Starting phenix.real_space_refine on Sat Mar 7 08:39:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v82_31787/03_2026/7v82_31787.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v82_31787/03_2026/7v82_31787.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v82_31787/03_2026/7v82_31787.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v82_31787/03_2026/7v82_31787.map" model { file = "/net/cci-nas-00/data/ceres_data/7v82_31787/03_2026/7v82_31787.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v82_31787/03_2026/7v82_31787.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 198 5.16 5 C 25566 2.51 5 N 6525 2.21 5 O 7803 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40092 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "C" Number of atoms: 8110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8110 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 52, 'TRANS': 985} Chain breaks: 7 Chain: "E" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} 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: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.11, per 1000 atoms: 0.23 Number of scatterers: 40092 At special positions: 0 Unit cell: (167.2, 181.5, 242, 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 198 16.00 O 7803 8.00 N 6525 7.00 C 25566 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 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 291 " - pdb=" SG CYS B 301 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 542 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.02 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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=0, symmetry=0 Links applied BETA1-4 " 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-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 234 " " NAG A2005 " - " ASN A 603 " " NAG A2006 " - " ASN A 657 " " NAG A2007 " - " ASN A 20 " " NAG A2008 " - " ASN A 188 " " 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 B2007 " - " ASN B 20 " " NAG B2008 " - " ASN B 188 " " NAG C2001 " - " ASN C 61 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 343 " " NAG C2006 " - " ASN C 603 " " NAG C2007 " - " ASN C 657 " " NAG C2008 " - " ASN C 20 " " NAG C2009 " - " ASN C 188 " " NAG D1001 " - " ASN D 53 " " NAG G 1 " - " ASN A 282 " " NAG H 1 " - " ASN A 331 " " NAG I 1 " - " ASN A 343 " " NAG J 1 " - " ASN A 616 " " NAG K 1 " - " ASN A 709 " " NAG L 1 " - " ASN A 717 " " NAG M 1 " - " ASN A 801 " " NAG N 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 122 " " NAG R 1 " - " ASN B 282 " " NAG S 1 " - " ASN B 331 " " NAG T 1 " - " ASN B 616 " " NAG U 1 " - " ASN B 709 " " NAG V 1 " - " ASN B 717 " " NAG W 1 " - " ASN B 801 " " NAG X 1 " - " ASN B1074 " " NAG Y 1 " - " ASN B1098 " " NAG Z 1 " - " ASN B1134 " " NAG a 1 " - " ASN C 282 " " NAG b 1 " - " ASN C 331 " " NAG d 1 " - " ASN C 709 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " Time building additional restraints: 3.31 Conformation dependent library (CDL) restraints added in 1.6 seconds 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9210 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 51 sheets defined 37.9% alpha, 15.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 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: 4.343A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.059A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 783 removed outlier: 3.513A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.688A 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 908 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.541A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 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: 3.788A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.550A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.657A 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 337 through 343 removed outlier: 3.652A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.686A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.786A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 4.166A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.611A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.943A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.965A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 767 " --> pdb=" O LEU B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.592A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.247A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) 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 982 removed outlier: 3.550A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.287A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.905A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.534A pdb=" N GLU C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.519A pdb=" N CYS C 743 " --> pdb=" O THR C 739 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.042A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 783 Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.557A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) 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 908 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.606A 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 984 removed outlier: 3.720A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1034 removed outlier: 4.432A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU C1034 " --> pdb=" O SER C1030 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 removed outlier: 4.072A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 53 removed outlier: 3.519A pdb=" N LYS E 26 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 57 No H-bonds generated for 'chain 'E' and resid 55 through 57' Processing helix chain 'E' and resid 58 through 80 removed outlier: 4.230A pdb=" N MET E 62 " --> pdb=" O ASN E 58 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU E 75 " --> pdb=" O ALA E 71 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN E 76 " --> pdb=" O PHE E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 102 removed outlier: 3.627A pdb=" N LEU E 100 " --> pdb=" O GLN E 96 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN E 102 " --> pdb=" O GLN E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.910A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 172 removed outlier: 3.647A pdb=" N VAL E 172 " --> pdb=" O TRP E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 194 removed outlier: 3.671A pdb=" N TYR E 180 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 205 Processing helix chain 'E' and resid 218 through 224 removed outlier: 3.921A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 218 through 224' Processing helix chain 'E' and resid 234 through 252 removed outlier: 3.708A pdb=" N GLU E 238 " --> pdb=" O LYS E 234 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 