resid 853 throu \ gh 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' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 24.670 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 25953 Z= 0.238 Angle : 0.671 18.371 35476 Z= 0.331 Chirality : 0.048 0.327 4234 Planarity : 0.003 0.050 4444 Dihedral : 13.996 105.187 10578 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.80 % Favored : 95.13 % 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: 0.24 (0.15), residues: 3040 helix: 2.25 (0.21), residues: 655 sheet: 0.67 (0.19), residues: 716 loop : -0.98 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.021 0.001 TYR A 871 PHE 0.042 0.001 PHE B 904 TRP 0.022 0.002 TRP B 884 HIS 0.003 0.001 HIS B1062 Details of bonding type rmsd covalent geometry : bond 0.00530 (25830) covalent geometry : angle 0.64460 (35147) SS BOND : bond 0.00342 ( 40) SS BOND : angle 1.83908 ( 80) hydrogen bonds : bond 0.12272 ( 1000) hydrogen bonds : angle 5.88034 ( 2730) link_BETA1-4 : bond 0.00293 ( 35) link_BETA1-4 : angle 1.84233 ( 105) link_NAG-ASN : bond 0.00263 ( 48) link_NAG-ASN : angle 2.29225 ( 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 207 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 ARG cc_start: 0.7592 (mpt-90) cc_final: 0.7360 (mmt90) REVERT: A 569 ASP cc_start: 0.7963 (m-30) cc_final: 0.7139 (t0) REVERT: B 118 LEU cc_start: 0.7678 (tt) cc_final: 0.7376 (tt) REVERT: B 955 GLN cc_start: 0.8379 (tm-30) cc_final: 0.8137 (tm-30) REVERT: B 985 PRO cc_start: 0.7529 (Cg_exo) cc_final: 0.7325 (Cg_endo) REVERT: B 1048 MET cc_start: 0.8057 (ptm) cc_final: 0.7734 (ptm) REVERT: C 375 PHE cc_start: 0.8181 (t80) cc_final: 0.7849 (t80) REVERT: C 434 TRP cc_start: 0.7422 (p-90) cc_final: 0.7195 (p90) outliers start: 0 outliers final: 3 residues processed: 207 average time/residue: 0.6403 time to fit residues: 153.6375 Evaluate side-chains 107 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 104 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 978 ILE Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 992 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 GLN A 237 GLN A 540 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN C 115 GLN C 899 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.140542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.082379 restraints weight = 44582.385| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 3.26 r_work: 0.3011 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 25953 Z= 0.215 Angle : 0.674 9.564 35476 Z= 0.334 Chirality : 0.049 0.365 4234 Planarity : 0.004 0.056 4444 Dihedral : 8.353 89.929 5059 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 0.67 % Allowed : 8.77 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3040 helix: 2.08 (0.21), residues: 678 sheet: 0.58 (0.19), residues: 684 loop : -1.07 (0.14), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1037 TYR 0.027 0.001 TYR A1065 PHE 0.030 0.002 PHE B 904 TRP 0.013 0.002 TRP B 884 HIS 0.005 0.001 HIS A1086 Details of bonding type rmsd covalent geometry : bond 0.00526 (25830) covalent geometry : angle 0.65021 (35147) SS BOND : bond 0.00431 ( 40) SS BOND : angle 2.08219 ( 80) hydrogen bonds : bond 0.06776 ( 1000) hydrogen bonds : angle 5.15706 ( 2730) link_BETA1-4 : bond 0.00345 ( 35) link_BETA1-4 : angle 1.69423 ( 105) link_NAG-ASN : bond 0.00302 ( 48) link_NAG-ASN : angle 2.03308 ( 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 146 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7725 (t60) cc_final: 0.6775 (t60) REVERT: A 188 ARG cc_start: 0.7865 (mpt-90) cc_final: 0.7584 (mmt90) REVERT: A 569 ASP cc_start: 0.8303 (m-30) cc_final: 0.7397 (t0) REVERT: B 53 ASP cc_start: 0.7473 (t70) cc_final: 0.7142 (t70) REVERT: B 774 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8835 (ttpp) REVERT: B 955 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8533 (tm-30) REVERT: B 1048 MET cc_start: 0.8551 (ptm) cc_final: 0.8248 (ptm) REVERT: C 301 LEU cc_start: 0.8454 (OUTLIER) cc_final: 0.8239 (mt) REVERT: C 375 PHE cc_start: 0.8027 (t80) cc_final: 0.7680 (t80) REVERT: C 434 TRP cc_start: 0.7519 (p-90) cc_final: 0.7253 (p90) outliers start: 18 outliers final: 5 residues processed: 141 average time/residue: 0.5329 time to fit residues: 90.5441 Evaluate side-chains 114 