Starting phenix.real_space_refine on Sun Jul 5 05:13:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.cif" model { file = "/net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7n_31775/07_2026/7v7n_31775.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.038 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 16152 2.51 5 N 4139 2.21 5 O 5031 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25430 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 4 Chain: "B" 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 chiralities: 4 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 chiralities: 4 Time building chain proxies: 6.01, per 1000 atoms: 0.24 Number of scatterers: 25430 At special positions: 0 Unit cell: (145.2, 148.5, 178.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5031 8.00 N 4139 7.00 C 16152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.04 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.03 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 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 D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 329 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 329 " " NAG B2003 " - " ASN B 601 " " NAG B2004 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 341 " " 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 232 " " NAG S 1 " - " ASN B 280 " " NAG T 1 " - " ASN B 341 " " NAG U 1 " - " ASN B 614 " " NAG V 1 " - " ASN B 707 " " NAG W 1 " - " ASN B 715 " " NAG X 1 " - " ASN B 799 " " NAG Y 1 " - " ASN B1072 " " NAG Z 1 " - " ASN B1096 " " NAG a 1 " - " ASN B1132 " " NAG b 1 " - " ASN C 122 " " NAG c 1 " - " ASN C 163 " " NAG d 1 " - " ASN C 232 " " NAG e 1 " - " ASN C 280 " " NAG f 1 " - " ASN C 341 " " NAG g 1 " - " ASN C 614 " " NAG h 1 " - " ASN C 707 " " NAG i 1 " - " ASN C 715 " " NAG j 1 " - " ASN C 799 " " NAG k 1 " - " ASN C1072 " " NAG l 1 " - " ASN C1096 " " NAG m 1 " - " ASN C1132 " Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.0 seconds 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 25.5% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 347 through 351 removed outlier: 3.577A pdb=" N TRP A 351 " --> pdb=" O VAL A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 381 through 388 removed outlier: 4.522A pdb=" N ASN A 386 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU A 388 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 408 removed outlier: 3.921A pdb=" N VAL A 405 " --> pdb=" O GLY A 402 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG A 406 " --> pdb=" O ASP A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 420 Processing helix chain 'A' and resid 436 through 441 removed outlier: 3.672A pdb=" N SER A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 636 removed outlier: 3.976A pdb=" N THR A 636 " --> pdb=" O VAL A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 744 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.645A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.502A pdb=" N LYS A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 824 " --> pdb=" O LEU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 882 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 911 through 916 removed outlier: 3.779A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU A 916 " --> pdb=" O ASN A 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 911 through 916' Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 980 Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.186A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1144 removed outlier: 4.009A pdb=" N ASP A1144 " --> pdb=" O GLN A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 302 Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.119A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N SER B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 385 Processing helix chain 'B' and resid 403 through 408 removed outlier: 4.685A pdb=" N ARG B 406 " --> pdb=" O ASP B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 420 Processing helix chain 'B' and resid 436 through 441 Processing helix chain 'B' and resid 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 753 removed outlier: 4.039A pdb=" N GLN B 753 " --> pdb=" O ASN B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.793A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.712A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 removed outlier: 3.638A pdb=" N GLY B 883 " --> pdb=" O THR B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 889 removed outlier: 3.975A 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: 3.567A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.576A 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: 3.647A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.364A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1143 Processing helix chain 'C' and resid 292 through 302 removed outlier: 3.577A pdb=" N GLU C 296 " --> pdb=" O ASP C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.721A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 3.607A pdb=" N LEU C 388 " --> pdb=" O LEU C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 408 removed outlier: 3.765A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 removed outlier: 3.591A pdb=" N TYR C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 441 removed outlier: 3.500A pdb=" N SER C 441 " --> pdb=" O ASN C 437 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.962A pdb=" N THR C 636 " --> pdb=" O