Starting phenix.real_space_refine on Sun Jul 5 03:59:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.map" model { file = "/net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v76_31760/07_2026/7v76_31760.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16043 2.51 5 N 4087 2.21 5 O 4978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 25219 Number of models: 1 Model: "" Number of chains: 37 Chain: "A" Number of atoms: 8014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1026, 8014 Classifications: {'peptide': 1026} Link IDs: {'PTRANS': 52, 'TRANS': 973} Chain breaks: 7 Chain: "B" Number of atoms: 8070 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8070 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 53, 'TRANS': 978} Chain breaks: 7 Chain: "C" Number of atoms: 8057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8057 Classifications: {'peptide': 1030} Link IDs: {'PTRANS': 53, 'TRANS': 976} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 4.39, per 1000 atoms: 0.17 Number of scatterers: 25219 At special positions: 0 Unit cell: (143, 146.3, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4978 8.00 N 4087 7.00 C 16043 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.03 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 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 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.04 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.03 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.03 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " 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 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.04 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " 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 D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 165 " " NAG C2003 " - " ASN C 328 " " NAG C2004 " - " ASN C 600 " " NAG C2005 " - " ASN C 654 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 234 " " NAG F 1 " - " ASN A 279 " " NAG G 1 " - " ASN A 328 " " NAG H 1 " - " ASN A 340 " " NAG I 1 " - " ASN A 613 " " NAG J 1 " - " ASN A 706 " " NAG K 1 " - " ASN A 714 " " NAG L 1 " - " ASN A 798 " " NAG M 1 " - " ASN A1071 " " NAG N 1 " - " ASN A1095 " " NAG O 1 " - " ASN A1131 " " NAG P 1 " - " ASN B 165 " " NAG Q 1 " - " ASN B 279 " " NAG R 1 " - " ASN B 340 " " NAG S 1 " - " ASN B 613 " " NAG T 1 " - " ASN B 706 " " NAG U 1 " - " ASN B 714 " " NAG V 1 " - " ASN B 798 " " NAG W 1 " - " ASN B1071 " " NAG X 1 " - " ASN B1095 " " NAG Y 1 " - " ASN B1131 " " NAG Z 1 " - " ASN C 279 " " NAG a 1 " - " ASN C 340 " " NAG b 1 " - " ASN C 613 " " NAG c 1 " - " ASN C 706 " " NAG d 1 " - " ASN C 714 " " NAG e 1 " - " ASN C 798 " " NAG f 1 " - " ASN C1071 " " NAG g 1 " - " ASN C1095 " " NAG h 1 " - " ASN C1131 " Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 988.7 milliseconds 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5780 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 24.7% alpha, 24.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 Processing helix chain 'A' and resid 335 through 340 Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.513A pdb=" N SER A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 Processing helix chain 'A' and resid 400 through 404 Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.613A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 780 removed outlier: 4.519A pdb=" N GLN A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 764 " --> pdb=" O LEU A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 823 Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.652A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 906 removed outlier: 3.817A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.967A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 979 removed outlier: 3.788A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.659A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 361 through 368 removed outlier: 4.118A pdb=" N LEU B 365 " --> pdb=" O ASP B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 4.118A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 407 removed outlier: 3.738A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 435 through 440 removed outlier: 3.664A pdb=" N SER B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 743 through 752 removed outlier: 4.005A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 756 through 780 removed outlier: 3.620A pdb=" N LEU B 760 " --> pdb=" O PHE B 756 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP B 772 " --> pdb=" O ALA B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.550A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 894 through 905 Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.692A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 removed outlier: 3.724A pdb=" N ILE B 977 " --> pdb=" O VAL B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 1030 removed outlier: 5.097A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.753A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.804A pdb=" N SER C 368 " --> pdb=" O VAL C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 386 removed outlier: 3.693A pdb=" N LEU C 384 " --> pdb=" O PRO C 381 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN C 385 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASP C 386 " --> pdb=" O LYS C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 407 removed outlier: 4.543A pdb=" N ARG C 405 " --> pdb=" O ASP C 402 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 440 removed outlier: 3.505A pdb=" N SER C 440 " --> pdb=" O ASN C 436 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 635 removed outlier: 4.046A pdb=" N THR C 635 " --> pdb=" O VAL C 632 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 743 through 751 Processing helix chain 'C' and resid 755 through 780 removed outlier: 3.576A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 771 " --> pdb=" O ILE C 767 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP C 772 " --> pdb=" O ALA C 768 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 Processing helix chain 'C' and resid 863 through 881 removed outlier: 3.565A pdb=" N ILE C 879 " --> pdb=" O LEU C 875 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 880 " --> pdb=" O ALA C 876 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 894 through 905 removed outlier: 3.530A pdb=" N ALA C 900 " --> pdb=" O ALA C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.980A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU C 915 " --> pdb=" O ASN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 Processing helix chain 'C' and resid 982 through 1030 removed outlier: 3.965A pdb=" N GLU C 987 " --> pdb=" O PRO C 983 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N GLN C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 removed outlier: 3.699A pdb=" N GLU C1141 " --> pdb=" O PRO C1137 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.355A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.022A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.675A pdb=" N GLY C 563 " --> pdb=" O ASP C 571 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ASP C 571 " --> pdb=" O ILE C 584 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.022A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.304A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.261A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA8, first strand: chain 'A' and resid 351 through 355 