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 82 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 305 optimal weight: 0.9990 chunk 227 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 236 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 220 optimal weight: 5.9990 chunk 292 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 216 optimal weight: 0.0980 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN B 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.142600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.085296 restraints weight = 44503.886| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 3.22 r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 25953 Z= 0.121 Angle : 0.595 10.018 35476 Z= 0.292 Chirality : 0.046 0.357 4234 Planarity : 0.004 0.054 4444 Dihedral : 7.618 85.951 5053 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 1.33 % Allowed : 10.48 % Favored : 88.19 % 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: 0.27 (0.15), residues: 3040 helix: 2.21 (0.21), residues: 672 sheet: 0.74 (0.19), residues: 703 loop : -0.97 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 188 TYR 0.017 0.001 TYR B1065 PHE 0.015 0.001 PHE A 757 TRP 0.010 0.001 TRP B 884 HIS 0.004 0.000 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00265 (25830) covalent geometry : angle 0.57144 (35147) SS BOND : bond 0.00445 ( 40) SS BOND : angle 1.70833 ( 80) hydrogen bonds : bond 0.05476 ( 1000) hydrogen bonds : angle 4.86603 ( 2730) link_BETA1-4 : bond 0.00373 ( 35) link_BETA1-4 : angle 1.70237 ( 105) link_NAG-ASN : bond 0.00295 ( 48) link_NAG-ASN : angle 1.91258 ( 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 169 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 133 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7696 (t60) cc_final: 0.6786 (t60) REVERT: A 124 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9040 (p) REVERT: A 188 ARG cc_start: 0.7832 (mpt-90) cc_final: 0.7587 (mmt90) REVERT: A 227 LEU cc_start: 0.8021 (mm) cc_final: 0.7791 (mt) REVERT: A 569 ASP cc_start: 0.8263 (m-30) cc_final: 0.7371 (t0) REVERT: B 53 ASP cc_start: 0.7395 (t70) cc_final: 0.7079 (t70) REVERT: B 955 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8382 (tp-100) REVERT: B 1048 MET cc_start: 0.8348 (ptm) cc_final: 0.8054 (ptm) REVERT: C 434 TRP cc_start: 0.7523 (p-90) cc_final: 0.7269 (p90) REVERT: C 1098 THR cc_start: 0.9088 (m) cc_final: 0.8842 (p) outliers start: 36 outliers final: 13 residues processed: 162 average time/residue: 0.4838 time to fit residues: 95.6406 Evaluate side-chains 125 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 240 LEU Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 982 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 233 optimal weight: 9.9990 chunk 200 optimal weight: 2.9990 chunk 245 optimal weight: 0.9990 chunk 273 optimal weight: 4.9990 chunk 301 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 148 optimal weight: 8.9990 chunk 146 optimal weight: 8.9990 chunk 189 optimal weight: 1.9990 chunk 173 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 854 ASN A 912 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN B 496 GLN B 760 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.140568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.083050 restraints weight = 44198.310| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 3.17 r_work: 0.3026 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 25953 Z= 0.180 Angle : 0.628 11.914 35476 Z= 0.308 Chirality : 0.047 0.368 4234 Planarity : 0.004 0.052 4444 Dihedral : 7.264 79.110 5053 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 1.59 % Allowed : 12.74 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3040 helix: 2.17 (0.21), residues: 673 sheet: 0.65 (0.19), residues: 678 loop : -1.07 (0.14), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 212 TYR 0.024 0.001 TYR A1065 PHE 0.018 0.001 PHE B1119 TRP 0.011 0.001 TRP B 884 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00436 (25830) covalent geometry : angle 0.60478 (35147) SS BOND : bond 0.00535 ( 40) SS BOND : angle 1.86025 ( 80) hydrogen bonds : bond 0.06234 ( 1000) hydrogen bonds : angle 4.90824 ( 2730) link_BETA1-4 : bond 0.00327 ( 35) link_BETA1-4 : angle 1.70166 ( 105) link_NAG-ASN : bond 0.00275 ( 48) link_NAG-ASN : angle 1.97159 ( 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 158 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7688 (t60) cc_final: 0.6737 (t60) REVERT: A 124 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9013 (p) REVERT: A 188 ARG cc_start: 0.7881 (mpt-90) cc_final: 0.7503 (mmt90) REVERT: A 569 ASP cc_start: 0.8400 (m-30) cc_final: 0.7333 (t0) REVERT: B 53 ASP cc_start: 0.7565 (t70) cc_final: 0.7187 (t70) REVERT: B 579 THR cc_start: 0.8798 (OUTLIER) cc_final: 0.8592 (p) REVERT: B 774 LYS cc_start: 0.9015 (OUTLIER) cc_final: 0.8793 (ttpp) REVERT: B 955 GLN cc_start: 0.8870 (tm-30) cc_final: 0.8387 (tp-100) REVERT: B 1037 ARG cc_start: 0.9209 (OUTLIER) cc_final: 0.8970 (mtp180) REVERT: B 1048 MET cc_start: 0.8444 (ptm) cc_final: 0.8223 (ptm) REVERT: C 434 TRP cc_start: 0.7511 (p-90) cc_final: 0.7261 (p90) REVERT: C 527 LYS cc_start: 0.8587 (mmmt) cc_final: 0.7760 (mmtt) REVERT: C 1000 GLN cc_start: 0.7900 (OUTLIER) cc_final: 0.7440 (mp10) outliers start: 43 outliers final: 23 residues processed: 153 average time/residue: 0.5137 time to fit residues: 95.0952 Evaluate side-chains 135 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 579 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 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 183 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 35 optimal weight: 0.2980 chunk 208 optimal weight: 7.9990 chunk 167 optimal weight: 1.9990 chunk 140 optimal weight: 6.9990 chunk 200 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 197 optimal weight: 0.8980 chunk 228 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B1104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.141597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.084162 restraints weight = 44168.074| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.19 r_work: 0.3042 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 25953 Z= 0.132 Angle : 0.591 11.166 35476 Z= 0.289 Chirality : 0.046 0.361 4234 Planarity : 0.004 0.049 4444 Dihedral : 6.796 72.087 5053 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.89 % Allowed : 13.66 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3040 helix: 2.21 (0.21), residues: 677 sheet: 0.70 (0.19), residues: 699 loop : -1.04 (0.14), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 188 TYR 0.019 0.001 TYR A1065 PHE 0.015 0.001 PHE C1119 TRP 0.010 0.001 TRP B 884 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00307 (25830) covalent geometry : angle 0.56818 (35147) SS BOND : bond 0.00428 ( 40) SS BOND : angle 1.63015 ( 80) hydrogen bonds : bond 0.05584 ( 1000) hydrogen bonds : angle 4.76559 ( 2730) link_BETA1-4 : bond 0.00370 ( 35) link_BETA1-4 : angle 1.71225 ( 105) link_NAG-ASN : bond 0.00279 ( 48) link_NAG-ASN : angle 1.90852 ( 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 167 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7690 (t60) cc_final: 0.6789 (t60) REVERT: A 124 THR cc_start: 0.9391 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 188 ARG cc_start: 0.7896 (mpt-90) cc_final: 0.7600 (mmt90) REVERT: A 227 LEU cc_start: 0.7997 (mm) cc_final: 0.7791 (mt) REVERT: A 569 ASP cc_start: 0.8390 (m-30) cc_final: 0.7327 (t0) REVERT: B 53 ASP cc_start: 0.7735 (t70) cc_final: 0.7451 (t70) REVERT: B 579 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8598 (p) REVERT: B 774 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8731 (ttpp) REVERT: B 955 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8363 (tp-100) REVERT: B 1037 ARG cc_start: 0.9188 (OUTLIER) cc_final: 0.8874 (mtp180) REVERT: B 1048 MET cc_start: 0.8325 (ptm) cc_final: 0.8076 (ptm) REVERT: B 1104 GLN cc_start: 0.9311 (OUTLIER) cc_final: 0.9048 (pt0) REVERT: C 434 TRP cc_start: 0.7498 (p-90) cc_final: 0.7253 (p90) REVERT: C 1000 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.7393 (mp10) outliers start: 51 outliers final: 25 residues processed: 160 average time/residue: 0.4637 time to fit residues: 90.9647 Evaluate side-chains 139 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 803 ILE Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 88 ASP Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1104 GLN Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 134 optimal weight: 6.9990 chunk 31 optimal