Starting phenix.real_space_refine on Sun Jul 5 04:21:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.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 { model { file = "/net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7o_31776/07_2026/7v7o_31776.map" } 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= 0.039 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 16085 2.51 5 N 4124 2.21 5 O 5008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 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: 25325 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8003 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 53, 'TRANS': 971} Chain breaks: 7 Chain: "B" Number of atoms: 8077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8077 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 53, 'TRANS': 979} Chain breaks: 7 Chain: "C" Number of atoms: 8083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8083 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 54, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 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: 5.61, per 1000 atoms: 0.22 Number of scatterers: 25325 At special positions: 0 Unit cell: (141.9, 149.6, 199.1, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 5008 8.00 N 4124 7.00 C 16085 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=2.02 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.03 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.03 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 536 " - pdb=" SG CYS A 588 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.04 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.03 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 536 " - pdb=" SG CYS B 588 " distance=2.04 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.02 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.03 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 536 " - pdb=" SG CYS C 588 " distance=2.04 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 341 " " NAG A2003 " - " ASN A 601 " " NAG A2004 " - " ASN A 655 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 232 " " NAG B2003 " - " ASN B 329 " " NAG B2004 " - " ASN B 601 " " NAG B2005 " - " ASN B 655 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 329 " " NAG C2003 " - " ASN C 601 " " NAG C2004 " - " ASN C 655 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 163 " " NAG F 1 " - " ASN A 232 " " NAG G 1 " - " ASN A 280 " " NAG H 1 " - " ASN A 329 " " NAG I 1 " - " ASN A 614 " " NAG J 1 " - " ASN A 707 " " NAG K 1 " - " ASN A 715 " " NAG L 1 " - " ASN A 799 " " NAG M 1 " - " ASN A1072 " " NAG N 1 " - " ASN A1096 " " NAG O 1 " - " ASN A1132 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 163 " " NAG R 1 " - " ASN B 280 " " NAG S 1 " - " ASN B 341 " " NAG T 1 " - " ASN B 614 " " NAG U 1 " - " ASN B 707 " " NAG V 1 " - " ASN B 715 " " NAG W 1 " - " ASN B 799 " " NAG X 1 " - " ASN B1072 " " NAG Y 1 " - " ASN B1096 " " NAG Z 1 " - " ASN B1132 " " NAG a 1 " - " ASN C 122 " " NAG b 1 " - " ASN C 163 " " NAG c 1 " - " ASN C 232 " " NAG d 1 " - " ASN C 280 " " NAG e 1 " - " ASN C 341 " " NAG f 1 " - " ASN C 614 " " NAG g 1 " - " ASN C 707 " " NAG h 1 " - " ASN C 715 " " NAG i 1 " - " ASN C 799 " " NAG j 1 " - " ASN C1072 " " NAG k 1 " - " ASN C1096 " " NAG l 1 " - " ASN C1132 " Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.1 seconds 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5794 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 45 sheets defined 25.0% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 292 through 302 Processing helix chain 'A' and resid 336 through 341 Processing helix chain 'A' and resid 362 through 369 removed outlier: 4.199A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.110A pdb=" N ASN A 386 " --> pdb=" O PRO A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 405 No H-bonds generated for 'chain 'A' and resid 403 through 405' Processing helix chain 'A' and resid 414 through 420 Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 4.003A pdb=" N GLN A 753 " --> pdb=" O ASN A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 781 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 906 Processing helix chain 'A' and resid 910 through 917 removed outlier: 4.286A pdb=" N LEU A 914 " --> pdb=" O THR A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 Processing helix chain 'A' and resid 943 through 963 Processing helix chain 'A' and resid 964 through 966 No H-bonds generated for 'chain 'A' and resid 964 through 966' Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.523A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 982 " --> pdb=" O ILE A 978 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1031 removed outlier: 4.565A pdb=" N VAL A 989 " --> pdb=" O PRO A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1138 through 1143 Processing helix chain 'B' and resid 292 through 302 removed outlier: 3.658A pdb=" N GLU B 296 " --> pdb=" O ASP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 341 Processing helix chain 'B' and resid 347 through 351 removed outlier: 3.514A pdb=" N TRP B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 369 removed outlier: 4.041A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) removed outlier: 3.549A 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: 4.740A 