Starting phenix.real_space_refine on Fri Sep 19 12:05:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v7g_31770/09_2025/7v7g_31770.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v7g_31770/09_2025/7v7g_31770.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v7g_31770/09_2025/7v7g_31770.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v7g_31770/09_2025/7v7g_31770.map" model { file = "/net/cci-nas-00/data/ceres_data/7v7g_31770/09_2025/7v7g_31770.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v7g_31770/09_2025/7v7g_31770.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 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 111 5.16 5 C 16179 2.51 5 N 4134 2.21 5 O 5037 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25461 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.20, per 1000 atoms: 0.24 Number of scatterers: 25461 At special positions: 0 Unit cell: (141.9, 149.6, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 5037 8.00 N 4134 7.00 C 16179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 343 " " NAG A2003 " - " ASN A 603 " " NAG A2004 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 165 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 343 " " NAG B2005 " - " ASN B 603 " " NAG B2006 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 234 " " NAG C2003 " - " ASN C 331 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 122 " " NAG E 1 " - " ASN A 165 " " NAG F 1 " - " ASN A 234 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 616 " " NAG J 1 " - " ASN A 709 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 282 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 709 " " NAG U 1 " - " ASN B 717 " " NAG V 1 " - " ASN B 801 " " NAG W 1 " - " ASN B1074 " " NAG X 1 " - " ASN B1098 " " NAG Y 1 " - " ASN B1134 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 282 " " NAG c 1 " - " ASN C 343 " " NAG d 1 " - " ASN C 616 " " NAG e 1 " - " ASN C 709 " " NAG f 1 " - " ASN C 717 " " NAG g 1 " - " ASN C 801 " " NAG h 1 " - " ASN C1074 " " NAG i 1 " - " ASN C1098 " " NAG j 1 " - " ASN C1134 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 978.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5832 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 51 sheets defined 24.4% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.727A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.516A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.930A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.015A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 941 removed outlier: 3.654A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.067A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.699A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.724A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.520A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.950A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.546A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.615A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.813A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.506A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.533A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.562A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.595A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 removed outlier: 3.989A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.639A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.834A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.153A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.971A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.601A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.587A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.468A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 6.881A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (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: 6.295A pdb=" N PHE A 43 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.550A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 126 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL A 171 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE A 128 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N GLU A 169 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL A 130 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASN A 165 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.550A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.382A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.511A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB2, first strand: chain 'A' and resid 361 through 362 removed outlier: 3.741A pdb=" N CYS A 525 " --> pdb=" O CYS A 361 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB5, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.654A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.967A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.751A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.502A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.598A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.796A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 