weight: 30.0000 chunk 267 optimal weight: 0.8980 chunk 65 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 27 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 162 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS A 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN B1104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.141668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.083729 restraints weight = 44870.748| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.25 r_work: 0.3046 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25953 Z= 0.138 Angle : 0.595 10.699 35476 Z= 0.291 Chirality : 0.046 0.362 4234 Planarity : 0.004 0.048 4444 Dihedral : 6.558 65.989 5053 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 1.96 % Allowed : 14.37 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.15), residues: 3040 helix: 2.24 (0.21), residues: 675 sheet: 0.69 (0.19), residues: 670 loop : -1.03 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1105 TYR 0.020 0.001 TYR A1065 PHE 0.019 0.001 PHE C 133 TRP 0.009 0.001 TRP B 884 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00326 (25830) covalent geometry : angle 0.57275 (35147) SS BOND : bond 0.00420 ( 40) SS BOND : angle 1.60070 ( 80) hydrogen bonds : bond 0.05619 ( 1000) hydrogen bonds : angle 4.74514 ( 2730) link_BETA1-4 : bond 0.00353 ( 35) link_BETA1-4 : angle 1.72718 ( 105) link_NAG-ASN : bond 0.00270 ( 48) link_NAG-ASN : angle 1.90390 ( 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 163 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 110 time to evaluate : 0.920 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7718 (t60) cc_final: 0.6766 (t60) REVERT: A 81 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7456 (p0) REVERT: A 124 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9041 (p) REVERT: A 188 ARG cc_start: 0.7911 (mpt-90) cc_final: 0.7611 (mmt90) REVERT: A 227 LEU cc_start: 0.8086 (mm) cc_final: 0.7879 (mt) REVERT: A 569 ASP cc_start: 0.8432 (m-30) cc_final: 0.7442 (t0) REVERT: A 976 ASN cc_start: 0.9094 (m-40) cc_final: 0.8682 (t0) REVERT: B 53 ASP cc_start: 0.7803 (t70) cc_final: 0.7533 (t70) REVERT: B 774 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8750 (ttpp) REVERT: B 955 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8348 (tp-100) REVERT: B 1037 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8885 (mtp180) REVERT: B 1048 MET cc_start: 0.8311 (ptm) cc_final: 0.8101 (ptm) REVERT: C 434 TRP cc_start: 0.7488 (p-90) cc_final: 0.7246 (p90) REVERT: C 876 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8826 (tt) REVERT: C 1000 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7443 (mp10) outliers start: 53 outliers final: 31 residues processed: 159 average time/residue: 0.4461 time to fit residues: 88.2657 Evaluate side-chains 143 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 238 THR Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL 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 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 93 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 152 optimal weight: 0.1980 chunk 303 optimal weight: 0.9990 chunk 172 optimal weight: 0.8980 chunk 288 optimal weight: 0.9990 chunk 145 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 912 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.142262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.084808 restraints weight = 44333.720| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.21 r_work: 0.3061 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 25953 Z= 0.120 Angle : 0.581 11.002 35476 Z= 0.283 Chirality : 0.045 0.359 4234 Planarity : 0.004 0.048 4444 Dihedral : 6.284 58.518 5053 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.52 % Favored : 96.41 % Rotamer: Outliers : 1.67 % Allowed : 14.96 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.15), residues: 3040 helix: 2.24 (0.21), residues: 685 sheet: 0.85 (0.19), residues: 674 loop : -1.01 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 102 TYR 0.018 0.001 TYR A1065 PHE 0.016 0.001 PHE A 133 TRP 0.009 0.001 TRP C 351 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00272 (25830) covalent geometry : angle 0.55845 (35147) SS BOND : bond 0.00365 ( 40) SS BOND : angle 1.59761 ( 