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 632 through 636 Processing helix chain 'B' and resid 736 through 741 Processing helix chain 'B' and resid 744 through 752 Processing helix chain 'B' and resid 753 through 755 No H-bonds generated for 'chain 'B' and resid 753 through 755' Processing helix chain 'B' and resid 756 through 781 removed outlier: 3.732A pdb=" N GLN B 760 " --> pdb=" O SER B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.624A pdb=" N VAL B 824 " --> pdb=" O LEU B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 864 through 883 Processing helix chain 'B' and resid 884 through 889 removed outlier: 4.016A 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: 3.637A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) removed outlier: 3.667A 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 982 removed outlier: 3.600A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1031 removed outlier: 4.339A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1144 removed outlier: 3.819A pdb=" N ASP B1144 " --> pdb=" O GLN B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 302 Processing helix chain 'C' and resid 336 through 341 Processing helix chain 'C' and resid 347 through 351 removed outlier: 3.675A pdb=" N TRP C 351 " --> pdb=" O VAL C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 363 through 369 removed outlier: 3.606A pdb=" N SER C 369 " --> pdb=" O VAL C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 381 through 387 removed outlier: 3.575A pdb=" N LEU C 385 " --> pdb=" O PRO C 382 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ASN C 386 " --> pdb=" O THR C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 408 removed outlier: 3.597A pdb=" N VAL C 405 " --> pdb=" O GLY C 402 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C 406 " --> pdb=" O ASP C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 420 Processing helix chain 'C' and resid 631 through 636 removed outlier: 3.832A 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 753 removed outlier: 3.993A pdb=" N GLN C 753 " --> pdb=" O ASN C 749 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.604A 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: 3.669A pdb=" N GLY C 883 " --> pdb=" O THR C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 906 Processing helix chain 'C' and resid 911 through 916 removed outlier: 3.847A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) removed outlier: 3.749A 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 1031 removed outlier: 4.533A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1144 removed outlier: 3.745A pdb=" N ASP C1144 " --> pdb=" O GLN C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.827A pdb=" N ASN A 61 " --> pdb=" O TYR A 267 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N TYR A 267 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.997A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.467A pdb=" N ASP C 572 " --> pdb=" O ILE C 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.044A pdb=" N ASP A 285 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.145A pdb=" N ARG A 235 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N PHE A 106 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N GLN A 237 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N TRP A 104 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU A 239 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 317 removed outlier: 7.057A pdb=" N VAL A 593 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASN A 315 " --> pdb=" O GLY A 591 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N GLY A 591 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLY A 592 " --> pdb=" O GLN A 611 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 324 removed outlier: 3.586A pdb=" N VAL A 574 " --> pdb=" O LEU A 583 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N ASP A 572 " --> pdb=" O ILE A 585 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLY A 564 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 356 Processing sheet with id=AA9, first strand: chain 'A' and resid 450 through 452 Processing sheet with id=AB1, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB2, first strand: chain 'A' and resid 652 through 653 removed outlier: 6.097A pdb=" N GLU A 652 " --> pdb=" O ALA A 692 " (cutoff:3.500A) removed outlier: 8.573A pdb=" N THR A 694 " --> pdb=" O GLU A 652 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N ALA A 670 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.805A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.701A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N MET A1048 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N TYR A1065 " --> pdb=" O HIS A1046 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N HIS A1046 " --> pdb=" O TYR A1065 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 709 through 726 removed outlier: 6.701A pdb=" N SER A 709 " --> pdb=" O THR A1074 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR A1074 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA A 711 " --> pdb=" O ASN A1072 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ASN A1072 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU A1070 " --> pdb=" O PRO A 713 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 731 through 734 removed outlier: 