VAL C 633 " (cutoff:3.500A) 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 756 through 781 removed outlier: 3.712A pdb=" N GLN C 760 " --> pdb=" O SER C 756 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 822 Processing helix chain 'C' and resid 864 through 883 removed outlier: 3.578A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 removed outlier: 3.633A pdb=" N GLY C 887 " --> pdb=" O TRP C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.931A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLU C 916 " --> pdb=" O ASN C 912 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 911 through 916' Processing helix chain 'C' and resid 917 through 939 Processing helix chain 'C' and resid 943 through 963 Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 980 Processing helix chain 'C' and resid 983 through 1032 removed outlier: 4.531A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C1032 " --> pdb=" O SER C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.731A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.635A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) removed outlier: 9.323A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.616A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.014A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.116A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N SER A 170 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.478A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 323 through 326 removed outlier: 5.097A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA7, first strand: chain 'A' and resid 359 through 360 removed outlier: 6.590A pdb=" N CYS A 359 " --> pdb=" O CYS A 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 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 652 through 653 removed outlier: 6.041A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 699 through 701 removed outlier: 7.083A pdb=" N ALA A 699 " --> pdb=" O ILE C 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.834A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.561A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB7, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB8, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.604A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.676A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.557A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 43 removed outlier: 6.337A pdb=" N GLY C 564 " --> pdb=" O ASP C 572 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP B 285 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.971A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.399A pdb=" N VAL B 126 " --> pdb=" O GLU B 167 " (cutoff:3.500A) removed outlier: 10.109A pdb=" N GLU B 167 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N ILE B 128 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR B 165 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N VAL B 130 " --> pdb=" O ASN B 163 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N ASN B 163 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLU B 132 " --> pdb=" O ALA B 161 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ALA B 161 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLN B 134 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.555A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.543A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY B 592 " --> pdb=" O GLN B 611 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 5.455A pdb=" N ASP B 572 " --> pdb=" O ILE B 585 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 564 " --> pdb=" O ALA B 573 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 352 through 356 Processing sheet with id=AC6, first strand: chain 'B' and resid 359 through 360 removed outlier: 6.374A pdb=" N CYS B 359 " --> pdb=" O CYS B 523 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 451 through 452 Processing sheet with id=AC8, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AC9, first strand: chain 'B' and resid 652 through 653 removed outlier: 6.058A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.724A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.127A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N SER B 719 " --> pdb=" O THR B1064 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.949A 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: 4.493A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 786 through 788 removed outlier: 5.745A pdb=" N ILE B 786 " --> pdb=" O ASN C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 5.049A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1092 through 1095 Processing sheet with id=AD6, first strand: chain 'C' and resid 26 through 30 removed outlier: 8.391A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.919A pdb=" N ASP C 285 " --> pdb=" O LYS C 276 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.069A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N PHE C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.582A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY C 592 " --> pdb=" O GLN C 611 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 352 through 356 Processing sheet with id=AE2, first strand: chain 'C' and resid 359 through 360 removed outlier: 3.892A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.212A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.946A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ALA C 670 " --> pdb=" O PRO C 663 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.810A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET C1048 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.598A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1118 through 1120 Processing sheet with id=AE9, first strand: chain 'C' and resid 1092 through 1095 993 hydrogen bonds defined for protein. 