1094 through 1096 Processing sheet with id=AC3, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.035A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.777A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.578A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.213A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.699A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 6.887A pdb=" N ASN B 437 " --> pdb=" O PHE B 374 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N PHE B 374 " --> pdb=" O ASN B 437 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.527A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 539 through 543 removed outlier: 5.640A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.000A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.511A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 701 through 703 Processing sheet with id=AD6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.369A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.549A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.824A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.742A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.826A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.556A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 134 through 135 removed outlier: 7.030A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.248A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 325 through 326 Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.325A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.118A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.920A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 979 hydrogen bonds defined for protein. 2694 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 3.02 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: 8015 1.34 - 1.46: 6076 1.46 - 1.58: 11790 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 26019 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C1 NAG P 2 " pdb=" O5 NAG P 2 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.68e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.444 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C1 NAG d 1 " pdb=" O5 NAG d 1 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.79e+00 bond pdb=" C1 NAG A2002 " pdb=" O5 NAG A2002 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.73e+00 ... (remaining 26014 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 34609 1.92 - 3.85: 744 3.85 - 5.77: 45 5.77 - 7.69: 10 7.69 - 9.61: 4 Bond angle restraints: 35412 Sorted by residual: angle pdb=" N ASN C 164 " pdb=" CA ASN C 164 " pdb=" C ASN C 164 " ideal model delta sigma weight residual 108.19 112.87 -4.68 1.29e+00 6.01e-01 1.32e+01 angle pdb=" N GLN C1002 " pdb=" CA GLN C1002 " pdb=" CB GLN C1002 " ideal model delta sigma weight residual 110.12 115.17 -5.05 1.47e+00 4.63e-01 1.18e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.65 -3.95 1.22e+00 6.72e-01 1.05e+01 angle pdb=" C ASN C 164 " pdb=" N ASN C 165 " pdb=" CA ASN C 165 " ideal model delta sigma weight residual 121.97 126.79 -4.82 1.73e+00 3.34e-01 7.76e+00 angle pdb=" CA LEU C 560 " pdb=" CB LEU C 560 " pdb=" CG LEU C 560 " ideal model delta sigma weight residual 116.30 125.91 -9.61 3.50e+00 8.16e-02 7.54e+00 ... (remaining 35407 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 14916 18.05 - 36.11: 1279 36.11 - 54.16: 253 54.16 - 72.22: 60 72.22 - 90.27: 22 Dihedral angle restraints: 16530 sinusoidal: 7467 harmonic: 9063 Sorted by residual: dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual 93.00 -176.73 -90.27 1 1.00e+01 1.00e-02 9.65e+01 dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -166.29 80.29 1 1.00e+01 1.00e-02 7.98e+01 dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 -162.93 76.93 1 1.00e+01 1.00e-02 7.43e+01 ... (remaining 16527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.191: 4249 0.191 - 0.381: 4 0.381 - 0.572: 1 0.572 - 0.763: 1 0.763 - 0.953: 2 Chirality restraints: 4257 Sorted by residual: chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN B 331 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.45 -0.95 2.00e-01 2.50e+01 2.27e+01 chirality pdb=" C1 NAG W 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG W 1 " pdb=" O5 NAG W 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.52 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" C1 NAG h 1 " pdb=" ND2 ASN C1074 " pdb=" C2 NAG h 1 " pdb=" O5 NAG h 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.09e+01 ... (remaining 4254 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO B 987 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO C 295 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN B 173 " 0.034 5.00e-02 4.00e+02 5.17e-02 4.28e+00 pdb=" N PRO B 174 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 174 