4.606A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 785 through 787 Processing sheet with id=AB8, first strand: chain 'A' and resid 1118 through 1120 Processing sheet with id=AB9, first strand: chain 'B' and resid 26 through 30 removed outlier: 7.957A pdb=" N ASN B 61 " --> pdb=" O TYR B 267 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR B 267 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) removed outlier: 9.560A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.426A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.965A 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: 7.099A pdb=" N ARG B 235 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE B 106 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLN B 237 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP B 104 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LEU B 239 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.426A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 4.414A 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 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: 6.417A 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 450 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: 6.101A pdb=" N GLU B 652 " --> pdb=" O ALA B 692 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N THR B 694 " --> pdb=" O GLU B 652 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ALA B 670 " --> pdb=" O PRO B 663 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 700 through 701 Processing sheet with id=AD2, first strand: chain 'B' and resid 713 through 726 removed outlier: 6.124A pdb=" N GLU B1070 " --> pdb=" O PRO B 713 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR B1065 " --> pdb=" O HIS B1046 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N HIS B1046 " --> pdb=" O TYR B1065 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 731 through 734 removed outlier: 4.508A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 4.998A 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 27 through 30 removed outlier: 7.944A pdb=" N ASN C 61 " --> pdb=" O TYR C 267 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TYR C 267 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N HIS C 205 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 9.695A pdb=" N LEU C 221 " --> pdb=" O HIS C 205 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 36 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.993A 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: 7.173A pdb=" N ARG C 235 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N PHE C 106 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N GLN C 237 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N TRP C 104 " --> pdb=" O GLN C 237 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C 239 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER C 170 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 4.561A 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: 7.037A pdb=" N VAL C 593 " --> pdb=" O THR C 313 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN C 315 " --> pdb=" O GLY C 591 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N GLY C 591 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 4.472A 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: 3.735A pdb=" N CYS C 523 " --> pdb=" O CYS C 359 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 450 through 452 Processing sheet with id=AE4, first strand: chain 'C' and resid 471 through 472 removed outlier: 3.513A pdb=" N TYR C 487 " --> pdb=" O TYR C 471 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 652 through 653 removed outlier: 6.081A pdb=" N GLU C 652 " --> pdb=" O ALA C 692 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR C 694 " --> pdb=" O GLU C 652 " (cutoff:3.500A) removed outlier: 5.930A 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: 6.739A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR C1065 " --> pdb=" O HIS C1046 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N HIS C1046 " --> pdb=" O TYR C1065 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 709 through 726 removed outlier: 6.739A pdb=" N SER C 709 " --> pdb=" O THR C1074 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N THR C1074 " --> pdb=" O SER C 709 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA C 711 " --> pdb=" O ASN C1072 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN C1072 " --> pdb=" O ALA C 711 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLU C1070 " --> pdb=" O PRO C 713 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 731 through 734 removed outlier: 4.606A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1118 through 1120 1025 hydrogen bonds defined for protein. 