80) hydrogen bonds : bond 0.05283 ( 1000) hydrogen bonds : angle 4.68685 ( 2730) link_BETA1-4 : bond 0.00365 ( 35) link_BETA1-4 : angle 1.73961 ( 105) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 1.87022 ( 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 162 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 117 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7587 (t60) cc_final: 0.6652 (t60) REVERT: A 81 ASN cc_start: 0.8160 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 124 THR cc_start: 0.9382 (OUTLIER) cc_final: 0.9028 (p) REVERT: A 188 ARG cc_start: 0.7858 (mpt-90) cc_final: 0.7544 (mmt90) REVERT: A 227 LEU cc_start: 0.8044 (mm) cc_final: 0.7840 (mt) REVERT: A 569 ASP cc_start: 0.8431 (m-30) cc_final: 0.7431 (t0) REVERT: A 976 ASN cc_start: 0.9101 (m-40) cc_final: 0.8687 (t0) REVERT: B 53 ASP cc_start: 0.7811 (t70) cc_final: 0.7494 (t70) REVERT: B 774 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.8707 (ttpp) REVERT: B 955 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8342 (tp-100) REVERT: B 1037 ARG cc_start: 0.9181 (OUTLIER) cc_final: 0.8884 (mtp180) REVERT: C 434 TRP cc_start: 0.7503 (p-90) cc_final: 0.7264 (p90) REVERT: C 876 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8773 (tt) REVERT: C 1000 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: C 1098 THR cc_start: 0.9139 (m) cc_final: 0.8907 (p) outliers start: 45 outliers final: 29 residues processed: 158 average time/residue: 0.4668 time to fit residues: 90.9261 Evaluate side-chains 142 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 107 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 566 ASP 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 740 ILE Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 106 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 212 optimal weight: 4.9990 chunk 278 optimal weight: 0.0670 chunk 181 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 257 optimal weight: 4.9990 chunk 195 optimal weight: 0.9990 chunk 176 optimal weight: 0.4980 chunk 288 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.142699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.085394 restraints weight = 44652.771| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.20 r_work: 0.3069 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25953 Z= 0.115 Angle : 0.590 15.651 35476 Z= 0.285 Chirality : 0.045 0.356 4234 Planarity : 0.004 0.051 4444 Dihedral : 6.086 56.775 5053 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.59 % Favored : 96.35 % Rotamer: Outliers : 1.55 % Allowed : 15.40 % Favored : 83.04 % 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: 0.32 (0.15), residues: 3040 helix: 2.27 (0.21), residues: 685 sheet: 0.86 (0.19), residues: 680 loop : -0.99 (0.14), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 212 TYR 0.017 0.001 TYR A1065 PHE 0.023 0.001 PHE A 757 TRP 0.011 0.001 TRP C 351 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00255 (25830) covalent geometry : angle 0.56845 (35147) SS BOND : bond 0.00408 ( 40) SS BOND : angle 1.48887 ( 80) hydrogen bonds : bond 0.05073 ( 1000) hydrogen bonds : angle 4.63880 ( 2730) link_BETA1-4 : bond 0.00368 ( 35) link_BETA1-4 : angle 1.74684 ( 105) link_NAG-ASN : bond 0.00283 ( 48) link_NAG-ASN : angle 1.84562 ( 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 158 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 116 time to evaluate : 0.947 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7592 (t60) cc_final: 0.6656 (t60) REVERT: A 124 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.8994 (p) REVERT: A 188 ARG cc_start: 0.7891 (mpt-90) cc_final: 0.7448 (mmt90) REVERT: A 227 LEU cc_start: 0.8085 (mm) cc_final: 0.7867 (mt) REVERT: A 569 ASP cc_start: 0.8419 (m-30) cc_final: 0.7431 (t0) REVERT: A 976 ASN cc_start: 0.9110 (m-40) cc_final: 0.8704 (t0) REVERT: B 53 ASP cc_start: 0.7759 (t70) cc_final: 0.7495 (t70) REVERT: B 955 GLN cc_start: 0.8873 (tm-30) cc_final: 0.8353 (tp-100) REVERT: B 979 LEU cc_start: 0.9081 (mt) cc_final: 0.8637 (pp) REVERT: C 64 TRP cc_start: 0.7833 (t60) cc_final: 0.7437 (t60) REVERT: C 434 TRP cc_start: 0.7497 (p-90) cc_final: 0.7247 (p90) REVERT: C 876 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8788 (tt) REVERT: C 1000 GLN cc_start: 0.7877 (OUTLIER) cc_final: 