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 174 " 0.029 5.00e-02 4.00e+02 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1047 2.71 - 3.26: 25458 3.26 - 3.81: 40025 3.81 - 4.35: 47227 4.35 - 4.90: 81878 Nonbonded interactions: 195635 Sorted by model distance: nonbonded pdb=" OG SER C 349 " pdb=" O ARG C 452 " model vdw 2.168 3.040 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.180 3.120 nonbonded pdb=" OG1 THR C 393 " pdb=" OE2 GLU C 516 " model vdw 2.198 3.040 nonbonded pdb=" OG SER B1123 " pdb=" OD1 ASN C 914 " model vdw 2.200 3.040 nonbonded pdb=" O ARG A 214 " pdb=" OH TYR A 266 " model vdw 2.215 3.040 ... (remaining 195630 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 2004) selection = (chain 'C' and resid 14 through 2004) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.220 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26137 Z= 0.197 Angle : 0.675 16.527 35727 Z= 0.321 Chirality : 0.052 0.953 4257 Planarity : 0.004 0.066 4476 Dihedral : 13.604 89.455 10590 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.61 % Favored : 94.32 % Rotamer: Outliers : 0.04 % Allowed : 0.22 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.15), residues: 3066 helix: 2.04 (0.21), residues: 661 sheet: 0.51 (0.19), residues: 716 loop : -1.30 (0.15), residues: 1689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 102 TYR 0.020 0.001 TYR B 636 PHE 0.028 0.001 PHE C 906 TRP 0.020 0.001 TRP B 353 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00417 (26019) covalent geometry : angle 0.62106 (35412) SS BOND : bond 0.00242 ( 36) SS BOND : angle 1.23890 ( 72) hydrogen bonds : bond 0.11624 ( 964) hydrogen bonds : angle 5.81618 ( 2694) Misc. bond : bond 0.00020 ( 1) link_BETA1-4 : bond 0.00428 ( 33) link_BETA1-4 : angle 2.43375 ( 99) link_NAG-ASN : bond 0.00372 ( 48) link_NAG-ASN : angle 3.63962 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 0.838 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.4437 (pmm) cc_final: 0.4165 (pmm) REVERT: A 360 ASN cc_start: 0.9045 (m-40) cc_final: 0.8682 (p0) REVERT: A 773 GLU cc_start: 0.6460 (tm-30) cc_final: 0.6242 (tm-30) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.1682 time to fit residues: 21.6761 Evaluate side-chains 48 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.0980 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.6980 chunk 298 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN ** C 484 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 = 0.3869 r_free = 0.3869 target = 0.081700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.052707 restraints weight = 107517.077| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 4.34 r_work: 0.2938 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26137 Z= 0.126 Angle : 0.605 14.060 35727 Z= 0.293 Chirality : 0.047 0.564 4257 Planarity : 0.004 0.061 4476 Dihedral : 7.048 92.597 5040 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.70 % Favored : 95.24 % Rotamer: Outliers : 0.11 % Allowed : 5.03 % Favored : 94.85 % 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 aren not related in a simple way. whole: -0.07 (0.15), residues: 3066 helix: 1.99 (0.21), residues: 683 sheet: 0.62 (0.20), residues: 713 loop : -1.28 (0.15), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 346 TYR 0.015 0.001 TYR C1067 PHE 0.026 0.001 PHE A 133 TRP 0.021 0.001 TRP B 353 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00283 (26019) covalent geometry : angle 0.56090 (35412) SS BOND : bond 0.00299 ( 36) SS BOND : angle 1.32570 ( 72) hydrogen bonds : bond 0.05042 ( 964) hydrogen bonds : angle 5.05203 ( 2694) Misc. bond : bond 0.00015 ( 1) link_BETA1-4 : bond 0.00379 ( 33) link_BETA1-4 : angle 2.10106 ( 99) link_NAG-ASN : bond 0.00380 ( 48) link_NAG-ASN : angle 3.06907 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5094 (pmm) cc_final: 0.4499 (pmm) REVERT: A 360 ASN cc_start: 0.9160 (m-40) cc_final: 0.8880 (p0) REVERT: A 773 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7517 (tm-30) REVERT: A 1002 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8140 (tp-100) REVERT: B 1017 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8948 (tm-30) outliers start: 3 outliers final: 3 residues processed: 72 average time/residue: 0.1500 time to fit residues: 18.6300 Evaluate side-chains 59 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 641 ASN Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 742 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 251 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 97 optimal weight: 0.0050 chunk 90 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 39 optimal weight: 20.0000 chunk 181 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 641 ASN C 394 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1088 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.080833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.051828 restraints weight = 107679.068| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 4.29 r_work: 0.2913 