2805 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.79 Time building geometry restraints manager: 3.19 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: 7991 1.34 - 1.46: 6434 1.46 - 1.58: 11318 1.58 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 25875 Sorted by residual: bond pdb=" C1 NAG X 1 " pdb=" O5 NAG X 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.48e+00 bond pdb=" CB ASN C 775 " pdb=" CG ASN C 775 " ideal model delta sigma weight residual 1.516 1.459 0.057 2.50e-02 1.60e+03 5.14e+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 4.28e+00 bond pdb=" C1 NAG B2003 " pdb=" O5 NAG B2003 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB CYS C 736 " pdb=" SG CYS C 736 " ideal model delta sigma weight residual 1.808 1.751 0.057 3.30e-02 9.18e+02 2.95e+00 ... (remaining 25870 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 33826 1.63 - 3.26: 1245 3.26 - 4.90: 108 4.90 - 6.53: 21 6.53 - 8.16: 8 Bond angle restraints: 35208 Sorted by residual: angle pdb=" C GLY B 646 " pdb=" N CYS B 647 " pdb=" CA CYS B 647 " ideal model delta sigma weight residual 122.29 117.14 5.15 1.65e+00 3.67e-01 9.74e+00 angle pdb=" N PRO B 984 " pdb=" CA PRO B 984 " pdb=" C PRO B 984 " ideal model delta sigma weight residual 110.70 114.43 -3.73 1.22e+00 6.72e-01 9.34e+00 angle pdb=" CA VAL A 727 " pdb=" C VAL A 727 " pdb=" N SER A 728 " ideal model delta sigma weight residual 116.60 120.73 -4.13 1.45e+00 4.76e-01 8.09e+00 angle pdb=" CA CYS C 758 " pdb=" CB CYS C 758 " pdb=" SG CYS C 758 " ideal model delta sigma weight residual 114.40 107.97 6.43 2.30e+00 1.89e-01 7.82e+00 angle pdb=" N PRO A 559 " pdb=" CA PRO A 559 " pdb=" C PRO A 559 " ideal model delta sigma weight residual 112.47 118.13 -5.66 2.06e+00 2.36e-01 7.56e+00 ... (remaining 35203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 13310 17.75 - 35.51: 1186 35.51 - 53.26: 204 53.26 - 71.01: 36 71.01 - 88.77: 31 Dihedral angle restraints: 14767 sinusoidal: 5768 harmonic: 8999 Sorted by residual: dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -166.21 80.21 1 1.00e+01 1.00e-02 7.97e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual -86.00 -163.60 77.60 1 1.00e+01 1.00e-02 7.54e+01 dihedral pdb=" CB CYS C1080 " pdb=" SG CYS C1080 " pdb=" SG CYS C1124 " pdb=" CB CYS C1124 " ideal model delta sinusoidal sigma weight residual -86.00 -9.17 -76.83 1 1.00e+01 1.00e-02 7.41e+01 ... (remaining 14764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4025 0.101 - 0.201: 208 0.201 - 0.302: 3 0.302 - 0.403: 2 0.403 - 0.503: 1 Chirality restraints: 4239 Sorted by residual: chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C 163 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.34e+00 chirality pdb=" C1 NAG c 1 " pdb=" ND2 ASN C 232 " pdb=" C2 NAG c 1 " pdb=" O5 NAG c 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 NAG B2004 " pdb=" ND2 ASN B 601 " pdb=" C2 NAG B2004 " pdb=" O5 NAG B2004 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 4236 not shown) Planarity restraints: 4498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 904 " 0.018 2.00e-02 2.50e+03 1.89e-02 6.24e+00 pdb=" CG PHE B 904 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE B 904 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 PHE B 904 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE B 904 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 904 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 904 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 904 " -0.018 2.00e-02 2.50e+03 1.85e-02 6.00e+00 pdb=" CG PHE C 904 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 PHE C 904 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE C 904 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE C 904 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE C 904 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE C 904 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1072 " 0.022 2.00e-02 2.50e+03 1.97e-02 4.87e+00 pdb=" CG ASN B1072 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN B1072 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B1072 " -0.021 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " 0.022 2.00e-02 2.50e+03 ... (remaining 4495 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1034 2.71 - 3.25: 24856 3.25 - 3.80: 39113 3.80 - 4.35: 46425 4.35 - 4.90: 81737 Nonbonded interactions: 193165 Sorted by model distance: nonbonded pdb=" OG1 THR A 124 " pdb=" OD1 ASN A 125 " model vdw 2.158 3.040 nonbonded pdb=" O GLU C 154 " pdb=" OH TYR C 158 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASP C 566 " pdb=" OG1 THR C 570 " model vdw 2.202 3.040 nonbonded pdb=" O ASN A 437 " pdb=" OG SER A 441 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR A 109 " pdb=" OD1 ASP A 111 " model vdw 2.232 3.040 ... (remaining 193160 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 619 or resid 637 through 825 or resid 853 throu \ gh 2004)) selection = (chain 'C' and (resid 14 through 619 or resid 637 through 825 or resid 853 throu \ gh 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 24.280 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 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 : 0.007 0.057 25998 Z= 0.321 Angle : 0.727 9.671 35537 Z= 0.359 Chirality : 0.050 0.503 4239 Planarity : 0.004 0.042 4450 Dihedral : 13.841 88.765 8853 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.49 % Favored : 94.45 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3044 helix: 1.85 (0.21), residues: 674 sheet: 0.51 (0.18), residues: 737 loop : -1.14 (0.15), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1037 TYR 0.019 0.001 TYR B1065 PHE 0.043 0.002 PHE B 904 TRP 0.027 0.002 TRP B 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00742 / 0.32 (25875) covalent geometry : angle 0.69108 / 0.35 (35208) SS BOND : bond 0.00480 / 0.31 ( 40) SS BOND : angle 2.02176 / 1.35 ( 80) hydrogen bonds : bond 0.12942 / 8.46 ( 1001) hydrogen bonds : angle 6.27634 / 4.33 ( 2805) link_BETA1-4 : bond 0.00381 / 0.23 ( 35) link_BETA1-4 : angle 2.17243 / 1.37 ( 105) link_NAG-ASN : bond 0.00483 / 0.32 ( 48) link_NAG-ASN : angle 2.79121 / 2.00 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 1.012 Fit side-chains revert: symmetry clash REVERT: B 454 PHE cc_start: 0.9154 (m-80) cc_final: 0.8844 (m-80) REVERT: C 400 ILE cc_start: 0.8810 (pt) cc_final: 0.8609 (pt) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.6865 time to fit residues: 59.5039 Evaluate side-chains 54 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 0.5980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN B 499 ASN B 562 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 ASN ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1000 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.077397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.046312 restraints weight = 86637.428| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.96 r_work: 0.2646 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.0651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 25998 Z= 0.164 Angle : 0.616 9.941 35537 Z= 0.308 Chirality : 0.046 0.377 4239 Planarity : 0.004 0.047 4450 Dihedral : 4.328 22.389 3315 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.70 % Rotamer: Outliers : 0.26 % Allowed : 6.06 % Favored : 93.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3044 helix: 2.04 (0.21), residues: 680 sheet: 0.54 (0.19), residues: 735 loop : -1.07 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 355 TYR 0.016 0.001 TYR A1065 PHE 0.028 0.001 PHE C 166 TRP 0.010 0.001 TRP B 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (25875) covalent geometry : angle 0.58617 / 0.30 (35208) SS BOND : bond 0.00375 / 0.23 ( 40) SS BOND : angle 1.67177 / 1.16 ( 80) hydrogen bonds : bond 0.06427 / 4.23 ( 1001) hydrogen bonds : angle 5.29742 / 3.65 ( 2805) link_BETA1-4 : bond 0.00385 / 0.26 ( 35) link_BETA1-4 : angle 1.84035 / 1.16 ( 105) link_NAG-ASN : bond 0.00350 / 0.21 ( 48) link_NAG-ASN : angle 2.35392 / 1.71 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8901 (tp40) REVERT: B 454 PHE cc_start: 0.9346 (m-80) cc_final: 0.8915 (m-80) REVERT: C 400 ILE cc_start: 0.9030 (pt) cc_final: 0.8797 (pt) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 0.7221 time to fit residues: 60.7868 Evaluate side-chains 57 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain B residue 1015 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 69 optimal weight: 0.6980 chunk 186 optimal weight: 3.9990 chunk 291 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 286 optimal weight: 3.9990 chunk 140 optimal weight: 20.0000 chunk 210 optimal weight: 0.9990 chunk 221 optimal weight: 0.9980 chunk 197 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.077404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.046386 restraints weight = 86532.966| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.96 r_work: 0.2648 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25998 Z= 0.160 Angle : 0.593 9.863 35537 Z= 0.296 Chirality : 0.045 0.375 4239 Planarity : 0.004 0.046 4450 Dihedral : 4.192 20.586 3315 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.60 % Favored : 95.34 % Rotamer: Outliers : 0.81 % Allowed : 8.54 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3044 helix: 2.08 (0.21), residues: 690 sheet: 0.61 (0.19), residues: 723 loop : -1.06 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 355 TYR 0.016 0.001 TYR B1065 PHE 0.023 0.001 PHE C 166 TRP 0.007 0.001 TRP B 884 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (25875) covalent geometry : angle 0.56466 / 0.29 (35208) SS BOND : bond 0.00351 / 0.22 ( 40) SS BOND : angle 1.50416 / 1.03 ( 80) hydrogen bonds : bond 0.06072 / 3.99 ( 1001) hydrogen bonds : angle 5.07380 / 3.50 ( 2805) link_BETA1-4 : bond 0.00386 / 0.26 ( 35) link_BETA1-4 : angle 1.79646 / 1.12 ( 105) link_NAG-ASN : bond 0.00348 / 0.21 ( 48) link_NAG-ASN : angle 2.28384 / 1.66 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8891 (tp40) REVERT: B 454 PHE cc_start: 0.9332 (m-80) cc_final: 0.8903 (m-80) REVERT: B 1027 MET cc_start: 0.9411 (tpp) cc_final: 0.9176 (tpp) REVERT: C 983 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7222 (p0) outliers start: 22 outliers final: 11 residues processed: 76 average time/residue: 0.6420 time to fit residues: 57.6275 Evaluate side-chains 66 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 20.0000 chunk 284 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 162 optimal weight: 0.4980 chunk 226 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 953 ASN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.077969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.047102 restraints weight = 86247.878| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 4.00 r_work: 0.2673 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25998 Z= 0.122 Angle : 0.560 9.894 35537 Z= 0.279 Chirality : 0.044 0.371 4239 Planarity : 0.004 0.045 4450 Dihedral : 4.020 19.318 3315 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.91 % Favored : 96.02 % Rotamer: Outliers : 1.04 % Allowed : 9.98 % Favored : 88.98 % 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: 3044 helix: 2.22 (0.21), residues: 682 sheet: 0.67 (0.19), residues: 724 loop : -1.00 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.016 0.001 