2709 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: 6.27 Time building geometry restraints manager: 3.36 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: 8014 1.34 - 1.46: 6436 1.46 - 1.58: 11402 1.58 - 1.70: 0 1.70 - 1.82: 132 Bond restraints: 25984 Sorted by residual: bond pdb=" C1 NAG Y 1 " pdb=" O5 NAG Y 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.89e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.28e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.13e+00 bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.20e+00 bond pdb=" C1 NAG U 1 " pdb=" O5 NAG U 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.68e+00 ... (remaining 25979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 34301 1.60 - 3.20: 937 3.20 - 4.80: 89 4.80 - 6.41: 24 6.41 - 8.01: 6 Bond angle restraints: 35357 Sorted by residual: angle pdb=" C CYS A 660 " pdb=" N ASP A 661 " pdb=" CA ASP A 661 " ideal model delta sigma weight residual 121.54 127.80 -6.26 1.91e+00 2.74e-01 1.07e+01 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.45 -3.75 1.22e+00 6.72e-01 9.45e+00 angle pdb=" N VAL C 339 " pdb=" CA VAL C 339 " pdb=" C VAL C 339 " ideal model delta sigma weight residual 113.39 109.20 4.19 1.47e+00 4.63e-01 8.14e+00 angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 122.29 117.99 4.30 1.65e+00 3.67e-01 6.80e+00 angle pdb=" C VAL B 481 " pdb=" N GLU B 482 " pdb=" CA GLU B 482 " ideal model delta sigma weight residual 121.76 127.45 -5.69 2.19e+00 2.09e-01 6.76e+00 ... (remaining 35352 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 13376 17.83 - 35.66: 1189 35.66 - 53.49: 190 53.49 - 71.32: 31 71.32 - 89.15: 29 Dihedral angle restraints: 14815 sinusoidal: 5788 harmonic: 9027 Sorted by residual: dihedral pdb=" CB CYS A1080 " pdb=" SG CYS A1080 " pdb=" SG CYS A1124 " pdb=" CB CYS A1124 " ideal model delta sinusoidal sigma weight residual -86.00 -2.39 -83.61 1 1.00e+01 1.00e-02 8.53e+01 dihedral pdb=" CB CYS B 536 " pdb=" SG CYS B 536 " pdb=" SG CYS B 588 " pdb=" CB CYS B 588 " ideal model delta sinusoidal sigma weight residual -86.00 -10.56 -75.44 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" CB CYS C 536 " pdb=" SG CYS C 536 " pdb=" SG CYS C 588 " pdb=" CB CYS C 588 " ideal model delta sinusoidal sigma weight residual -86.00 -11.49 -74.51 1 1.00e+01 1.00e-02 7.04e+01 ... (remaining 14812 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 4230 0.137 - 0.275: 26 0.275 - 0.412: 2 0.412 - 0.550: 1 0.550 - 0.687: 2 Chirality restraints: 4261 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 163 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.71 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 163 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.85 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.37e+00 ... (remaining 4258 not shown) Planarity restraints: 4511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.027 2.00e-02 2.50e+03 2.51e-02 7.90e+00 pdb=" CG ASN B1072 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.027 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 232 " -0.001 2.00e-02 2.50e+03 2.26e-02 6.36e+00 pdb=" CG ASN B 232 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B 232 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN B 232 " -0.026 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 904 " -0.019 2.00e-02 2.50e+03 1.75e-02 5.36e+00 pdb=" CG PHE C 904 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE C 904 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE C 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE C 904 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 904 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE C 904 " -0.001 2.00e-02 2.50e+03 ... (remaining 4508 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1156 2.72 - 3.26: 25010 3.26 - 3.81: 39404 3.81 - 4.35: 45870 4.35 - 4.90: 81156 Nonbonded interactions: 192596 Sorted by model distance: nonbonded pdb=" OD1 ASP C 566 " pdb=" OG1 THR C 570 " model vdw 2.171 3.040 nonbonded pdb=" OG1 THR C 714 " pdb=" O GLN C1069 " model vdw 2.190 3.040 nonbonded pdb=" O GLU A 154 " pdb=" OH TYR A 158 " model vdw 2.195 3.040 nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.211 3.040 nonbonded pdb=" O ARG A 212 " pdb=" OH TYR A 264 " model vdw 2.212 3.040 ... (remaining 192591 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 619 or resid 631 through 2004)) selection = (chain 'B' and (resid 14 through 825 or resid 852 through 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 631 through 2004)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.210 Find NCS groups from input model: 1.040 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: 0.000 Load rotamer database and sin/cos tables:6.