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26137 Z= 0.167 Angle : 0.610 13.467 35727 Z= 0.295 Chirality : 0.047 0.568 4257 Planarity : 0.004 0.060 4476 Dihedral : 6.580 85.217 5040 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.88 % Rotamer: Outliers : 0.62 % Allowed : 8.01 % Favored : 91.36 % 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 aren not related in a simple way. whole: -0.13 (0.15), residues: 3066 helix: 1.91 (0.21), residues: 688 sheet: 0.52 (0.19), residues: 720 loop : -1.29 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1039 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.001 PHE B 133 TRP 0.012 0.001 TRP B 353 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00389 (26019) covalent geometry : angle 0.56808 (35412) SS BOND : bond 0.00306 ( 36) SS BOND : angle 1.35679 ( 72) hydrogen bonds : bond 0.05231 ( 964) hydrogen bonds : angle 4.99895 ( 2694) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00363 ( 33) link_BETA1-4 : angle 2.06826 ( 99) link_NAG-ASN : bond 0.00332 ( 48) link_NAG-ASN : angle 3.03696 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5068 (pmm) cc_final: 0.4505 (pmm) REVERT: A 360 ASN cc_start: 0.9171 (m-40) cc_final: 0.8904 (p0) REVERT: A 1002 GLN cc_start: 0.8556 (tm-30) cc_final: 0.8134 (tp-100) REVERT: B 1017 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8912 (tm-30) outliers start: 17 outliers final: 8 residues processed: 73 average time/residue: 0.1438 time to fit residues: 18.4789 Evaluate side-chains 60 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 148 optimal weight: 50.0000 chunk 66 optimal weight: 3.9990 chunk 258 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 172 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 chunk 218 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 207 HIS A 901 GLN B 914 ASN ** C 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.079804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.050371 restraints weight = 107041.528| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.33 r_work: 0.2879 rms_B_bonded: 4.57 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 26137 Z= 0.220 Angle : 0.651 13.647 35727 Z= 0.316 Chirality : 0.048 0.579 4257 Planarity : 0.004 0.061 4476 Dihedral : 6.424 77.817 5040 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.26 % Rotamer: Outliers : 1.07 % Allowed : 10.40 % Favored : 88.53 % 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 aren not related in a simple way. whole: -0.26 (0.15), residues: 3066 helix: 1.81 (0.21), residues: 682 sheet: 0.25 (0.19), residues: 758 loop : -1.31 (0.15), residues: 1626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1039 TYR 0.018 0.001 TYR B1067 PHE 0.025 0.002 PHE A 906 TRP 0.015 0.001 TRP B 886 HIS 0.004 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00512 (26019) covalent geometry : angle 0.61029 (35412) SS BOND : bond 0.00335 ( 36) SS BOND : angle 1.56692 ( 72) hydrogen bonds : bond 0.05826 ( 964) hydrogen bonds : angle 5.12991 ( 2694) Misc. bond : bond 0.00014 ( 1) link_BETA1-4 : bond 0.00322 ( 33) link_BETA1-4 : angle 2.07146 ( 99) link_NAG-ASN : bond 0.00363 ( 48) link_NAG-ASN : angle 3.06539 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 51 time to evaluate : 0.935 Fit side-chains REVERT: A 153 MET cc_start: 0.5255 (pmm) cc_final: 0.4617 (pmm) REVERT: A 873 TYR cc_start: 0.9505 (OUTLIER) cc_final: 0.9211 (m-80) REVERT: A 1002 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8364 (tm-30) REVERT: C 212 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6916 (tt) outliers start: 29 outliers final: 12 residues processed: 79 average time/residue: 0.1359 time to fit residues: 19.3876 Evaluate side-chains 63 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 49 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 47 optimal weight: 6.9990 chunk 31 optimal weight: 20.0000 chunk 177 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 267 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 143 optimal weight: 20.0000 chunk 260 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 306 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 ASN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 484 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 = 0.3832 r_free = 0.3832 target = 0.079928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.050768 restraints weight = 107490.413| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.30 r_work: 0.2882 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 26137 Z= 0.199 Angle : 0.632 14.272 35727 Z= 0.306 Chirality : 0.047 0.567 4257 Planarity : 0.004 0.061 4476 Dihedral : 6.280 73.661 5040 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % Rotamer: Outliers : 1.14 % Allowed : 12.05 % Favored : 86.81 % 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 aren not related in a simple way. whole: -0.28 (0.15), residues: 3066 helix: 1.84 (0.21), residues: 682 sheet: 0.30 (0.19), residues: 741 loop : -1.35 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.017 0.001 