TYR A1065 PHE 0.021 0.001 PHE C 166 TRP 0.008 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (25875) covalent geometry : angle 0.53248 / 0.27 (35208) SS BOND : bond 0.00296 / 0.19 ( 40) SS BOND : angle 1.35551 / 0.94 ( 80) hydrogen bonds : bond 0.05469 / 3.60 ( 1001) hydrogen bonds : angle 4.88824 / 3.37 ( 2805) link_BETA1-4 : bond 0.00426 / 0.29 ( 35) link_BETA1-4 : angle 1.75857 / 1.10 ( 105) link_NAG-ASN : bond 0.00346 / 0.21 ( 48) link_NAG-ASN : angle 2.17111 / 1.58 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8793 (tp40) REVERT: B 454 PHE cc_start: 0.9312 (m-80) cc_final: 0.8897 (m-80) REVERT: B 856 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8802 (mt) REVERT: C 983 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7086 (p0) outliers start: 28 outliers final: 11 residues processed: 88 average time/residue: 0.6229 time to fit residues: 65.1703 Evaluate side-chains 69 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 703 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 898 MET Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 30 optimal weight: 20.0000 chunk 224 optimal weight: 4.9990 chunk 231 optimal weight: 7.9990 chunk 215 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 146 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 10.0000 chunk 181 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 216 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 963 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.076124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.044873 restraints weight = 86386.908| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.97 r_work: 0.2602 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 25998 Z= 0.286 Angle : 0.664 10.204 35537 Z= 0.332 Chirality : 0.048 0.367 4239 Planarity : 0.004 0.049 4450 Dihedral : 4.351 20.346 3315 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.93 % Favored : 94.97 % Rotamer: Outliers : 1.22 % Allowed : 11.42 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3044 helix: 2.01 (0.21), residues: 689 sheet: 0.47 (0.19), residues: 729 loop : -1.13 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1037 TYR 0.020 0.001 TYR B1065 PHE 0.021 0.002 PHE C 904 TRP 0.009 0.001 TRP B 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00685 / 0.29 (25875) covalent geometry : angle 0.63550 / 0.33 (35208) SS BOND : bond 0.00447 / 0.30 ( 40) SS BOND : angle 1.80598 / 1.23 ( 80) hydrogen bonds : bond 0.06975 / 4.57 ( 1001) hydrogen bonds : angle 5.14291 / 3.55 ( 2805) link_BETA1-4 : bond 0.00313 / 0.21 ( 35) link_BETA1-4 : angle 1.85013 / 1.15 ( 105) link_NAG-ASN : bond 0.00443 / 0.29 ( 48) link_NAG-ASN : angle 2.36494 / 1.73 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 454 PHE cc_start: 0.9315 (m-80) cc_final: 0.8904 (m-80) outliers start: 33 outliers final: 15 residues processed: 88 average time/residue: 0.5866 time to fit residues: 61.6894 Evaluate side-chains 71 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 75 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 228 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 17 optimal weight: 0.0870 chunk 268 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 80 optimal weight: 0.9990 overall best weight: 0.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 81 ASN ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.077791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046880 restraints weight = 86987.486| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.02 r_work: 0.2663 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25998 Z= 0.115 Angle : 0.569 9.775 35537 Z= 0.283 Chirality : 0.044 0.371 4239 Planarity : 0.004 0.047 4450 Dihedral : 4.056 19.135 3315 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.94 % Favored : 95.96 % Rotamer: Outliers : 1.22 % Allowed : 12.09 % Favored : 86.69 % 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: 3044 helix: 2.16 (0.21), residues: 689 sheet: 0.63 (0.19), residues: 724 loop : -1.03 (0.15), residues: 1631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 355 TYR 0.015 0.001 TYR A1065 PHE 0.012 0.001 PHE C1119 TRP 0.009 0.001 TRP C 434 HIS 0.002 0.000 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (25875) covalent geometry : angle 0.54312 / 0.28 (35208) SS BOND : bond 0.00338 / 0.22 ( 40) SS BOND : angle 1.36073 / 0.95 ( 80) hydrogen bonds : bond 0.05494 / 3.62 ( 1001) hydrogen bonds : angle 4.85337 / 3.34 ( 2805) link_BETA1-4 : bond 0.00445 / 0.30 ( 35) link_BETA1-4 : angle 1.78061 / 1.11 ( 105) link_NAG-ASN : bond 0.00357 / 0.22 ( 48) link_NAG-ASN : angle 2.12780 / 1.55 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8809 (tp40) REVERT: B 81 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.8029 (p0) REVERT: B 227 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9005 (mm) REVERT: B 454 PHE cc_start: 0.9308 (m-80) cc_final: 0.8904 (m-80) REVERT: C 579 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.9006 (p) REVERT: C 983 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7154 (p0) outliers start: 33 outliers final: 17 residues processed: 91 average time/residue: 0.5508 time to fit residues: 60.0244 Evaluate side-chains 76 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 111 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 228 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 64 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 214 optimal weight: 5.9990 chunk 169 optimal weight: 0.6980 overall best weight: 2.5388 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.076453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.045275 restraints weight = 86895.822| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 4.00 r_work: 0.2611 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 25998 Z= 0.233 Angle : 0.634 10.019 35537 Z= 0.316 Chirality : 0.047 0.366 4239 Planarity : 0.004 0.049 4450 Dihedral : 4.228 20.353 3315 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 1.00 % Allowed : 12.79 % Favored : 86.