301 Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.601A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 331 Processing helix chain 'E' and resid 365 through 385 removed outlier: 3.810A pdb=" N TYR E 385 " --> pdb=" O TYR E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 393 Processing helix chain 'E' and resid 398 through 413 removed outlier: 4.268A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 421 removed outlier: 3.688A pdb=" N ILE E 421 " --> pdb=" O HIS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.621A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 474 through 485 Processing helix chain 'E' and resid 503 through 507 removed outlier: 3.704A pdb=" N VAL E 506 " --> pdb=" O LEU E 503 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N SER E 507 " --> pdb=" O PHE E 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 503 through 507' Processing helix chain 'E' and resid 513 through 532 removed outlier: 4.180A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 559 removed outlier: 3.661A pdb=" N LYS E 553 " --> pdb=" O GLU E 549 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 560 through 564 removed outlier: 3.640A pdb=" N GLU E 564 " --> pdb=" O GLY E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 570 Processing helix chain 'E' and resid 582 through 588 removed outlier: 3.777A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE E 588 " --> pdb=" O LEU E 584 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 597 removed outlier: 3.591A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 53 removed outlier: 3.541A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR D 27 " --> pdb=" O GLU D 23 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU D 35 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 80 removed outlier: 3.928A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLN D 76 " --> pdb=" O PHE D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.573A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 Processing helix chain 'D' and resid 147 through 154 Processing helix chain 'D' and resid 158 through 171 Processing helix chain 'D' and resid 175 through 194 removed outlier: 3.960A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.677A pdb=" N TYR D 202 " --> pdb=" O ASP D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 227 removed outlier: 4.035A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N GLU D 227 " --> pdb=" O ILE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 232 No H-bonds generated for 'chain 'D' and resid 230 through 232' Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.581A pdb=" N GLY D 268 " --> pdb=" O HIS D 265 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 removed outlier: 4.091A pdb=" N PHE D 314 " --> pdb=" O GLU D 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.750A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.751A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 removed outlier: 3.603A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.525A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 473 through 485 Processing helix chain 'D' and resid 503 through 507 removed outlier: 3.884A pdb=" N SER D 507 " --> pdb=" O PHE D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 532 removed outlier: 3.695A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG D 518 " --> pdb=" O ARG D 514 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLN D 524 " --> pdb=" O LEU D 520 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.679A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 560 through 564 removed outlier: 3.564A pdb=" N SER D 563 " --> pdb=" O LEU D 560 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N GLU D 564 " --> pdb=" O GLY D 561 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 560 through 564' Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 582 through 588 removed outlier: 3.714A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 597 removed outlier: 3.505A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 53 removed outlier: 4.293A pdb=" N THR F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 80 removed outlier: 3.808A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASN F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU F 75 " --> pdb=" O ALA F 71 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 76 " --> pdb=" O PHE F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 101 Processing helix chain 'F' and resid 109 through 128 removed outlier: 3.572A pdb=" N SER F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 154 removed outlier: 3.755A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 158 through 169 removed outlier: 3.715A pdb=" N ALA F 164 " --> pdb=" O GLU F 160 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 194 removed outlier: 3.951A pdb=" N LEU F 179 " --> pdb=" O GLN F 175 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.844A pdb=" N TYR F 202 " --> pdb=" O ASP F 198 " (cutoff:3.500A) Processing helix chain 'F' and resid 218 through 229 removed outlier: 3.867A pdb=" N LEU F 222 " --> pdb=" O SER F 218 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE F 223 " --> pdb=" O ARG F 219 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N GLU F 227 " --> pdb=" O ILE F 223 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS F 228 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR F 229 " --> pdb=" O ASP F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 232 No H-bonds generated for 'chain 'F' and resid 230 through 232' Processing helix chain 'F' and resid 233 through 252 Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 301 Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.665A pdb=" N LYS F 313 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE F 314 " --> pdb=" O GLU F 310 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N PHE F 315 " --> pdb=" O ALA F 311 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N VAL F 316 " --> pdb=" O GLU F 312 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 331 Processing helix chain 'F' and resid 365 through 385 Processing helix chain 'F' and resid 386 through 388 No H-bonds generated for 'chain 'F' and resid 386 through 388' Processing helix chain 'F' and resid 389 through 393 removed outlier: 3.565A pdb=" N ARG F 393 " --> pdb=" O PHE F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 removed outlier: 3.867A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 431 through 447 removed outlier: 4.290A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL F 447 " --> pdb=" O ALA F 443 " (cutoff:3.500A) Processing helix chain 'F' and resid 449 through 465 Processing helix chain 'F' and resid 474 through 485 Processing helix chain 'F' and resid 503 through 507 removed outlier: 3.633A pdb=" N VAL F 506 " --> pdb=" O LEU F 503 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER F 507 " --> pdb=" O PHE F 504 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 503 through 507' Processing helix chain 'F' and resid 513 through 532 removed outlier: 3.782A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 547 through 559 removed outlier: 3.713A pdb=" N GLY F 551 " --> pdb=" O SER F 547 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN F 552 " --> pdb=" O THR F 548 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS F 553 " --> pdb=" O GLU F 549 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 559 " --> pdb=" O PHE F 555 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 570 Processing helix chain 'F' and resid 582 through 588 removed outlier: 3.672A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 597 removed outlier: 3.556A pdb=" N ASP F 597 " --> pdb=" O THR F 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.732A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.533A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.458A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.454A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ILE C 587 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.954A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.027A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 573 through 576 removed outlier: 3.984A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.961A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.627A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB4, first strand: chain 'A' and resid 717 through 728 removed outlier: 6.019A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.452A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.723A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.840A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.335A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.054A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 134 through 135 removed outlier: 3.799A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.360A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.558A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 326 removed outlier: 3.670A pdb=" N VAL B 576 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.567A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.915A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 712 Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.119A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.725A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.042A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.286A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.568A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.896A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.770A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE C 105 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 11.496A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 10.178A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.431A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.803A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.052A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.684A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.941A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AE6, first strand: chain 'C' and resid 717 through 728 removed outlier: 5.991A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.633A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.950A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'E' and resid 132 through 133 Processing sheet with id=AF2, first strand: chain 'E' and resid 347 through 350 Processing sheet with id=AF3, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.138A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 132 through 133 Processing sheet with id=AF6, first strand: chain 'F' and resid 347 through 352 removed outlier: 6.005A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) 1670 hydrogen bonds defined for protein. 4686 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: 9.16 Time building geometry restraints manager: 4.42 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: 12688 1.34 - 1.46: 10170 1.46 - 1.58: 17920 1.58 - 1.70: 1 1.70 - 1.83: 288 Bond restraints: 41067 Sorted by residual: bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.33e+00 bond pdb=" C1 NAG b 1 " pdb=" O5 NAG b 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.18e+00 bond pdb=" CB PRO E 492 " pdb=" CG PRO E 492 " ideal model delta sigma weight residual 1.492 1.599 -0.107 5.00e-02 4.00e+02 4.61e+00 bond pdb=" C1 NAG B2008 " pdb=" O5 NAG B2008 " ideal model delta sigma weight residual 1.406 1.447 -0.041 2.00e-02 2.50e+03 4.26e+00 ... (remaining 41062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 54575 1.85 - 3.71: 1130 3.71 - 5.56: 124 5.56 - 7.42: 23 7.42 - 9.27: 8 Bond angle restraints: 55860 Sorted by residual: angle pdb=" C LEU C 984 " pdb=" N ASP C 985 " pdb=" CA ASP C 985 " ideal model delta sigma weight residual 120.67 129.49 -8.82 1.34e+00 5.57e-01 4.34e+01 angle pdb=" CA PRO E 492 " pdb=" N PRO E 492 " pdb=" CD PRO E 492 " ideal model delta sigma weight residual 112.00 104.52 7.48 1.40e+00 5.10e-01 2.85e+01 angle pdb=" C GLU E 375 " pdb=" N MET E 376 " pdb=" CA MET E 376 " ideal model delta sigma weight residual 121.58 114.21 7.37 1.95e+00 2.63e-01 1.43e+01 angle pdb=" N THR B 618 " pdb=" CA THR B 618 " pdb=" C THR B 618 " ideal model delta sigma weight residual 114.04 109.55 4.49 1.24e+00 6.50e-01 1.31e+01 angle pdb=" N ILE F 21 " pdb=" CA ILE F 21 " pdb=" C ILE F 21 " ideal model delta sigma weight residual 113.42 109.28 4.14 1.17e+00 7.31e-01 1.25e+01 ... (remaining 55855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.93: 23900 24.93 - 49.85: 1294 49.85 - 74.78: 156 74.78 - 99.71: 50 99.71 - 124.64: 34 Dihedral angle restraints: 25434 sinusoidal: 11115 harmonic: 14319 Sorted by residual: 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 93.00 -177.52 -89.48 1 1.00e+01 1.00e-02 9.51e+01 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 -178.04 -88.96 1 1.00e+01 1.00e-02 9.43e+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 93.00 177.81 -84.81 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 25431 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 6077 0.096 - 0.192: 306 0.192 - 0.288: 5 0.288 - 0.385: 5 0.385 - 0.481: 1 Chirality restraints: 6394 Sorted by residual: chirality pdb=" C1 NAG K 1 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG K 1 " pdb=" O5 NAG K 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.78e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C 282 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.53e+00 ... (remaining 6391 not shown) Planarity restraints: 7163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 491 " 0.091 5.00e-02 4.00e+02 1.34e-01 2.86e+01 pdb=" N PRO E 492 " -0.231 5.00e-02 