0.7367 (mp10) REVERT: C 1098 THR cc_start: 0.9138 (m) cc_final: 0.8922 (p) outliers start: 42 outliers final: 28 residues processed: 155 average time/residue: 0.4540 time to fit residues: 87.3735 Evaluate side-chains 139 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 108 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 579 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 740 ILE Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 266 optimal weight: 4.9990 chunk 206 optimal weight: 0.0980 chunk 254 optimal weight: 0.0970 chunk 174 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 102 optimal weight: 20.0000 chunk 131 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 111 optimal weight: 8.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.142546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.085092 restraints weight = 44518.973| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 3.25 r_work: 0.3083 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25953 Z= 0.122 Angle : 0.596 13.954 35476 Z= 0.287 Chirality : 0.045 0.356 4234 Planarity : 0.004 0.050 4444 Dihedral : 5.917 56.837 5053 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.62 % Favored : 96.32 % Rotamer: Outliers : 1.55 % Allowed : 15.88 % Favored : 82.56 % 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: 0.33 (0.15), residues: 3040 helix: 2.26 (0.21), residues: 685 sheet: 0.84 (0.19), residues: 681 loop : -0.97 (0.15), residues: 1674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 212 TYR 0.018 0.001 TYR A1065 PHE 0.015 0.001 PHE C 390 TRP 0.013 0.001 TRP C 351 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00278 (25830) covalent geometry : angle 0.57461 (35147) SS BOND : bond 0.00414 ( 40) SS BOND : angle 1.48350 ( 80) hydrogen bonds : bond 0.05105 ( 1000) hydrogen bonds : angle 4.61656 ( 2730) link_BETA1-4 : bond 0.00369 ( 35) link_BETA1-4 : angle 1.75455 ( 105) link_NAG-ASN : bond 0.00277 ( 48) link_NAG-ASN : angle 1.83788 ( 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 156 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7711 (t60) cc_final: 0.6782 (t60) REVERT: A 124 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.8994 (p) REVERT: A 188 ARG cc_start: 0.8029 (mpt-90) cc_final: 0.7737 (mmt90) REVERT: A 227 LEU cc_start: 0.8129 (mm) cc_final: 0.7895 (mt) REVERT: A 569 ASP cc_start: 0.8556 (m-30) cc_final: 0.7491 (t0) REVERT: A 976 ASN cc_start: 0.9150 (m-40) cc_final: 0.8732 (t0) REVERT: B 53 ASP cc_start: 0.7898 (t70) cc_final: 0.7624 (t70) REVERT: B 774 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8753 (ttpp) REVERT: B 955 GLN cc_start: 0.9022 (tm-30) cc_final: 0.8493 (tp-100) REVERT: B 979 LEU cc_start: 0.9098 (mt) cc_final: 0.8623 (pp) REVERT: B 1037 ARG cc_start: 0.9216 (OUTLIER) cc_final: 0.8920 (mtp180) REVERT: C 64 TRP cc_start: 0.8011 (t60) cc_final: 0.7569 (t60) REVERT: C 434 TRP cc_start: 0.7480 (p-90) cc_final: 0.7241 (p90) REVERT: C 876 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8858 (tt) REVERT: C 1000 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7612 (mp10) REVERT: C 1098 THR cc_start: 0.9157 (m) cc_final: 0.8889 (p) outliers start: 42 outliers final: 30 residues processed: 151 average time/residue: 0.4584 time to fit residues: 85.7964 Evaluate side-chains 144 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 579 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 740 ILE Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 24 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 226 optimal weight: 2.9990 chunk 125 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 235 optimal weight: 3.9990 chunk 233 optimal weight: 10.