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 3044 helix: 2.07 (0.21), residues: 690 sheet: 0.54 (0.19), residues: 728 loop : -1.10 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1037 TYR 0.019 0.001 TYR B1065 PHE 0.017 0.001 PHE B 140 TRP 0.007 0.001 TRP A 884 HIS 0.004 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (25875) covalent geometry : angle 0.60640 / 0.31 (35208) SS BOND : bond 0.00422 / 0.28 ( 40) SS BOND : angle 1.68627 / 1.13 ( 80) hydrogen bonds : bond 0.06510 / 4.27 ( 1001) hydrogen bonds : angle 5.00846 / 3.45 ( 2805) link_BETA1-4 : bond 0.00326 / 0.22 ( 35) link_BETA1-4 : angle 1.82788 / 1.14 ( 105) link_NAG-ASN : bond 0.00401 / 0.26 ( 48) link_NAG-ASN : angle 2.27460 / 1.66 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 56 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9112 (tm-30) cc_final: 0.8826 (tp40) REVERT: B 227 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8986 (mm) REVERT: B 454 PHE cc_start: 0.9306 (m-80) cc_final: 0.8905 (m-80) REVERT: C 579 THR cc_start: 0.9241 (OUTLIER) cc_final: 0.9015 (p) REVERT: C 983 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7145 (p0) outliers start: 27 outliers final: 18 residues processed: 81 average time/residue: 0.5520 time to fit residues: 53.4100 Evaluate side-chains 76 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 296 optimal weight: 0.6980 chunk 132 optimal weight: 9.9990 chunk 21 optimal weight: 0.7980 chunk 121 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 173 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 134 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.077361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.046382 restraints weight = 86709.131| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 4.01 r_work: 0.2647 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25998 Z= 0.140 Angle : 0.586 9.781 35537 Z= 0.291 Chirality : 0.045 0.369 4239 Planarity : 0.004 0.048 4450 Dihedral : 4.079 20.408 3315 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.98 % Favored : 95.93 % Rotamer: Outliers : 0.92 % Allowed : 13.23 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3044 helix: 2.11 (0.21), residues: 695 sheet: 0.67 (0.19), residues: 714 loop : -1.05 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C1037 TYR 0.015 0.001 TYR A1065 PHE 0.012 0.001 PHE C 375 TRP 0.007 0.001 TRP C 434 HIS 0.002 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (25875) covalent geometry : angle 0.55995 / 0.29 (35208) SS BOND : bond 0.00342 / 0.22 ( 40) SS BOND : angle 1.44416 / 0.99 ( 80) hydrogen bonds : bond 0.05716 / 3.76 ( 1001) hydrogen bonds : angle 4.85889 / 3.35 ( 2805) link_BETA1-4 : bond 0.00418 / 0.29 ( 35) link_BETA1-4 : angle 1.79290 / 1.12 ( 105) link_NAG-ASN : bond 0.00340 / 0.21 ( 48) link_NAG-ASN : angle 2.13828 / 1.56 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9104 (tm-30) cc_final: 0.8822 (tp40) REVERT: B 227 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9009 (mm) REVERT: B 454 PHE cc_start: 0.9300 (m-80) cc_final: 0.8902 (m-80) REVERT: C 579 THR cc_start: 0.9225 (OUTLIER) cc_final: 0.8996 (p) REVERT: C 983 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7170 (p0) outliers start: 25 outliers final: 19 residues processed: 83 average time/residue: 0.5270 time to fit residues: 52.6942 Evaluate side-chains 79 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 138 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.076161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.044959 restraints weight = 87086.150| |-----------------------------------------------------------------------------| r_work (start): 0.2762 rms_B_bonded: 3.99 r_work: 0.2603 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 25998 Z= 0.249 Angle : 0.651 10.062 35537 Z= 0.325 Chirality : 0.047 0.366 4239 Planarity : 0.004 0.048 4450 Dihedral : 4.303 20.999 3315 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.45 % Favored : 94.45 % Rotamer: Outliers : 1.07 % Allowed : 13.31 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.15), residues: 3044 helix: 2.06 (0.21), residues: 686 sheet: 0.50 (0.19), residues: 729 loop : -1.12 (0.15), residues: 1629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1037 TYR 0.019 0.001 TYR B1065 PHE 0.016 0.001 PHE B1119 TRP 0.007 0.001 TRP B 884 HIS 0.003 0.001 HIS B1046 Details of bonding type rmsd/Z covalent geometry : bond 0.00593 / 0.25 (25875) covalent geometry : angle 0.62387 / 0.32 (35208) SS BOND : bond 0.00439 / 0.29 ( 40) SS BOND : angle 1.74282 / 1.17 ( 80) hydrogen bonds : bond 0.06752 / 4.43 ( 1001) hydrogen bonds : angle 5.04892 / 3.48 ( 2805) link_BETA1-4 : bond 0.00320 / 0.22 ( 35) link_BETA1-4 : angle 1.86820 / 1.16 ( 105) link_NAG-ASN : bond 0.00429 / 0.28 ( 48) link_NAG-ASN : angle 2.29217 / 1.67 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 227 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8964 (mm) REVERT: B 454 PHE cc_start: 0.9296 (m-80) cc_final: 0.8914 (m-80) REVERT: C 114 THR cc_start: 0.7535 (OUTLIER) cc_final: 0.7311 (p) REVERT: C 579 THR cc_start: 0.9234 (OUTLIER) cc_final: 0.9008 (p) REVERT: C 983 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7172 (p0) outliers start: 29 outliers final: 21 residues processed: 83 average time/residue: 0.5965 time to fit residues: 59.6672 Evaluate side-chains 77 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 52 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 205 optimal weight: 30.0000 chunk 166 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 262 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 51 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 207 optimal weight: 0.6980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.077068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.046061 restraints weight = 86733.533| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 4.00 r_work: 0.2637 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 25998 Z= 0.157 Angle : 0.603 10.408 35537 Z= 0.300 Chirality : 0.045 0.371 4239 Planarity : 0.004 0.048 4450 Dihedral : 4.146 20.592 3315 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.34 % Favored : 95.57 % Rotamer: Outliers : 0.96 % Allowed : 13.49 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.15), residues: 3044 helix: 2.06 (0.21), residues: 697 sheet: 0.62 (0.19), residues: 707 loop : -1.06 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1037 TYR 0.015 0.001 TYR A1065 PHE 0.012 0.001 PHE B 140 TRP 0.007 0.001 TRP C 884 HIS 0.003 0.001 HIS B1086 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (25875) covalent geometry : angle 0.57640 / 0.29 (35208) SS BOND : bond 0.00355 / 0.23 ( 40) SS BOND : angle 1.51100 / 1.04 ( 80) hydrogen bonds : bond 0.05921 / 3.90 ( 1001) hydrogen bonds : angle 4.90014 / 3.38 ( 2805) link_BETA1-4 : bond 0.00399 / 0.27 ( 35) link_BETA1-4 : angle 1.83131 / 1.14 ( 105) link_NAG-ASN : bond 0.00343 / 0.21 ( 48) link_NAG-ASN : angle 2.15558 / 1.57 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6088 Ramachandran restraints generated. 3044 Oldfield, 0 Emsley, 3044 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8837 (tp40) REVERT: B 227 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9023 (mm) REVERT: B 454 PHE cc_start: 0.9296 (m-80) cc_final: 0.8918 (m-80) REVERT: C 114 THR cc_start: 0.7508 (OUTLIER) cc_final: 0.7289 (p) REVERT: C 579 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.9001 (p) REVERT: C 983 ASP cc_start: 0.7850 (OUTLIER) cc_final: 0.7130 (p0) outliers start: 26 outliers final: 22 residues processed: 83 average time/residue: 0.5919 time to fit residues: 58.7195 Evaluate side-chains 81 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 597 THR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 932 ILE Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1041 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 157 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain B residue 583 LEU Chi-restraints excluded: chain B residue 586 THR Chi-restraints excluded: chain B residue 647 CYS Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 722 THR Chi-restraints excluded: chain B residue 856 LEU Chi-restraints excluded: chain B residue 932 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 579 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 736 CYS Chi-restraints excluded: chain C residue 983 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 75 optimal weight: 2.9990 chunk 271 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 286 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 157 optimal weight: 3.9990 chunk 191 optimal weight: 2.9990 chunk 156 optimal weight: 0.9980 chunk 36 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.076356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.045185 restraints weight = 86674.745| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 4.00 r_work: 0.2610 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25998 Z= 0.221 Angle : 0.636 9.951 35537 Z= 0.316 Chirality : 0.046 0.368 4239 Planarity : 0.004 0.048 4450 Dihedral : 4.257 20.827 3315 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.09 % Favored : 94.81 % Rotamer: Outliers : 1.07 % Allowed : 13.49 % Favored : 85.43 % 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: 0.08 (0.15), residues: 3044 helix: 2.09 (0.21), residues: 686 sheet: 0.54 (0.19), residues: 711 loop : -1.10 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1037 TYR 0.018 0.001 TYR B1065 PHE 0.014 0.001 PHE B1119 TRP 0.007 0.001 TRP B 884 HIS 0.003 0.001 HIS A1062 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (25875) covalent geometry : angle 0.60935 / 0.31 (35208) SS BOND : bond 0.00418 / 0.28 ( 40) SS BOND : angle 1.67165 / 1.13 ( 80) hydrogen bonds : bond 0.06486 / 4.26 ( 1001) hydrogen bonds : angle 4.99655 / 3.44 ( 2805) link_BETA1-4 : bond 0.00343 / 0.24 ( 35) link_BETA1-4 : angle 1.87507 / 1.16 ( 105) link_NAG-ASN : bond 0.00399 / 0.26 ( 48) link_NAG-ASN : angle 2.24715 / 1.64 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7846.01 seconds wall clock time: 134 minutes 46.15 seconds (8086.15 seconds total)