4.00e+02 pdb=" CA PRO E 492 " 0.070 5.00e-02 4.00e+02 pdb=" CD PRO E 492 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1074 " 0.030 2.00e-02 2.50e+03 2.79e-02 9.72e+00 pdb=" CG ASN C1074 " -0.034 2.00e-02 2.50e+03 pdb=" OD1 ASN C1074 " 0.005 2.00e-02 2.50e+03 pdb=" ND2 ASN C1074 " -0.031 2.00e-02 2.50e+03 pdb=" C1 NAG g 1 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.046 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO C 987 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.039 5.00e-02 4.00e+02 ... (remaining 7160 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1169 2.70 - 3.25: 40074 3.25 - 3.80: 63496 3.80 - 4.35: 78915 4.35 - 4.90: 132798 Nonbonded interactions: 316452 Sorted by model distance: nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.150 3.040 nonbonded pdb=" O ASP B 442 " pdb=" ND2 ASN B 448 " model vdw 2.186 3.120 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.192 3.040 nonbonded pdb=" O ILE E 151 " pdb=" OG SER E 155 " model vdw 2.196 3.040 nonbonded pdb=" OD2 ASP B 796 " pdb=" O6 NAG K 1 " model vdw 2.200 3.040 ... (remaining 316447 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' selection = (chain 'C' and resid 14 through 2008) } ncs_group { reference = (chain 'D' and resid 19 through 614) selection = chain 'E' selection = chain 'F' } ncs_group { reference = 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.800 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: 0.040 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.970 Find NCS groups from input model: 1.330 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 41197 Z= 0.209 Angle : 0.650 13.793 56202 Z= 0.326 Chirality : 0.046 0.481 6394 Planarity : 0.004 0.134 7110 Dihedral : 15.217 124.636 16080 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.12), residues: 4848 helix: 1.24 (0.14), residues: 1592 sheet: 0.01 (0.18), residues: 747 loop : -1.40 (0.12), residues: 2509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.021 0.001 TYR A 873 PHE 0.040 0.001 PHE C 906 TRP 0.035 0.001 TRP C 886 HIS 0.013 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00461 (41067) covalent geometry : angle 0.62321 (55860) SS BOND : bond 0.00355 ( 48) SS BOND : angle 1.43973 ( 96) hydrogen bonds : bond 0.14104 ( 1670) hydrogen bonds : angle 5.94014 ( 4686) link_BETA1-4 : bond 0.00454 ( 29) link_BETA1-4 : angle 2.69391 ( 87) link_NAG-ASN : bond 0.00410 ( 53) link_NAG-ASN : angle 2.75207 ( 159) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5302 (ppp) cc_final: 0.5060 (pp-130) REVERT: E 163 TRP cc_start: 0.8195 (m100) cc_final: 0.7553 (t60) REVERT: E 360 MET cc_start: 0.1436 (ptm) cc_final: -0.0109 (tpt) REVERT: E 480 MET cc_start: 0.1033 (mpp) cc_final: 0.0387 (ttp) REVERT: D 366 MET cc_start: 0.5490 (tpt) cc_final: 0.5127 (tpp) REVERT: F 332 MET cc_start: 0.1101 (ppp) cc_final: 0.0296 (pmm) REVERT: F 366 MET cc_start: 0.1461 (tpt) cc_final: 0.1176 (mmm) REVERT: F 462 MET cc_start: 0.6590 (ptm) cc_final: 0.6124 (mmt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.7762 time to fit residues: 113.4861 Evaluate side-chains 107 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 40.0000 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 20.0000 chunk 455 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 8.9990 chunk 470 optimal weight: 50.0000 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 901 GLN ** C 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN E 195 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 505 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.122148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.073994 restraints weight = 181420.566| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 6.39 r_work: 0.2834 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.0776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.135 41197 Z= 0.318 Angle : 0.692 10.871 56202 Z= 0.345 Chirality : 0.047 0.349 6394 Planarity : 0.004 0.073 7110 Dihedral : 10.421 113.673 7029 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 0.28 % Allowed : 6.47 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.12), residues: 4848 helix: 1.12 (0.13), residues: 1606 sheet: -0.01 (0.18), residues: 749 loop : -1.43 (0.12), residues: 2493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1039 TYR 0.024 0.001 TYR F 385 PHE 0.033 0.002 PHE C 906 TRP 0.026 0.001 TRP C 886 HIS 0.014 0.001 HIS E 195 Details of bonding type rmsd covalent geometry : bond 0.00746 (41067) covalent geometry : angle 0.66913 (55860) SS BOND : bond 0.00412 ( 48) SS BOND : angle 1.81305 ( 96) hydrogen bonds : bond 0.06060 ( 1670) hydrogen bonds : angle 5.22765 ( 4686) link_BETA1-4 : bond 0.00433 ( 29) link_BETA1-4 : angle 2.16535 ( 87) link_NAG-ASN : bond 0.00603 ( 53) link_NAG-ASN : angle 2.70381 ( 159) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 1.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.6821 (ppp) cc_final: 0.6546 (pp-130) REVERT: C 153 MET cc_start: 0.7368 (tmm) cc_final: 0.7000 (tmm) REVERT: E 163 TRP cc_start: 0.8200 (m100) cc_final: 0.7924 (t60) REVERT: E 376 MET cc_start: 0.4459 (pmm) cc_final: 0.4018 (pmm) REVERT: D 332 MET cc_start: 0.5804 (pp-130) cc_final: 0.5445 (ppp) REVERT: F 366 MET cc_start: 0.2861 (tpt) cc_final: 0.2449 (mmm) REVERT: F 480 MET cc_start: 0.6248 (pp-130) cc_final: 0.5713 (pp-130) outliers start: 12 outliers final: 2 residues processed: 111 average time/residue: 0.7704 time to fit residues: 103.6775 Evaluate side-chains 109 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain D residue 249 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 276 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 320 optimal weight: 8.9990 chunk 42 optimal weight: 50.0000 chunk 185 optimal weight: 0.8980 chunk 300 optimal weight: 1.9990 chunk 217 optimal weight: 20.0000 chunk 254 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 157 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN C 360 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN C 926 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.082348 restraints weight = 180915.692| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 7.51 r_work: 0.2862 rms_B_bonded: 5.76 restraints_weight: 2.0000 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 41197 Z= 0.111 Angle : 0.570 12.074 56202 Z= 0.279 Chirality : 0.043 0.332 6394 Planarity : 0.004 0.071 7110 Dihedral : 9.304 113.813 7029 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.56 % Allowed : 8.61 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.28 (0.12), residues: 4848 helix: 1.33 (0.13), residues: 1609 sheet: 0.16 (0.18), residues: 740 loop : -1.37 (0.12), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 518 TYR 0.021 0.001 TYR F 385 PHE 0.014 0.001 PHE B1121 TRP 0.016 0.001 TRP E 610 HIS 0.005 0.001 HIS E 373 Details of bonding type rmsd covalent geometry : bond 0.00239 (41067) covalent geometry : angle 0.54823 (55860) SS BOND : bond 0.00322 ( 48) SS BOND : angle 1.19182 ( 96) hydrogen bonds : bond 0.04709 ( 1670) hydrogen bonds : angle 4.81146 ( 4686) link_BETA1-4 : bond 0.00526 ( 29) link_BETA1-4 : angle 2.21432 ( 87) link_NAG-ASN : bond 0.00417 ( 53) link_NAG-ASN : angle 2.37878 ( 159) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 153 MET cc_start: 0.5446 (ppp) cc_final: 0.5016 (pp-130) REVERT: B 1132 ILE cc_start: 0.9434 (OUTLIER) cc_final: 0.9185 (pp) REVERT: C 153 MET cc_start: 0.6817 (tmm) cc_final: 0.6108 (tmm) REVERT: E 163 TRP cc_start: 0.8164 (m100) cc_final: 0.7740 (t60) REVERT: E 480 MET cc_start: 0.2028 (ttt) cc_final: 0.1550 (tmm) REVERT: D 332 MET cc_start: 0.4516 (pp-130) cc_final: 0.3956 (ppp) REVERT: D 455 MET cc_start: 0.4427 (OUTLIER) cc_final: 0.4140 (pp-130) REVERT: D 480 MET cc_start: 0.4684 (ppp) cc_final: 0.4262 (pp-130) REVERT: F 332 MET cc_start: 0.3681 (OUTLIER) cc_final: 0.2994 (tmm) REVERT: F 366 MET cc_start: 0.2222 (tpt) cc_final: 0.1851 (mmm) REVERT: F 480 MET cc_start: 0.5348 (pp-130) cc_final: 0.4901 (pp-130) outliers start: 24 outliers final: 5 residues processed: 118 average time/residue: 0.7567 time to fit residues: 109.2202 Evaluate side-chains 112 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 104 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 286 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 438 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 3.9990 chunk 157 optimal weight: 0.9990 chunk 403 optimal weight: 20.0000 chunk 419 optimal weight: 20.0000 chunk 172 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 703 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN E 239 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 524 GLN F 81 GLN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 493 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.122806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.075528 restraints weight = 180529.677| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 6.14 r_work: 0.2866 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 41197 Z= 0.203 Angle : 0.595 9.793 56202 Z= 0.293 Chirality : 0.044 0.346 6394 Planarity : 0.004 0.072 7110 Dihedral : 8.690 114.480 7029 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.05 % Allowed : 9.89 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.12), residues: 4848 helix: 1.37 (0.13), residues: 1608 sheet: 0.09 (0.18), residues: 732 loop : -1.31 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1039 TYR 0.019 0.001 TYR B1067 PHE 0.018 0.001 PHE A1121 TRP 0.017 0.001 TRP F 610 HIS 0.013 0.001 HIS E 239 Details of bonding type rmsd covalent geometry : bond 0.00476 (41067) covalent geometry : angle 0.57307 (55860) SS BOND : bond 0.00333 ( 48) SS BOND : angle 1.38291 ( 96) hydrogen bonds : bond 0.05056 ( 1670) hydrogen bonds : angle 4.82603 ( 4686) link_BETA1-4 : bond 0.00507 ( 29) link_BETA1-4 : angle 2.20915 ( 87) link_NAG-ASN : bond 0.00449 ( 53) link_NAG-ASN : angle 2.41967 ( 159) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 106 time to evaluate : 1.387 Fit side-chains revert: symmetry clash REVERT: A 1039 ARG cc_start: 0.9448 (OUTLIER) cc_final: 0.8965 (ptm160) REVERT: B 108 THR cc_start: 0.8061 (OUTLIER) cc_final: 0.7775 (m) REVERT: B 153 MET cc_start: 0.6525 (ppp) cc_final: 0.6083 (pp-130) REVERT: B 984 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9132 (pp) REVERT: B 1132 ILE cc_start: 0.9451 (OUTLIER) cc_final: 0.9172 (pp) REVERT: C 153 MET cc_start: 0.7411 (tmm) cc_final: 0.6532 (tmm) REVERT: C 1040 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9358 (m) REVERT: E 163 TRP cc_start: 0.8163 (m100) cc_final: 0.7827 (t60) REVERT: E 480 MET cc_start: 0.1886 (ttt) cc_final: 0.1431 (tmm) REVERT: D 332 MET cc_start: 0.5040 (pp-130) cc_final: 0.4557 (ppp) REVERT: F 332 MET cc_start: 0.4072 (OUTLIER) cc_final: 0.3450 (tmm) REVERT: F 366 MET cc_start: 0.2414 (tpt) cc_final: 0.2095 (mmm) REVERT: F 480 MET cc_start: 0.5383 (pp-130) cc_final: 0.4969 (pp-130) outliers start: 45 outliers final: 14 residues processed: 136 average time/residue: 0.6946 time to fit residues: 116.0068 Evaluate side-chains 125 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 274 optimal weight: 0.8980 chunk 193 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 3.9990 chunk 273 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 482 optimal weight: 20.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN D 241 HIS ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 49 ASN ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.123751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.083324 restraints weight = 180781.737| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 6.90 r_work: 0.2879 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41197 Z= 0.107 Angle : 0.547 10.563 56202 Z= 0.268 Chirality : 0.043 0.349 6394 Planarity : 0.004 0.070 7110 Dihedral : 7.991 111.838 7029 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.02 % Allowed : 11.01 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.12), residues: 4848 helix: 1.48 (0.13), residues: 1612 sheet: 0.20 (0.19), residues: 739 loop : -1.26 (0.12), residues: 2497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 460 TYR 0.021 0.001 TYR F 385 PHE 0.014 0.001 PHE E 592 TRP 0.011 0.001 TRP D 165 HIS 0.004 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00234 (41067) covalent geometry : angle 0.52802 (55860) SS BOND : bond 0.00294 ( 48) SS BOND : angle 1.13323 ( 96) hydrogen bonds : bond 0.04287 ( 1670) hydrogen bonds : angle 4.61174 ( 4686) link_BETA1-4 : bond 0.00516 ( 29) link_BETA1-4 : angle 2.14967 ( 87) link_NAG-ASN : bond 0.00380 ( 53) link_NAG-ASN : angle 2.15240 ( 159) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 670 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8883 (pp) REVERT: A 1039 ARG cc_start: 0.9380 (OUTLIER) cc_final: 0.8853 (ptm160) REVERT: B 108 THR cc_start: 0.7910 (OUTLIER) cc_final: 0.7599 (m) REVERT: B 153 MET cc_start: 0.5796 (ppp) cc_final: 0.5264 (pp-130) REVERT: B 581 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8991 (p) REVERT: B 984 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9109 (pp) REVERT: B 1132 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9230 (pp) REVERT: C 153 MET cc_start: 0.7012 (tmm) cc_final: 0.5783 (tmm) REVERT: E 163 TRP cc_start: 0.8148 (m100) cc_final: 0.7782 (t60) REVERT: E 270 MET cc_start: 0.3580 (tpp) cc_final: 0.2074 (ptm) REVERT: E 480 MET cc_start: 0.2554 (ttt) cc_final: 0.1897 (tmm) REVERT: D 224 GLU cc_start: 0.8937 (mp0) cc_final: 0.8606 (pp20) REVERT: D 323 MET cc_start: 0.6676 (tmt) cc_final: 0.6239 (tmt) REVERT: D 327 PHE cc_start: 0.7986 (OUTLIER) cc_final: 0.7774 (t80) REVERT: D 332 MET cc_start: 0.5247 (pp-130) cc_final: 0.4653 (ppp) REVERT: D 408 MET cc_start: 0.5960 (mmp) cc_final: 0.5428 (tpt) REVERT: D 455 MET cc_start: 0.4318 (OUTLIER) cc_final: 0.4117 (pp-130) REVERT: D 480 MET cc_start: 0.4647 (ppp) cc_final: 0.4285 (pp-130) REVERT: D 536 GLU cc_start: 0.8171 (pm20) cc_final: 0.7639 (tm-30) REVERT: F 332 MET cc_start: 0.3872 (OUTLIER) cc_final: 0.3071 (tmm) REVERT: F 366 MET cc_start: 0.2804 (tpt) cc_final: 0.2342 (mmm) outliers start: 44 outliers final: 15 residues processed: 147 average time/residue: 0.7012 time to fit residues: 126.6165 Evaluate side-chains 132 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 670 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 323 optimal weight: 50.0000 chunk 481 optimal weight: 50.0000 chunk 120 optimal weight: 3.9990 chunk 407 optimal weight: 50.0000 chunk 141 optimal weight: 50.0000 chunk 393 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 304 optimal weight: 1.9990 chunk 389 optimal weight: 50.0000 chunk 377 optimal weight: 9.9990 overall best weight: 8.