TYR B1067 PHE 0.017 0.001 PHE C1121 TRP 0.014 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00465 (26019) covalent geometry : angle 0.59092 (35412) SS BOND : bond 0.00330 ( 36) SS BOND : angle 1.52912 ( 72) hydrogen bonds : bond 0.05614 ( 964) hydrogen bonds : angle 5.06818 ( 2694) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00329 ( 33) link_BETA1-4 : angle 2.07930 ( 99) link_NAG-ASN : bond 0.00341 ( 48) link_NAG-ASN : angle 3.02566 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 52 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.5001 (pmm) cc_final: 0.4356 (pmm) REVERT: A 360 ASN cc_start: 0.9295 (m110) cc_final: 0.8969 (p0) REVERT: A 560 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8921 (mp) REVERT: A 1002 GLN cc_start: 0.8699 (tm-30) cc_final: 0.8337 (tm-30) outliers start: 31 outliers final: 16 residues processed: 82 average time/residue: 0.1418 time to fit residues: 20.9505 Evaluate side-chains 65 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 149 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 178 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 277 optimal weight: 0.0070 chunk 37 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN ** C 484 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 = 0.3834 r_free = 0.3834 target = 0.080041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.050910 restraints weight = 108237.410| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 4.31 r_work: 0.2886 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26137 Z= 0.176 Angle : 0.624 14.896 35727 Z= 0.299 Chirality : 0.047 0.558 4257 Planarity : 0.004 0.061 4476 Dihedral : 6.159 70.573 5040 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.19 % Favored : 94.75 % Rotamer: Outliers : 1.25 % Allowed : 13.12 % Favored : 85.63 % 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 aren not related in a simple way. whole: -0.25 (0.15), residues: 3066 helix: 1.89 (0.21), residues: 683 sheet: 0.29 (0.19), residues: 740 loop : -1.34 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.016 0.001 TYR B1067 PHE 0.016 0.001 PHE C1121 TRP 0.015 0.001 TRP B 353 HIS 0.002 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00410 (26019) covalent geometry : angle 0.58312 (35412) SS BOND : bond 0.00341 ( 36) SS BOND : angle 1.42809 ( 72) hydrogen bonds : bond 0.05465 ( 964) hydrogen bonds : angle 4.99259 ( 2694) Misc. bond : bond 0.00001 ( 1) link_BETA1-4 : bond 0.00342 ( 33) link_BETA1-4 : angle 2.09079 ( 99) link_NAG-ASN : bond 0.00333 ( 48) link_NAG-ASN : angle 2.98148 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 50 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.5089 (pmm) cc_final: 0.4454 (pmm) REVERT: A 360 ASN cc_start: 0.9301 (m110) cc_final: 0.8988 (p0) REVERT: A 560 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8888 (mp) REVERT: A 873 TYR cc_start: 0.9511 (OUTLIER) cc_final: 0.9194 (m-80) REVERT: A 1002 GLN cc_start: 0.8696 (tm-30) cc_final: 0.8333 (tm-30) REVERT: C 1002 GLN cc_start: 0.9155 (mp10) cc_final: 0.8929 (mp10) outliers start: 34 outliers final: 19 residues processed: 83 average time/residue: 0.1401 time to fit residues: 21.1269 Evaluate side-chains 67 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 46 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 221 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 249 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 289 optimal weight: 4.9990 chunk 154 optimal weight: 0.0870 chunk 86 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 chunk 139 optimal weight: 1.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.081182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.052323 restraints weight = 107745.927| |-----------------------------------------------------------------------------| r_work (start): 0.3074 rms_B_bonded: 4.31 r_work: 0.2932 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26137 Z= 0.105 Angle : 0.575 15.197 35727 Z= 0.275 Chirality : 0.045 0.517 4257 Planarity : 0.004 0.061 4476 Dihedral : 5.845 67.424 5040 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.11 % Favored : 95.83 % Rotamer: Outliers : 0.81 % Allowed : 13.93 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.07 (0.15), residues: 3066 helix: 2.04 (0.21), residues: 683 sheet: 0.49 (0.20), residues: 717 loop : -1.25 (0.15), residues: 1666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 346 TYR 0.017 0.001 TYR C1067 PHE 0.020 0.001 PHE A 515 TRP 0.017 0.001 TRP B 353 HIS 0.001 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00227 (26019) covalent geometry : angle 0.53446 (35412) SS BOND : bond 0.00250 ( 36) SS BOND : angle 1.14768 ( 72) hydrogen bonds : bond 0.04598 ( 964) hydrogen bonds : angle 4.73135 ( 2694) Misc. bond : bond 0.00035 ( 1) link_BETA1-4 : bond 0.00427 ( 33) link_BETA1-4 : angle 2.10264 ( 99) link_NAG-ASN : bond 0.00377 ( 48) link_NAG-ASN : angle 2.86444 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 55 time to evaluate : 0.948 Fit side-chains REVERT: A 153 MET cc_start: 0.4894 (pmm) cc_final: 0.4245 (pmm) REVERT: A 360 ASN cc_start: 0.9275 (m110) cc_final: 0.8919 (p0) REVERT: A 560 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8883 (mp) REVERT: A 1002 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8144 (tp-100) REVERT: B 581 THR cc_start: 0.9331 (OUTLIER) cc_final: 0.9119 (p) REVERT: C 133 PHE cc_start: 0.8526 (m-80) cc_final: 0.8282 (m-80) outliers start: 22 outliers final: 12 residues processed: 75 average time/residue: 0.1444 time to fit residues: 19.5256 Evaluate side-chains 65 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 51 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 39 optimal weight: 30.0000 chunk 244 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 224 optimal weight: 0.0010 chunk 223 optimal weight: 3.9990 overall best weight: 2.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.080040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.050904 restraints weight = 107904.276| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 4.33 r_work: 0.2889 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 26137 Z= 0.189 Angle : 0.620 15.351 35727 Z= 0.298 Chirality : 0.046 0.554 4257 Planarity : 0.004 0.059 4476 Dihedral : 5.898 62.595 5040 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.38 % Favored : 94.55 % Rotamer: Outliers : 0.99 % Allowed : 14.26 % Favored : 84.75 % 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 aren not related in a simple way. whole: -0.14 (0.15), residues: 3066 helix: 1.99 (0.21), residues: 683 sheet: 0.39 (0.19), residues: 740 loop : -1.29 (0.15), residues: 1643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 346 TYR 0.017 0.001 TYR B1067 PHE 0.017 0.001 PHE A1089 TRP 0.016 0.001 TRP B 353 HIS 0.003 0.001 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.00441 (26019) covalent geometry : angle 0.58090 (35412) SS BOND : bond 0.00282 ( 36) SS BOND : angle 1.34058 ( 72) hydrogen bonds : bond 0.05352 ( 964) hydrogen bonds : angle 4.89323 ( 2694) Misc. bond : bond 0.00004 ( 1) link_BETA1-4 : bond 0.00336 ( 33) link_BETA1-4 : angle 2.09206 ( 99) link_NAG-ASN : bond 0.00332 ( 48) link_NAG-ASN : angle 2.92537 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.948 Fit side-chains REVERT: A 153 MET cc_start: 0.5060 (pmm) cc_final: 0.4364 (pmm) REVERT: A 360 ASN cc_start: 0.9275 (m110) cc_final: 0.8924 (p0) REVERT: A 560 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8832 (mp) REVERT: A 873 TYR cc_start: 0.9498 (OUTLIER) cc_final: 0.9194 (m-80) REVERT: A 985 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7099 (t0) REVERT: A 1002 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8311 (tm-30) REVERT: C 133 PHE cc_start: 0.8575 (m-80) cc_final: 0.8317 (m-80) REVERT: C 1002 GLN cc_start: 0.9147 (mp10) cc_final: 0.8912 (mp10) outliers start: 27 outliers final: 20 residues processed: 78 average time/residue: 0.1378 time to fit residues: 19.5472 Evaluate side-chains 72 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 49 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 203 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 241 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 103 optimal weight: 30.0000 chunk 189 optimal weight: 2.9990 chunk 305 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 246 optimal weight: 30.0000 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 HIS ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.080349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.051275 restraints weight = 108186.451| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 4.35 r_work: 0.2902 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26137 Z= 0.150 Angle : 0.598 15.044 35727 Z= 0.287 Chirality : 0.046 0.532 4257 Planarity : 0.004 0.094 4476 Dihedral : 5.859 60.907 5040 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.92 % Favored : 95.01 % Rotamer: Outliers : 1.18 % Allowed : 14.48 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.15), residues: 3066 helix: 2.03 (0.21), residues: 677 sheet: 0.41 (0.19), residues: 742 loop : -1.30 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 346 TYR 0.015 0.001 TYR B1067 PHE 0.015 0.001 PHE C1121 TRP 0.039 0.001 TRP B 353 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00348 (26019) covalent geometry : angle 0.55816 (35412) SS BOND : bond 0.00261 ( 36) SS BOND : angle 1.25679 ( 72) hydrogen bonds : bond 0.05096 ( 964) hydrogen bonds : angle 4.80853 ( 2694) Misc. bond : bond 0.00011 ( 1) link_BETA1-4 : bond 0.00351 ( 33) link_BETA1-4 : angle 2.09721 ( 99) link_NAG-ASN : bond 0.00322 ( 48) link_NAG-ASN : angle 2.88736 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 52 time to evaluate : 0.968 Fit side-chains REVERT: A 153 MET cc_start: 0.4894 (pmm) cc_final: 0.4225 (pmm) REVERT: A 360 ASN cc_start: 0.9278 (m110) cc_final: 0.8948 (p0) REVERT: A 560 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8819 (mp) REVERT: A 873 TYR cc_start: 0.9498 (OUTLIER) cc_final: 0.9214 (m-80) REVERT: A 985 ASP cc_start: 0.7379 (OUTLIER) cc_final: 