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 GLN B 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.140477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.082686 restraints weight = 44578.771| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.22 r_work: 0.3015 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25953 Z= 0.176 Angle : 0.636 12.909 35476 Z= 0.310 Chirality : 0.047 0.364 4234 Planarity : 0.004 0.053 4444 Dihedral : 5.929 57.438 5053 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.74 % Allowed : 16.25 % Favored : 82.01 % 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: 0.14 (0.15), residues: 3040 helix: 2.10 (0.21), residues: 689 sheet: 0.65 (0.19), residues: 665 loop : -1.05 (0.14), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 212 TYR 0.023 0.001 TYR A1065 PHE 0.025 0.001 PHE A 757 TRP 0.013 0.001 TRP C 351 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00425 (25830) covalent geometry : angle 0.61483 (35147) SS BOND : bond 0.00491 ( 40) SS BOND : angle 1.69210 ( 80) hydrogen bonds : bond 0.06124 ( 1000) hydrogen bonds : angle 4.76652 ( 2730) link_BETA1-4 : bond 0.00325 ( 35) link_BETA1-4 : angle 1.79467 ( 105) link_NAG-ASN : bond 0.00270 ( 48) link_NAG-ASN : angle 1.89869 ( 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 161 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 114 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 64 TRP cc_start: 0.7677 (t60) cc_final: 0.6730 (t60) REVERT: A 188 ARG cc_start: 0.7900 (mpt-90) cc_final: 0.7579 (mmt90) REVERT: A 227 LEU cc_start: 0.8070 (mm) cc_final: 0.7858 (mt) REVERT: A 569 ASP cc_start: 0.8485 (m-30) cc_final: 0.7414 (t0) REVERT: A 976 ASN cc_start: 0.9114 (m-40) cc_final: 0.8707 (t0) REVERT: B 53 ASP cc_start: 0.7857 (t70) cc_final: 0.7559 (t70) REVERT: B 774 LYS cc_start: 0.9090 (OUTLIER) cc_final: 0.8765 (ttpp) REVERT: B 955 GLN cc_start: 0.8865 (tm-30) cc_final: 0.8343 (tp-100) REVERT: B 1037 ARG cc_start: 0.9204 (OUTLIER) cc_final: 0.8902 (mtp180) REVERT: C 64 TRP cc_start: 0.7838 (t60) cc_final: 0.7365 (t60) REVERT: C 434 TRP cc_start: 0.7471 (p-90) cc_final: 0.7225 (p90) REVERT: C 876 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 1000 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7455 (mp10) outliers start: 47 outliers final: 33 residues processed: 158 average time/residue: 0.4772 time to fit residues: 92.9522 Evaluate side-chains 146 residues out of total 2701 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 109 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 272 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 737 THR Chi-restraints excluded: chain A residue 975 LEU Chi-restraints excluded: chain A residue 1102 VAL Chi-restraints excluded: chain B residue 431 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 579 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 740 ILE Chi-restraints excluded: chain B residue 774 LYS Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 964 LEU Chi-restraints excluded: chain B residue 1037 ARG Chi-restraints excluded: chain B residue 1075 THR Chi-restraints excluded: chain B residue 1120 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 982 LEU Chi-restraints excluded: chain C residue 1000 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 307 random chunks: chunk 220 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 196 optimal weight: 0.2980 chunk 95 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 172 optimal weight: 0.7980 chunk 142 optimal weight: 0.0370 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.142205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.084916 restraints weight = 44359.821| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 3.18 r_work: 0.3063 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 25953 Z= 0.117 Angle : 0.598 12.352 35476 Z= 0.290 Chirality : 0.045 0.356 4234 Planarity : 0.004 0.051 4444 Dihedral : 5.729 56.858 5053 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.42 % Favored : 96.51 % Rotamer: Outliers : 1.63 % Allowed : 16.44 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3040 helix: 2.24 (0.21), residues: 685 sheet: 0.76 (0.19), residues: 683 loop : -0.96 (0.15), residues: 1672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 212 TYR 0.017 0.001 TYR A1065 PHE 0.014 0.001 PHE C1119 TRP 0.012 0.001 TRP C 351 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd covalent geometry : bond 0.00256 (25830) covalent geometry : angle 0.57688 (35147) SS BOND : bond 0.00398 ( 40) SS BOND : angle 1.48583 ( 80) hydrogen bonds : bond 0.05266 ( 1000) hydrogen bonds : angle 4.66094 ( 2730) link_BETA1-4 : bond 0.00371 ( 35) link_BETA1-4 : angle 1.76659 ( 105) link_NAG-ASN : bond 0.00282 ( 48) link_NAG-ASN : angle 1.83020 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8477.84 seconds wall clock time: 145 minutes 16.85 seconds (8716.85 seconds total)