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 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 0.053 26109 Z= 0.225 Angle : 0.661 13.572 35692 Z= 0.317 Chirality : 0.050 0.687 4261 Planarity : 0.004 0.043 4463 Dihedral : 13.700 89.152 8883 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.44 % Favored : 94.43 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.11 (0.15), residues: 3053 helix: 2.05 (0.22), residues: 646 sheet: 0.76 (0.19), residues: 721 loop : -1.08 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1037 TYR 0.019 0.001 TYR A 871 PHE 0.040 0.001 PHE C 904 TRP 0.024 0.001 TRP B 884 HIS 0.003 0.001 HIS C1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.22 (25984) covalent geometry : angle 0.61953 / 0.31 (35357) SS BOND : bond 0.00396 / 0.27 ( 40) SS BOND : angle 1.61997 / 1.06 ( 80) hydrogen bonds : bond 0.12281 / 8.29 ( 981) hydrogen bonds : angle 6.00593 / 4.12 ( 2709) link_BETA1-4 : bond 0.00465 / 0.32 ( 37) link_BETA1-4 : angle 2.06123 / 1.51 ( 111) link_NAG-ASN : bond 0.00392 / 0.26 ( 48) link_NAG-ASN : angle 3.05298 / 2.55 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8171 (t0) cc_final: 0.7906 (t0) REVERT: B 415 LYS cc_start: 0.9143 (tptm) cc_final: 0.8836 (tppt) REVERT: C 416 ILE cc_start: 0.9070 (mp) cc_final: 0.8841 (pp) outliers start: 0 outliers final: 0 residues processed: 110 average time/residue: 0.5474 time to fit residues: 72.2129 Evaluate side-chains 72 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.3980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.0270 overall best weight: 1.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.079647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049602 restraints weight = 86556.795| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 4.00 r_work: 0.2766 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 26109 Z= 0.167 Angle : 0.604 13.180 35692 Z= 0.302 Chirality : 0.045 0.429 4261 Planarity : 0.004 0.060 4463 Dihedral : 4.172 22.767 3326 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.36 % Favored : 95.51 % Rotamer: Outliers : 0.59 % Allowed : 6.41 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.15), residues: 3053 helix: 2.02 (0.22), residues: 663 sheet: 0.82 (0.19), residues: 697 loop : -1.01 (0.15), residues: 1693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 406 TYR 0.015 0.001 TYR A1065 PHE 0.023 0.001 PHE C 904 TRP 0.013 0.001 TRP A 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (25984) covalent geometry : angle 0.57128 / 0.29 (35357) SS BOND : bond 0.00386 / 0.27 ( 40) SS BOND : angle 1.56552 / 1.05 ( 80) hydrogen bonds : bond 0.06237 / 4.16 ( 981) hydrogen bonds : angle 5.09518 / 3.51 ( 2709) link_BETA1-4 : bond 0.00370 / 0.23 ( 37) link_BETA1-4 : angle 1.70101 / 1.23 ( 111) link_NAG-ASN : bond 0.00345 / 0.24 ( 48) link_NAG-ASN : angle 2.58559 / 2.25 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8840 (t0) cc_final: 0.8481 (t0) REVERT: B 415 LYS cc_start: 0.9109 (tptm) cc_final: 0.8866 (tppt) REVERT: C 367 TYR cc_start: 0.8764 (t80) cc_final: 0.8541 (t80) REVERT: C 387 ASP cc_start: 0.9341 (t0) cc_final: 0.9134 (m-30) REVERT: C 421 TYR cc_start: 0.6438 (t80) cc_final: 0.6186 (t80) REVERT: C 454 PHE cc_start: 0.9145 (m-10) cc_final: 0.8840 (m-80) REVERT: C 760 GLN cc_start: 0.8865 (mt0) cc_final: 0.8535 (mt0) outliers start: 16 outliers final: 3 residues processed: 86 average time/residue: 0.6285 time to fit residues: 63.9801 Evaluate side-chains 72 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 778 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 233 optimal weight: 10.0000 chunk 181 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 255 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 185 optimal weight: 6.9990 chunk 278 optimal weight: 0.6980 chunk 215 optimal weight: 8.9990 chunk 265 optimal weight: 0.0770 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 14 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 912 ASN C1104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.079871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.049841 restraints weight = 87018.978| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 4.02 r_work: 0.2777 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.0762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26109 Z= 0.142 Angle : 0.574 12.385 35692 Z= 0.286 Chirality : 0.045 0.418 4261 Planarity : 0.004 0.061 4463 Dihedral : 4.071 22.143 3326 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.26 % Favored : 95.64 % Rotamer: Outliers : 0.81 % Allowed : 9.69 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 3053 helix: 2.07 (0.21), residues: 671 sheet: 0.82 (0.19), residues: 697 loop : -1.01 (0.15), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 406 TYR 0.015 0.001 TYR A1065 PHE 0.016 0.001 PHE A 904 TRP 0.011 0.001 TRP B 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (25984) covalent geometry : angle 0.54441 / 0.28 (35357) SS BOND : bond 0.00353 / 0.23 ( 40) SS BOND : angle 1.39258 / 0.96 ( 80) hydrogen bonds : bond 0.05802 / 3.88 ( 981) hydrogen bonds : angle 4.89699 / 3.36 ( 2709) link_BETA1-4 : bond 0.00417 / 0.27 ( 37) link_BETA1-4 : angle 1.62295 / 1.17 ( 111) link_NAG-ASN : bond 0.00330 / 0.24 ( 48) link_NAG-ASN : angle 2.42256 / 2.11 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8885 (t0) cc_final: 0.8520 (t0) REVERT: B 375 PHE cc_start: 0.8680 (t80) cc_final: 0.8468 (t80) REVERT: B 415 LYS cc_start: 0.9168 (tptm) cc_final: 0.8924 (tppt) REVERT: C 367 TYR cc_start: 0.8795 (t80) cc_final: 0.8529 (t80) REVERT: C 387 ASP cc_start: 0.9396 (t0) cc_final: 0.9153 (m-30) REVERT: C 406 ARG cc_start: 0.9063 (tmm160) cc_final: 0.8682 (ppt170) REVERT: C 421 TYR cc_start: 0.6490 (t80) cc_final: 0.6276 (t80) REVERT: C 453 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9015 (mt) REVERT: C 454 PHE cc_start: 0.9208 (m-10) cc_final: 0.8962 (m-80) REVERT: C 658 TYR cc_start: 0.8938 (OUTLIER) cc_final: 0.8018 (p90) REVERT: C 988 GLU cc_start: 0.7795 (pm20) cc_final: 0.7511 (pm20) outliers start: 22 outliers final: 6 residues processed: 96 average time/residue: 0.6012 time to fit residues: 67.8423 Evaluate side-chains 81 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 778 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 56 optimal weight: 0.6980 chunk 204 optimal weight: 1.9990 chunk 167 optimal weight: 0.0770 chunk 256 optimal weight: 4.9990 chunk 206 optimal weight: 20.0000 chunk 19 optimal weight: 4.9990 chunk 306 optimal weight: 0.9980 chunk 278 optimal weight: 0.2980 chunk 258 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 chunk 11 optimal weight: 7.