0.7118 (t0) REVERT: A 1002 GLN cc_start: 0.8676 (tm-30) cc_final: 0.8286 (tm-30) REVERT: C 153 MET cc_start: 0.0053 (ttt) cc_final: -0.0200 (tpp) REVERT: C 346 ARG cc_start: 0.8328 (mmm160) cc_final: 0.8116 (mmp80) REVERT: C 1002 GLN cc_start: 0.9138 (mp10) cc_final: 0.8906 (mp10) outliers start: 32 outliers final: 21 residues processed: 83 average time/residue: 0.1398 time to fit residues: 20.9579 Evaluate side-chains 72 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 48 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 200 optimal weight: 0.3980 chunk 112 optimal weight: 5.9990 chunk 9 optimal weight: 2.9990 chunk 74 optimal weight: 0.0270 chunk 4 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 75 optimal weight: 0.9990 chunk 202 optimal weight: 0.9980 chunk 249 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.080839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.052002 restraints weight = 107281.229| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.31 r_work: 0.2920 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26137 Z= 0.115 Angle : 0.577 14.140 35727 Z= 0.276 Chirality : 0.045 0.514 4257 Planarity : 0.004 0.077 4476 Dihedral : 5.729 58.206 5040 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.63 % Favored : 95.30 % Rotamer: Outliers : 0.88 % Allowed : 14.66 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.15), residues: 3066 helix: 2.05 (0.21), residues: 683 sheet: 0.48 (0.19), residues: 716 loop : -1.27 (0.15), residues: 1667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG C 346 TYR 0.016 0.001 TYR C1067 PHE 0.013 0.001 PHE A1121 TRP 0.042 0.001 TRP B 353 HIS 0.002 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00260 (26019) covalent geometry : angle 0.53683 (35412) SS BOND : bond 0.00237 ( 36) SS BOND : angle 1.17325 ( 72) hydrogen bonds : bond 0.04706 ( 964) hydrogen bonds : angle 4.68461 ( 2694) Misc. bond : bond 0.00059 ( 1) link_BETA1-4 : bond 0.00390 ( 33) link_BETA1-4 : angle 2.10318 ( 99) link_NAG-ASN : bond 0.00338 ( 48) link_NAG-ASN : angle 2.85170 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6132 Ramachandran restraints generated. 3066 Oldfield, 0 Emsley, 3066 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.870 Fit side-chains REVERT: A 153 MET cc_start: 0.4875 (pmm) cc_final: 0.4220 (pmm) REVERT: A 360 ASN cc_start: 0.9272 (m110) cc_final: 0.8946 (p0) REVERT: A 560 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8857 (mp) REVERT: A 869 MET cc_start: 0.9230 (mtt) cc_final: 0.8997 (mtm) REVERT: A 985 ASP cc_start: 0.7414 (OUTLIER) cc_final: 0.7117 (t0) REVERT: A 1002 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8155 (tp-100) REVERT: C 153 MET cc_start: -0.0093 (ttt) cc_final: -0.0320 (tpp) REVERT: C 360 ASN cc_start: 0.9140 (t0) cc_final: 0.8482 (m-40) REVERT: C 1002 GLN cc_start: 0.9116 (mp10) cc_final: 0.8874 (mp10) outliers start: 24 outliers final: 20 residues processed: 77 average time/residue: 0.1320 time to fit residues: 18.5029 Evaluate side-chains 75 residues out of total 2721 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 53 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 985 ASP Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1104 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 194 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 109 optimal weight: 9.9990 chunk 200 optimal weight: 0.4980 chunk 172 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 240 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 0.6980 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 641 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.080359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.051351 restraints weight = 107575.921| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 4.29 r_work: 0.2894 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 26137 Z= 0.154 Angle : 0.590 12.912 35727 Z= 0.283 Chirality : 0.046 0.530 4257 Planarity : 0.004 0.059 4476 Dihedral : 5.757 57.974 5040 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.89 % Favored : 95.04 % Rotamer: Outliers : 0.88 % Allowed : 14.85 % Favored : 84.27 % 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 aren not related in a simple way. whole: -0.10 (0.15), residues: 3066 helix: 2.04 (0.21), residues: 683 sheet: 0.45 (0.19), residues: 742 loop : -1.29 (0.15), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 346 TYR 0.016 0.001 TYR B1067 PHE 0.015 0.001 PHE C1121 TRP 0.040 0.001 TRP B 353 HIS 0.003 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00359 (26019) covalent geometry : angle 0.54955 (35412) SS BOND : bond 0.00266 ( 36) SS BOND : angle 1.23459 ( 72) hydrogen bonds : bond 0.04995 ( 964) hydrogen bonds : angle 4.75395 ( 2694) Misc. bond : bond 0.00006 ( 1) link_BETA1-4 : bond 0.00327 ( 33) link_BETA1-4 : angle 2.10651 ( 99) link_NAG-ASN : bond 0.00313 ( 48) link_NAG-ASN : angle 2.85928 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8199.08 seconds wall clock time: 140 minutes 49.94 seconds (8449.94 seconds total)