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 675 GLN A 955 ASN C 360 ASN C 641 ASN E 305 GLN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.120797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.072305 restraints weight = 183748.318| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 6.12 r_work: 0.2794 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.196 41197 Z= 0.547 Angle : 0.846 12.781 56202 Z= 0.420 Chirality : 0.052 0.389 6394 Planarity : 0.005 0.075 7110 Dihedral : 8.491 116.634 7029 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.48 % Favored : 93.50 % Rotamer: Outliers : 1.58 % Allowed : 12.06 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.68 (0.12), residues: 4848 helix: 0.94 (0.13), residues: 1614 sheet: -0.21 (0.18), residues: 722 loop : -1.49 (0.12), residues: 2512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1091 TYR 0.027 0.002 TYR B 91 PHE 0.035 0.002 PHE A1121 TRP 0.026 0.001 TRP A 886 HIS 0.009 0.002 HIS B1088 Details of bonding type rmsd covalent geometry : bond 0.01277 (41067) covalent geometry : angle 0.82452 (55860) SS BOND : bond 0.00518 ( 48) SS BOND : angle 2.27525 ( 96) hydrogen bonds : bond 0.06710 ( 1670) hydrogen bonds : angle 5.30358 ( 4686) link_BETA1-4 : bond 0.00854 ( 29) link_BETA1-4 : angle 2.33864 ( 87) link_NAG-ASN : bond 0.00995 ( 53) link_NAG-ASN : angle 2.88403 ( 159) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 107 time to evaluate : 1.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.9229 (tt0) cc_final: 0.8978 (tm-30) REVERT: B 108 THR cc_start: 0.8115 (OUTLIER) cc_final: 0.7845 (m) REVERT: B 153 MET cc_start: 0.6676 (ppp) cc_final: 0.6154 (pp-130) REVERT: B 581 THR cc_start: 0.9223 (OUTLIER) cc_final: 0.8983 (p) REVERT: B 984 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9054 (pp) REVERT: B 1132 ILE cc_start: 0.9548 (OUTLIER) cc_final: 0.9332 (pp) REVERT: C 153 MET cc_start: 0.7610 (tmm) cc_final: 0.6747 (tmm) REVERT: C 581 THR cc_start: 0.9099 (OUTLIER) cc_final: 0.8709 (p) REVERT: C 984 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8830 (pp) REVERT: E 163 TRP cc_start: 0.8142 (m100) cc_final: 0.7821 (t60) REVERT: E 480 MET cc_start: 0.2042 (ttt) cc_final: 0.1527 (tmm) REVERT: D 323 MET cc_start: 0.7215 (tmt) cc_final: 0.6908 (tmt) REVERT: D 332 MET cc_start: 0.5175 (pp-130) cc_final: 0.4694 (ppp) REVERT: D 408 MET cc_start: 0.6215 (mmp) cc_final: 0.5575 (tpt) REVERT: F 366 MET cc_start: 0.2659 (tpt) cc_final: 0.2166 (mmm) REVERT: F 480 MET cc_start: 0.5528 (pp-130) cc_final: 0.5111 (pp-130) outliers start: 68 outliers final: 28 residues processed: 161 average time/residue: 0.6321 time to fit residues: 127.8195 Evaluate side-chains 138 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 104 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 984 LEU Chi-restraints excluded: chain C residue 1039 ARG Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 260 optimal weight: 0.9990 chunk 206 optimal weight: 30.0000 chunk 198 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 chunk 465 optimal weight: 50.0000 chunk 344 optimal weight: 30.0000 chunk 449 optimal weight: 50.0000 chunk 145 optimal weight: 40.0000 chunk 430 optimal weight: 20.0000 chunk 156 optimal weight: 0.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN E 397 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.121868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.073392 restraints weight = 180525.864| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 6.35 r_work: 0.2823 rms_B_bonded: 5.35 restraints_weight: 2.0000 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.126 41197 Z= 0.304 Angle : 0.678 11.634 56202 Z= 0.334 Chirality : 0.046 0.379 6394 Planarity : 0.004 0.074 7110 Dihedral : 8.107 115.111 7029 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 1.49 % Allowed : 12.78 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.55 (0.12), residues: 4848 helix: 1.05 (0.13), residues: 1632 sheet: -0.11 (0.18), residues: 718 loop : -1.46 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 460 TYR 0.021 0.001 TYR B1067 PHE 0.024 0.002 PHE A1121 TRP 0.015 0.001 TRP A 886 HIS 0.006 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00710 (41067) covalent geometry : angle 0.65593 (55860) SS BOND : bond 0.00433 ( 48) SS BOND : angle 1.78752 ( 96) hydrogen bonds : bond 0.05737 ( 1670) hydrogen bonds : angle 5.05704 ( 4686) link_BETA1-4 : bond 0.00467 ( 29) link_BETA1-4 : angle 2.19023 ( 87) link_NAG-ASN : bond 0.00563 ( 53) link_NAG-ASN : angle 2.56418 ( 159) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 106 time to evaluate : 1.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9029 (p) REVERT: A 1039 ARG cc_start: 0.9499 (OUTLIER) cc_final: 0.8936 (ptm160) REVERT: A 1132 ILE cc_start: 0.9430 (OUTLIER) cc_final: 0.9196 (tp) REVERT: B 108 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.8012 (m) REVERT: B 153 MET cc_start: 0.6995 (ppp) cc_final: 0.6542 (pp-130) REVERT: B 581 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8992 (p) REVERT: B 984 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9110 (pp) REVERT: B 1132 ILE cc_start: 0.9514 (OUTLIER) cc_final: 0.9281 (pp) REVERT: C 153 MET cc_start: 0.7656 (tmm) cc_final: 0.6895 (tmm) REVERT: C 242 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9096 (pp) REVERT: C 581 THR cc_start: 0.9052 (OUTLIER) cc_final: 0.8669 (p) REVERT: E 163 TRP cc_start: 0.8162 (m100) cc_final: 0.7892 (t60) REVERT: E 270 MET cc_start: 0.3543 (tpp) cc_final: 0.2173 (ptm) REVERT: E 480 MET cc_start: 0.2276 (ttt) cc_final: 0.1711 (tmm) REVERT: D 332 MET cc_start: 0.5796 (pp-130) cc_final: 0.5361 (ppp) REVERT: D 408 MET cc_start: 0.6015 (mmp) cc_final: 0.5464 (tpt) REVERT: D 455 MET cc_start: 0.3958 (pp-130) cc_final: 0.3671 (pp-130) REVERT: D 474 MET cc_start: 0.2559 (tmt) cc_final: 0.2340 (tmt) REVERT: D 480 MET cc_start: 0.4619 (ppp) cc_final: 0.4295 (pp-130) REVERT: F 332 MET cc_start: 0.4291 (OUTLIER) cc_final: 0.2931 (ppp) REVERT: F 366 MET cc_start: 0.2678 (tpt) cc_final: 0.2157 (mmm) outliers start: 64 outliers final: 24 residues processed: 159 average time/residue: 0.6142 time to fit residues: 122.2949 Evaluate side-chains 137 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 103 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 549 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 469 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 chunk 362 optimal weight: 50.0000 chunk 402 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 405 optimal weight: 8.9990 chunk 72 optimal weight: 0.6980 chunk 251 optimal weight: 8.9990 chunk 424 optimal weight: 0.9980 chunk 341 optimal weight: 9.