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 162 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 912 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.080804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.051074 restraints weight = 86474.385| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.95 r_work: 0.2810 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 26109 Z= 0.105 Angle : 0.547 12.054 35692 Z= 0.272 Chirality : 0.044 0.410 4261 Planarity : 0.004 0.062 4463 Dihedral : 3.884 21.305 3326 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.93 % Favored : 95.97 % Rotamer: Outliers : 1.22 % Allowed : 10.87 % Favored : 87.91 % 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: 0.31 (0.16), residues: 3053 helix: 2.13 (0.22), residues: 677 sheet: 0.88 (0.19), residues: 697 loop : -0.94 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 406 TYR 0.021 0.001 TYR B 471 PHE 0.015 0.001 PHE A 398 TRP 0.009 0.001 TRP A 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.10 (25984) covalent geometry : angle 0.51967 / 0.27 (35357) SS BOND : bond 0.00302 / 0.20 ( 40) SS BOND : angle 1.16963 / 0.79 ( 80) hydrogen bonds : bond 0.05110 / 3.42 ( 981) hydrogen bonds : angle 4.71642 / 3.23 ( 2709) link_BETA1-4 : bond 0.00454 / 0.29 ( 37) link_BETA1-4 : angle 1.58865 / 1.14 ( 111) link_NAG-ASN : bond 0.00355 / 0.26 ( 48) link_NAG-ASN : angle 2.28753 / 2.01 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 92 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8879 (t0) cc_final: 0.8527 (t0) REVERT: B 415 LYS cc_start: 0.9190 (tptm) cc_final: 0.8957 (tppt) REVERT: B 983 ASP cc_start: 0.7418 (p0) cc_final: 0.7022 (p0) REVERT: C 387 ASP cc_start: 0.9449 (t0) cc_final: 0.9187 (m-30) REVERT: C 406 ARG cc_start: 0.9093 (tmm160) cc_final: 0.8722 (ppt170) REVERT: C 421 TYR cc_start: 0.6844 (t80) cc_final: 0.6579 (t80) REVERT: C 453 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9021 (mt) REVERT: C 454 PHE cc_start: 0.9332 (m-10) cc_final: 0.8971 (m-80) REVERT: C 579 THR cc_start: 0.9205 (OUTLIER) cc_final: 0.8876 (p) REVERT: C 658 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.7930 (p90) REVERT: C 988 GLU cc_start: 0.7764 (pm20) cc_final: 0.7457 (pm20) outliers start: 33 outliers final: 9 residues processed: 116 average time/residue: 0.5117 time to fit residues: 71.5682 Evaluate side-chains 88 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 99 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 242 optimal weight: 10.0000 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 203 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.078569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.048301 restraints weight = 86879.317| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 3.99 r_work: 0.2725 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 26109 Z= 0.246 Angle : 0.637 11.429 35692 Z= 0.319 Chirality : 0.046 0.415 4261 Planarity : 0.004 0.063 4463 Dihedral : 4.229 21.778 3326 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.31 % Favored : 94.56 % Rotamer: Outliers : 1.29 % Allowed : 12.12 % Favored : 86.59 % 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: 3053 helix: 2.03 (0.21), residues: 674 sheet: 0.66 (0.19), residues: 718 loop : -1.04 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 406 TYR 0.026 0.001 TYR B 471 PHE 0.024 0.001 PHE A 904 TRP 0.019 0.001 TRP A 884 HIS 0.005 0.001 HIS C1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (25984) covalent geometry : angle 0.60895 / 0.31 (35357) SS BOND : bond 0.00411 / 0.28 ( 40) SS BOND : angle 1.67110 / 1.11 ( 80) hydrogen bonds : bond 0.06639 / 4.39 ( 981) hydrogen bonds : angle 4.96912 / 3.40 ( 2709) link_BETA1-4 : bond 0.00318 / 0.21 ( 37) link_BETA1-4 : angle 1.59563 / 1.14 ( 111) link_NAG-ASN : bond 0.00352 / 0.25 ( 48) link_NAG-ASN : angle 2.47678 / 2.09 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 75 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8915 (t0) cc_final: 0.8505 (t0) REVERT: B 415 LYS cc_start: 0.9206 (tptm) cc_final: 0.9001 (tppt) REVERT: B 579 THR cc_start: 0.9373 (OUTLIER) cc_final: 0.9148 (p) REVERT: B 856 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9082 (pp) REVERT: C 387 ASP cc_start: 0.9498 (t0) cc_final: 0.9219 (m-30) REVERT: C 421 TYR cc_start: 0.6975 (t80) cc_final: 0.6720 (t80) REVERT: C 453 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8917 (mt) REVERT: C 454 PHE cc_start: 0.9343 (m-10) cc_final: 0.8972 (m-80) REVERT: C 579 THR cc_start: 0.9231 (OUTLIER) cc_final: 0.8909 (p) REVERT: C 658 TYR cc_start: 0.9011 (OUTLIER) cc_final: 0.7871 (p90) REVERT: C 898 MET cc_start: 0.9489 (OUTLIER) cc_final: 0.9155 (mtp) REVERT: C 988 GLU cc_start: 0.8025 (pm20) cc_final: 0.7718 (pm20) REVERT: C 1027 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.8814 (tpp) outliers start: 35 outliers final: 13 residues processed: 101 average time/residue: 0.5749 time to fit residues: 69.5330 Evaluate side-chains 92 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 876 LEU Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 243 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 181 optimal weight: 0.8980 chunk 200 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 176 optimal weight: 0.7980 chunk 242 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 204 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 504 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.079973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.050104 restraints weight = 85991.577| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 3.98 r_work: 0.2780 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 26109 Z= 0.119 Angle : 0.569 11.593 35692 Z= 0.283 Chirality : 0.044 0.392 4261 Planarity : 0.004 0.060 4463 Dihedral : 3.991 20.841 3326 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.03 % Favored : 95.84 % Rotamer: Outliers : 1.29 % Allowed : 13.19 % Favored : 85.52 % 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: 0.26 (0.16), residues: 3053 helix: 2.10 (0.21), residues: 680 sheet: 0.72 (0.19), residues: 711 loop : -0.94 (0.15), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.012 0.001 PHE A 398 TRP 0.013 0.001 TRP A 884 HIS 0.002 0.000 HIS C1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25984) covalent geometry : angle 0.54207 / 0.28 (35357) SS BOND : bond 0.00331 / 0.22 ( 40) SS BOND : angle 1.33460 / 0.90 ( 80) hydrogen bonds : bond 0.05477 / 3.67 ( 981) hydrogen bonds : angle 4.75528 / 3.26 ( 2709) link_BETA1-4 : bond 0.00455 / 0.30 ( 37) link_BETA1-4 : angle 1.58141 / 1.14 ( 111) link_NAG-ASN : bond 0.00332 / 0.24 ( 48) link_NAG-ASN : angle 2.25220 / 1.96 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8878 (t0) cc_final: 0.8510 (t0) REVERT: B 453 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7604 (tm) REVERT: B 454 PHE cc_start: 0.8228 (OUTLIER) cc_final: 0.7787 (m-10) REVERT: B 579 THR cc_start: 0.9467 (OUTLIER) cc_final: 0.9254 (p) REVERT: B 856 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.8950 (pp) REVERT: C 387 ASP cc_start: 0.9493 (t0) cc_final: 0.9220 (m-30) REVERT: C 421 TYR cc_start: 0.6975 (t80) cc_final: 0.6730 (t80) REVERT: C 453 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8940 (mt) REVERT: C 454 PHE cc_start: 0.9309 (m-10) cc_final: 0.8948 (m-80) REVERT: C 658 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.7770 (p90) REVERT: C 988 GLU cc_start: 0.7987 (pm20) cc_final: 0.7703 (pm20) outliers start: 35 outliers final: 11 residues processed: 112 average time/residue: 0.5569 time to fit residues: 74.8818 Evaluate side-chains 96 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 195 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 243 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 172 optimal weight: 0.1980 chunk 43 optimal weight: 10.0000 chunk 8 optimal weight: 0.0470 chunk 2 optimal weight: 5.9990 overall best weight: 1.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 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 = 0.3683 r_free = 0.3683 target = 0.079138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.049053 restraints weight = 86383.630| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.97 r_work: 0.2750 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26109 Z= 0.178 Angle : 0.603 11.171 35692 Z= 0.301 Chirality : 0.045 0.397 4261 Planarity : 0.004 0.060 4463 Dihedral : 4.086 21.161 3326 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.98 % Favored : 94.89 % Rotamer: Outliers : 1.47 % Allowed : 13.71 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 3053 helix: 2.10 (0.21), residues: 676 sheet: 0.74 (0.19), residues: 713 loop : -0.98 (0.15), residues: 1664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG C 406 TYR 0.015 0.001 TYR A1065 PHE 0.014 0.001 PHE A 398 TRP 0.016 0.001 TRP A 884 HIS 0.003 0.001 HIS C1056 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 (25984) covalent geometry : angle 0.57622 / 0.29 (35357) SS BOND : bond 0.00376 / 0.26 ( 40) SS BOND : angle 1.56145 / 1.03 ( 80) hydrogen bonds : bond 0.06002 / 3.99 ( 981) hydrogen bonds : angle 4.82552 / 3.30 ( 2709) link_BETA1-4 : bond 0.00359 / 0.24 ( 37) link_BETA1-4 : angle 1.57101 / 1.12 ( 111) link_NAG-ASN : bond 0.00312 / 0.23 ( 48) link_NAG-ASN : angle 2.32475 / 1.98 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8911 (t0) cc_final: 0.8486 (t0) REVERT: B 415 LYS cc_start: 0.9096 (tppt) cc_final: 0.8878 (tptm) REVERT: B 453 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7811 (pp) REVERT: B 454 PHE cc_start: 0.8189 (OUTLIER) cc_final: 0.7763 (m-10) REVERT: B 579 THR cc_start: 0.9385 (OUTLIER) cc_final: 0.9168 (p) REVERT: B 856 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9017 (pp) REVERT: C 421 TYR cc_start: 0.6995 (t80) cc_final: 0.6701 (t80) REVERT: C 453 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8911 (mt) REVERT: C 454 PHE cc_start: 0.9316 (m-10) cc_final: 0.8949 (m-80) REVERT: C 579 THR cc_start: 0.9220 (OUTLIER) cc_final: 0.8905 (p) REVERT: C 658 TYR cc_start: 0.9020 (OUTLIER) cc_final: 0.7807 (p90) REVERT: C 988 GLU cc_start: 0.8060 (pm20) cc_final: 0.7750 (pm20) outliers start: 40 outliers final: 16 residues processed: 114 average time/residue: 