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** 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 = 0.4460 r_free = 0.4460 target = 0.122555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.074308 restraints weight = 180157.354| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 6.09 r_work: 0.2867 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 41197 Z= 0.198 Angle : 0.621 11.529 56202 Z= 0.304 Chirality : 0.044 0.362 6394 Planarity : 0.004 0.073 7110 Dihedral : 7.612 112.123 7029 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 1.16 % Allowed : 13.62 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.12), residues: 4848 helix: 1.22 (0.13), residues: 1629 sheet: -0.03 (0.19), residues: 725 loop : -1.37 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1039 TYR 0.019 0.001 TYR F 385 PHE 0.018 0.001 PHE A1121 TRP 0.012 0.001 TRP A 886 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00462 (41067) covalent geometry : angle 0.60063 (55860) SS BOND : bond 0.00380 ( 48) SS BOND : angle 1.51063 ( 96) hydrogen bonds : bond 0.05088 ( 1670) hydrogen bonds : angle 4.86566 ( 4686) link_BETA1-4 : bond 0.00436 ( 29) link_BETA1-4 : angle 2.15172 ( 87) link_NAG-ASN : bond 0.00406 ( 53) link_NAG-ASN : angle 2.37685 ( 159) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 107 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9051 (p) REVERT: A 1039 ARG cc_start: 0.9437 (OUTLIER) cc_final: 0.8940 (ptm160) REVERT: B 108 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7844 (m) REVERT: B 153 MET cc_start: 0.6413 (ppp) cc_final: 0.5896 (pp-130) REVERT: B 563 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8168 (mt0) REVERT: B 581 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 984 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9035 (pp) REVERT: B 1132 ILE cc_start: 0.9495 (OUTLIER) cc_final: 0.9201 (tt) REVERT: C 153 MET cc_start: 0.7445 (tmm) cc_final: 0.6361 (tmm) REVERT: C 581 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8666 (p) REVERT: C 1040 VAL cc_start: 0.9549 (OUTLIER) cc_final: 0.9338 (m) REVERT: E 163 TRP cc_start: 0.8140 (m100) cc_final: 0.7869 (t60) REVERT: E 270 MET cc_start: 0.3864 (tpp) cc_final: 0.2590 (ptm) REVERT: E 480 MET cc_start: 0.2616 (ttt) cc_final: 0.2015 (tmm) REVERT: E 610 TRP cc_start: 0.6443 (OUTLIER) cc_final: 0.6172 (p-90) REVERT: D 224 GLU cc_start: 0.8982 (mp0) cc_final: 0.8677 (pp20) REVERT: D 332 MET cc_start: 0.5894 (pp-130) cc_final: 0.5375 (ppp) REVERT: D 408 MET cc_start: 0.5721 (mmp) cc_final: 0.5221 (tpt) REVERT: D 455 MET cc_start: 0.3873 (pp-130) cc_final: 0.3609 (pp-130) REVERT: D 480 MET cc_start: 0.5091 (ppp) cc_final: 0.4769 (pp-130) REVERT: D 536 GLU cc_start: 0.8303 (mp0) cc_final: 0.7972 (tm-30) REVERT: F 332 MET cc_start: 0.4316 (OUTLIER) cc_final: 0.2974 (ppp) REVERT: F 366 MET cc_start: 0.2886 (tpt) cc_final: 0.2388 (mmm) REVERT: F 480 MET cc_start: 0.6074 (pp-130) cc_final: 0.5733 (pp-130) outliers start: 50 outliers final: 20 residues processed: 148 average time/residue: 0.6620 time to fit residues: 122.1810 Evaluate side-chains 138 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain E residue 62 MET Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 128 optimal weight: 3.9990 chunk 477 optimal weight: 30.0000 chunk 328 optimal weight: 5.9990 chunk 228 optimal weight: 4.9990 chunk 382 optimal weight: 50.0000 chunk 333 optimal weight: 30.0000 chunk 25 optimal weight: 1.9990 chunk 41 optimal weight: 40.0000 chunk 397 optimal weight: 30.0000 chunk 362 optimal weight: 50.0000 chunk 68 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN E 194 ASN E 397 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.122417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.073698 restraints weight = 182988.752| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 6.05 r_work: 0.2869 rms_B_bonded: 5.11 restraints_weight: 2.0000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 41197 Z= 0.232 Angle : 0.639 11.686 56202 Z= 0.313 Chirality : 0.045 0.362 6394 Planarity : 0.004 0.073 7110 Dihedral : 7.386 110.128 7029 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.35 % Allowed : 13.57 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.12), residues: 4848 helix: 1.23 (0.13), residues: 1623 sheet: -0.09 (0.18), residues: 734 loop : -1.35 (0.12), residues: 2491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.020 0.001 TYR B1067 PHE 0.022 0.001 PHE A1121 TRP 0.011 0.001 TRP A 886 HIS 0.004 0.001 HIS C1048 Details of bonding type rmsd covalent geometry : bond 0.00543 (41067) covalent geometry : angle 0.61868 (55860) SS BOND : bond 0.00415 ( 48) SS BOND : angle 1.60855 ( 96) hydrogen bonds : bond 0.05242 ( 1670) hydrogen bonds : angle 4.88622 ( 4686) link_BETA1-4 : bond 0.00427 ( 29) link_BETA1-4 : angle 2.17042 ( 87) link_NAG-ASN : bond 0.00448 ( 53) link_NAG-ASN : angle 2.40659 ( 159) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 108 time to evaluate : 1.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9459 (OUTLIER) cc_final: 0.9023 (p) REVERT: A 1039 ARG cc_start: 0.9475 (OUTLIER) cc_final: 0.8996 (ptm160) REVERT: B 108 THR cc_start: 0.8137 (OUTLIER) cc_final: 0.7918 (m) REVERT: B 153 MET cc_start: 0.6920 (ppp) cc_final: 0.6482 (pp-130) REVERT: B 563 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8267 (mt0) REVERT: B 581 THR cc_start: 0.9196 (OUTLIER) cc_final: 0.8958 (p) REVERT: B 984 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9160 (pp) REVERT: B 1132 ILE cc_start: 0.9506 (OUTLIER) cc_final: 0.9255 (pp) REVERT: C 153 MET cc_start: 0.7565 (tmm) cc_final: 0.6828 (tmm) REVERT: C 581 THR cc_start: 0.9056 (OUTLIER) cc_final: 0.8675 (p) REVERT: C 1040 VAL cc_start: 0.9571 (OUTLIER) cc_final: 0.9347 (m) REVERT: E 163 TRP cc_start: 0.8170 (m100) cc_final: 0.7877 (t60) REVERT: E 270 MET cc_start: 0.3933 (tpp) cc_final: 0.2395 (ptm) REVERT: E 480 MET cc_start: 0.2024 (ttt) cc_final: 0.1437 (tmm) REVERT: E 610 TRP cc_start: 0.6610 (OUTLIER) cc_final: 0.6316 (p-90) REVERT: D 224 GLU cc_start: 0.8980 (mp0) cc_final: 0.8644 (pp20) REVERT: D 332 MET cc_start: 0.5738 (pp-130) cc_final: 0.5335 (ppp) REVERT: D 408 MET cc_start: 0.6033 (mmp) cc_final: 0.5451 (tpt) REVERT: D 455 MET cc_start: 0.4023 (pp-130) cc_final: 0.3709 (pp-130) REVERT: D 480 MET cc_start: 0.4445 (ppp) cc_final: 0.4029 (pp-130) REVERT: D 536 GLU cc_start: 0.8237 (mp0) cc_final: 0.7974 (tm-30) REVERT: F 332 MET cc_start: 0.4095 (OUTLIER) cc_final: 0.2606 (ppp) REVERT: F 366 MET cc_start: 0.2532 (tpt) cc_final: 0.2114 (mmm) REVERT: F 480 MET cc_start: 0.5761 (pp-130) cc_final: 0.5433 (pp-130) outliers start: 58 outliers final: 30 residues processed: 155 average time/residue: 0.6232 time to fit residues: 120.9331 Evaluate side-chains 149 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 108 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain B residue 1043 CYS Chi-restraints excluded: chain B residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1040 VAL Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 308 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 137 optimal weight: 9.9990 chunk 436 optimal weight: 1.9990 chunk 275 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 175 optimal weight: 0.5980 chunk 340 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 238 optimal weight: 9.9990 chunk 171 optimal weight: 0.8980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 472 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.123335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.081562 restraints weight = 179694.269| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 6.62 r_work: 0.2882 rms_B_bonded: 6.24 restraints_weight: 2.0000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 41197 Z= 0.122 Angle : 0.592 12.448 56202 Z= 0.287 Chirality : 0.043 0.343 6394 Planarity : 0.004 0.071 7110 Dihedral : 6.846 103.079 7029 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.91 % Allowed : 14.13 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.12), residues: 4848 helix: 1.37 (0.13), residues: 1633 sheet: 0.07 (0.19), residues: 734 loop : -1.27 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 518 TYR 0.018 0.001 TYR F 385 PHE 0.015 0.001 PHE D 327 TRP 0.013 0.001 TRP D 48 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00274 (41067) covalent geometry : angle 0.57345 (55860) SS BOND : bond 0.00331 ( 48) SS BOND : angle 1.20949 ( 96) hydrogen bonds : bond 0.04421 ( 1670) hydrogen bonds : angle 4.67098 ( 4686) link_BETA1-4 : bond 0.00503 ( 29) link_BETA1-4 : angle 2.16249 ( 87) link_NAG-ASN : bond 0.00365 ( 53) link_NAG-ASN : angle 2.18825 ( 159) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9696 Ramachandran restraints generated. 4848 Oldfield, 0 Emsley, 4848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 108 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 581 THR cc_start: 0.9462 (OUTLIER) cc_final: 0.9052 (p) REVERT: A 1039 ARG cc_start: 0.9408 (OUTLIER) cc_final: 0.8856 (ptm160) REVERT: B 108 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7769 (m) REVERT: B 153 MET cc_start: 0.5361 (ppp) cc_final: 0.4847 (pp-130) REVERT: B 563 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8246 (mt0) REVERT: B 581 THR cc_start: 0.9201 (OUTLIER) cc_final: 0.8937 (p) REVERT: B 984 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9140 (pp) REVERT: C 153 MET cc_start: 0.6463 (tmm) cc_final: 0.5302 (tmm) REVERT: C 581 THR cc_start: 0.9107 (OUTLIER) cc_final: 0.8749 (p) REVERT: E 163 TRP cc_start: 0.8151 (m100) cc_final: 0.7799 (t60) REVERT: E 270 MET cc_start: 0.3794 (tpp) cc_final: 0.2488 (ptm) REVERT: E 480 MET cc_start: 0.2426 (ttt) cc_final: 0.1783 (tmm) REVERT: E 557 MET cc_start: 0.5192 (ppp) cc_final: 0.4982 (ppp) REVERT: E 610 TRP cc_start: 0.6453 (OUTLIER) cc_final: 0.6153 (p-90) REVERT: D 224 GLU cc_start: 0.8932 (mp0) cc_final: 0.8593 (pp20) REVERT: D 332 MET cc_start: 0.5193 (pp-130) cc_final: 0.4236 (ppp) REVERT: D 455 MET cc_start: 0.4167 (pp-130) cc_final: 0.3879 (pp-130) REVERT: D 474 MET cc_start: 0.1973 (tmt) cc_final: 0.1627 (tmt) REVERT: D 480 MET cc_start: 0.4249 (ppp) cc_final: 0.3763 (pp-130) REVERT: D 536 GLU cc_start: 0.8138 (mp0) cc_final: 0.7821 (tm-30) REVERT: F 332 MET cc_start: 0.3659 (OUTLIER) cc_final: 0.1994 (ppp) REVERT: F 366 MET cc_start: 0.2299 (tpt) cc_final: 0.1876 (mmm) REVERT: F 480 MET cc_start: 0.5856 (pp-130) cc_final: 0.5391 (pp-130) outliers start: 39 outliers final: 20 residues processed: 138 average time/residue: 0.7001 time to fit residues: 119.1819 Evaluate side-chains 136 residues out of total 4296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1043 CYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 984 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 1117 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain E residue 610 TRP Chi-restraints excluded: chain D residue 20 THR Chi-restraints excluded: chain D residue 123 MET Chi-restraints excluded: chain D residue 209 VAL Chi-restraints excluded: chain F residue 332 MET Chi-restraints excluded: chain F residue 579 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 66 optimal weight: 3.9990 chunk 245 optimal weight: 30.0000 chunk 102 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 365 optimal weight: 9.9990 chunk 135 optimal weight: 30.0000 chunk 110 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 180 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 44 optimal weight: 20.0000 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 955 ASN ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 641 ASN ** E 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 397 ASN ** E 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.123278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.082345 restraints weight = 180784.234| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 7.69 r_work: 0.2916 rms_B_bonded: 6.14 restraints_weight: 2.0000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 41197 Z= 0.124 Angle : 0.597 23.054 56202 Z= 0.288 Chirality : 0.043 0.333 6394 Planarity : 0.004 0.071 7110 Dihedral : 6.396 92.941 7029 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.07 % Allowed : 14.08 % Favored : 84.85 % 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 are not related in a simple way. whole: -0.14 (0.12), residues: 4848 helix: 1.43 (0.13), residues: 1631 sheet: 0.13 (0.19), residues: 733 loop : -1.23 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 518 TYR 0.018 0.001 TYR F 385 PHE 0.014 0.001 PHE B1121 TRP 0.011 0.001 TRP F 461 HIS 0.005 0.001 HIS E 374 Details of bonding type rmsd covalent geometry : bond 0.00282 (41067) covalent geometry : angle 0.57929 (55860) SS BOND : bond 0.00342 ( 48) SS BOND : angle 1.17607 ( 96) hydrogen bonds : bond 0.04347 ( 1670) hydrogen bonds : angle 4.63839 ( 4686) link_BETA1-4 : bond 0.00450 ( 29) link_BETA1-4 : angle 2.16898 ( 87) link_NAG-ASN : bond 0.00343 ( 53) link_NAG-ASN : angle 2.19045 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25534.84 seconds wall clock time: 431 minutes 55.80 seconds (25915.80 seconds total)