0.5550 time to fit residues: 76.2414 Evaluate side-chains 99 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 932 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 71 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 186 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 chunk 225 optimal weight: 7.9990 chunk 229 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 216 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.079547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.049593 restraints weight = 86233.354| |-----------------------------------------------------------------------------| r_work (start): 0.2908 rms_B_bonded: 3.96 r_work: 0.2766 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 26109 Z= 0.142 Angle : 0.593 11.176 35692 Z= 0.296 Chirality : 0.045 0.384 4261 Planarity : 0.004 0.070 4463 Dihedral : 4.047 20.914 3326 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.32 % Favored : 95.55 % Rotamer: Outliers : 1.29 % Allowed : 14.37 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.15), residues: 3053 helix: 2.12 (0.21), residues: 680 sheet: 0.69 (0.19), residues: 710 loop : -0.94 (0.15), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 406 TYR 0.016 0.001 TYR A1065 PHE 0.013 0.001 PHE A 398 TRP 0.014 0.001 TRP A 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (25984) covalent geometry : angle 0.56726 / 0.29 (35357) SS BOND : bond 0.00362 / 0.25 ( 40) SS BOND : angle 1.43347 / 0.95 ( 80) hydrogen bonds : bond 0.05718 / 3.82 ( 981) hydrogen bonds : angle 4.77390 / 3.27 ( 2709) link_BETA1-4 : bond 0.00403 / 0.26 ( 37) link_BETA1-4 : angle 1.57194 / 1.12 ( 111) link_NAG-ASN : bond 0.00307 / 0.23 ( 48) link_NAG-ASN : angle 2.25085 / 1.94 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 82 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8902 (t0) cc_final: 0.8517 (t0) REVERT: B 453 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.7876 (pp) REVERT: B 454 PHE cc_start: 0.8157 (OUTLIER) cc_final: 0.7736 (m-10) REVERT: B 579 THR cc_start: 0.9434 (OUTLIER) cc_final: 0.9222 (p) REVERT: B 856 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.8991 (pp) REVERT: B 898 MET cc_start: 0.9451 (OUTLIER) cc_final: 0.9109 (mtp) REVERT: C 421 TYR cc_start: 0.7054 (t80) cc_final: 0.6753 (t80) REVERT: C 453 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8883 (mt) REVERT: C 454 PHE cc_start: 0.9298 (m-10) cc_final: 0.8936 (m-80) REVERT: C 579 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8903 (p) REVERT: C 658 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.7757 (p90) REVERT: C 867 MET cc_start: 0.9217 (OUTLIER) cc_final: 0.8854 (mtp) REVERT: C 988 GLU cc_start: 0.8036 (pm20) cc_final: 0.7755 (pm20) outliers start: 35 outliers final: 16 residues processed: 109 average time/residue: 0.5664 time to fit residues: 74.1844 Evaluate side-chains 99 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 898 MET Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 101 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 453 LEU Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 932 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 57 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 233 optimal weight: 9.9990 chunk 276 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.080332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.050477 restraints weight = 86421.981| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.98 r_work: 0.2794 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26109 Z= 0.116 Angle : 0.583 11.134 35692 Z= 0.290 Chirality : 0.044 0.370 4261 Planarity : 0.004 0.074 4463 Dihedral : 3.930 21.447 3326 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 0.99 % Allowed : 14.85 % Favored : 84.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.16), residues: 3053 helix: 2.20 (0.21), residues: 683 sheet: 0.72 (0.20), residues: 700 loop : -0.90 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.012 0.001 PHE A 398 TRP 0.012 0.001 TRP A 884 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (25984) covalent geometry : angle 0.55925 / 0.28 (35357) SS BOND : bond 0.00365 / 0.24 ( 40) SS BOND : angle 1.26519 / 0.86 ( 80) hydrogen bonds : bond 0.05241 / 3.51 ( 981) hydrogen bonds : angle 4.65620 / 3.19 ( 2709) link_BETA1-4 : bond 0.00442 / 0.29 ( 37) link_BETA1-4 : angle 1.54834 / 1.11 ( 111) link_NAG-ASN : bond 0.00329 / 0.24 ( 48) link_NAG-ASN : angle 2.17814 / 1.89 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 86 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8909 (t0) cc_final: 0.8547 (t0) REVERT: B 52 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8464 (tm-30) REVERT: B 415 LYS cc_start: 0.9147 (tptm) cc_final: 0.8940 (tppt) REVERT: B 453 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7739 (pp) REVERT: B 454 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7811 (m-10) REVERT: B 579 THR cc_start: 0.9466 (OUTLIER) cc_final: 0.9256 (p) REVERT: B 856 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8929 (pp) REVERT: C 406 ARG cc_start: 0.9239 (tmm-80) cc_final: 0.8978 (pmt-80) REVERT: C 421 TYR cc_start: 0.6865 (t80) cc_final: 0.6618 (t80) REVERT: C 453 LEU cc_start: 0.9239 (tp) cc_final: 0.8939 (mt) REVERT: C 454 PHE cc_start: 0.9288 (m-10) cc_final: 0.8924 (m-80) REVERT: C 579 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8807 (p) REVERT: C 658 TYR cc_start: 0.9005 (OUTLIER) cc_final: 0.7667 (p90) REVERT: C 867 MET cc_start: 0.9197 (OUTLIER) cc_final: 0.8921 (mtp) REVERT: C 988 GLU cc_start: 0.7998 (pm20) cc_final: 0.7730 (pm20) outliers start: 27 outliers final: 13 residues processed: 108 average time/residue: 0.5801 time to fit residues: 74.9353 Evaluate side-chains 98 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 932 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 262 optimal weight: 0.2980 chunk 301 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 238 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 6 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.080327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.050436 restraints weight = 86416.406| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.99 r_work: 0.2793 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26109 Z= 0.122 Angle : 0.587 10.966 35692 Z= 0.293 Chirality : 0.044 0.364 4261 Planarity : 0.004 0.067 4463 Dihedral : 3.912 20.598 3326 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.77 % Rotamer: Outliers : 1.03 % Allowed : 14.74 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.16), residues: 3053 helix: 2.19 (0.21), residues: 682 sheet: 0.69 (0.19), residues: 716 loop : -0.90 (0.15), residues: 1655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.014 0.001 PHE A 398 TRP 0.012 0.001 TRP A 884 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (25984) covalent geometry : angle 0.56338 / 0.29 (35357) SS BOND : bond 0.00327 / 0.22 ( 40) SS BOND : angle 1.27211 / 0.87 ( 80) hydrogen bonds : bond 0.05241 / 3.50 ( 981) hydrogen bonds : angle 4.63301 / 3.17 ( 2709) link_BETA1-4 : bond 0.00421 / 0.28 ( 37) link_BETA1-4 : angle 1.53634 / 1.09 ( 111) link_NAG-ASN : bond 0.00316 / 0.23 ( 48) link_NAG-ASN : angle 2.16716 / 1.88 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6106 Ramachandran restraints generated. 3053 Oldfield, 0 Emsley, 3053 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 854 ASN cc_start: 0.8920 (t0) cc_final: 0.8553 (t0) REVERT: B 52 GLN cc_start: 0.8980 (tm-30) cc_final: 0.8477 (tm-30) REVERT: B 415 LYS cc_start: 0.9124 (tptm) cc_final: 0.8897 (tppt) REVERT: B 453 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7742 (pp) REVERT: B 454 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7777 (m-10) REVERT: B 579 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9257 (p) REVERT: B 856 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.8935 (pp) REVERT: B 1015 GLU cc_start: 0.8903 (tm-30) cc_final: 0.8700 (tp30) REVERT: C 406 ARG cc_start: 0.9245 (tmm-80) cc_final: 0.8995 (pmt-80) REVERT: C 421 TYR cc_start: 0.6975 (t80) cc_final: 0.6732 (t80) REVERT: C 453 LEU cc_start: 0.9264 (tp) cc_final: 0.8977 (mt) REVERT: C 454 PHE cc_start: 0.9280 (m-10) cc_final: 0.8920 (m-80) REVERT: C 579 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8793 (p) REVERT: C 658 TYR cc_start: 0.8991 (OUTLIER) cc_final: 0.7650 (p90) REVERT: C 867 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8941 (mtp) REVERT: C 988 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7699 (pm20) REVERT: C 1027 MET cc_start: 0.8957 (OUTLIER) cc_final: 0.8579 (tpp) outliers start: 28 outliers final: 15 residues processed: 104 average time/residue: 0.5771 time to fit residues: 71.5687 Evaluate side-chains 105 residues out of total 2714 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 PHE Chi-restraints excluded: chain A residue 586 THR Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 454 PHE Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 588 CYS Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 231 ILE Chi-restraints excluded: chain C residue 372 PHE Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 658 TYR Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 867 MET Chi-restraints excluded: chain C residue 932 ILE Chi-restraints excluded: chain C residue 988 GLU Chi-restraints excluded: chain C residue 1027 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 199 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 201 optimal weight: 0.0870 chunk 276 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 141 optimal weight: 20.0000 chunk 233 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.079872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.049902 restraints weight = 86082.390| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 3.96 r_work: 0.2781 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26109 Z= 0.144 Angle : 0.598 10.794 35692 Z= 0.298 Chirality : 0.045 0.358 4261 Planarity : 0.004 0.067 4463 Dihedral : 3.953 21.023 3326 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.49 % Favored : 95.38 % Rotamer: Outliers : 1.03 % Allowed : 14.92 % Favored : 84.05 % 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: 0.28 (0.16), residues: 3053 helix: 2.11 (0.21), residues: 685 sheet: 0.66 (0.19), residues: 716 loop : -0.90 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 406 TYR 0.016 0.001 TYR A1065 PHE 0.014 0.001 PHE A 398 TRP 0.014 0.001 TRP A 884 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (25984) covalent geometry : angle 0.57411 / 0.29 (35357) SS BOND : bond 0.00350 / 0.24 ( 40) SS BOND : angle 1.37478 / 0.93 ( 80) hydrogen bonds : bond 0.05534 / 3.69 ( 981) hydrogen bonds : angle 4.66927 / 3.19 ( 2709) link_BETA1-4 : bond 0.00393 / 0.26 ( 37) link_BETA1-4 : angle 1.52857 / 1.09 ( 111) link_NAG-ASN : bond 0.00301 / 0.22 ( 48) link_NAG-ASN : angle 2.18713 / 1.88 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7115.55 seconds wall clock time: 122 minutes 45.19 seconds (7365.19 seconds total)