Processing sheet with id=AA9, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AB1, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB2, first strand: chain 'A' and resid 570 through 573 removed outlier: 3.559A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N PHE A 562 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 651 through 652 removed outlier: 6.488A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.870A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 699 through 700 Processing sheet with id=AB5, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.618A pdb=" N GLY A1056 " --> pdb=" O ALA A1053 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 6.012A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.476A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1073 through 1075 removed outlier: 3.573A pdb=" N THR A1073 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ALA A1075 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N PHE A1092 " --> pdb=" O ALA A1075 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.810A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.981A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.164A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.853A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.579A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 313 " --> pdb=" O VAL B 592 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY B 645 " --> pdb=" O THR B 642 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 5.374A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC7, first strand: chain 'B' and resid 470 through 471 removed outlier: 3.735A pdb=" N TYR B 470 " --> pdb=" O TYR B 486 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 486 " --> pdb=" O TYR B 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.090A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.903A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AD1, first strand: chain 'B' and resid 712 through 716 removed outlier: 6.162A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 712 through 716 removed outlier: 6.162A pdb=" N GLU B1069 " --> pdb=" O PRO B 712 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.472A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 4.644A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 4.849A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 6.206A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.383A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.110A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.058A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.377A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.937A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 10.130A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 308 through 316 removed outlier: 5.528A pdb=" N ILE C 309 " --> pdb=" O THR C 596 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N THR C 596 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLN C 311 " --> pdb=" O VAL C 594 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 594 " --> pdb=" O GLN C 311 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER C 313 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 351 through 355 removed outlier: 6.769A pdb=" N CYS C 358 " --> pdb=" O CYS C 522 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 351 through 355 removed outlier: 6.405A pdb=" N ASN C 391 " --> pdb=" O GLU C 513 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU C 513 " --> pdb=" O ASN C 391 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN C 434 " --> pdb=" O PHE C 371 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N PHE C 371 " --> pdb=" O ASN C 434 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 470 through 471 removed outlier: 3.658A pdb=" N TYR C 470 " --> pdb=" O TYR C 486 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR C 486 " --> pdb=" O TYR C 470 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 651 through 652 removed outlier: 5.939A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 709 through 725 removed outlier: 6.679A pdb=" N GLN C1068 " --> pdb=" O THR C 713 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N PHE C 715 " --> pdb=" O PRO C1066 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N ILE C 717 " --> pdb=" O TYR C1064 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N TYR C1064 " --> pdb=" O ILE C 717 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL C 719 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL C1062 " --> pdb=" O VAL C 719 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 721 " --> pdb=" O LEU C1060 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C1060 " --> pdb=" O THR C 721 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE C 723 " --> pdb=" O VAL C1058 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL C1058 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLY C1056 " --> pdb=" O PRO C 725 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY C1056 " --> pdb=" O ALA C1053 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.657A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1117 through 1119 Processing sheet with id=AE9, first strand: chain 'C' and resid 1091 through 1094 975 hydrogen bonds defined for protein. 2655 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.78 Time building geometry restraints manager: 2.72 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: 7934 1.34 - 1.46: 6337 1.46 - 1.58: 11368 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25777 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.469 -0.063 2.00e-02 2.50e+03 9.85e+00 bond pdb=" C1 NAG W 1 " pdb=" O5 NAG W 1 " ideal model delta sigma weight residual 1.406 1.452 -0.046 2.00e-02 2.50e+03 5.28e+00 bond pdb=" C1 NAG a 2 " pdb=" O5 NAG a 2 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.31e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.07e+00 ... (remaining 25772 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 34083 1.57 - 3.15: 901 3.15 - 4.72: 69 4.72 - 6.30: 22 6.30 - 7.87: 7 Bond angle restraints: 35082 Sorted by residual: angle pdb=" N ILE C 802 " pdb=" CA ILE C 802 " pdb=" C ILE C 802 " ideal model delta sigma weight residual 113.53 109.72 3.81 9.80e-01 1.04e+00 1.51e+01 angle pdb=" N LEU C 452 " pdb=" CA LEU C 452 " pdb=" C LEU C 452 " ideal model delta sigma weight residual 114.56 110.32 4.24 1.27e+00 6.20e-01 1.12e+01 angle pdb=" N PRO B 983 " pdb=" CA PRO B 983 " pdb=" C PRO B 983 " ideal model delta sigma weight residual 110.70 114.36 -3.66 1.22e+00 6.72e-01 8.98e+00 angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 126.88 -5.34 1.91e+00 2.74e-01 7.83e+00 angle pdb=" N VAL A 726 " pdb=" CA VAL A 726 " pdb=" C VAL A 726 " ideal model delta sigma weight residual 113.71 111.14 2.57 9.50e-01 1.11e+00 7.29e+00 ... (remaining 35077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13292 17.98 - 35.95: 1159 35.95 - 53.93: 202 53.93 - 71.91: 37 71.91 - 89.89: 27 Dihedral angle restraints: 14717 sinusoidal: 5729 harmonic: 8988 Sorted by residual: dihedral pdb=" CB CYS B 131 " pdb=" SG CYS B 131 " pdb=" SG CYS B 166 " pdb=" CB CYS B 166 " ideal model delta sinusoidal sigma weight residual 93.00 4.62 88.38 1 1.00e+01 1.00e-02 9.33e+01 dihedral pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -1.35 -84.65 1 1.00e+01 1.00e-02 8.70e+01 dihedral pdb=" CB CYS A 388 " pdb=" SG CYS A 388 " pdb=" SG CYS A 522 " pdb=" CB CYS A 522 " ideal model delta sinusoidal sigma weight residual -86.00 -3.50 -82.50 1 1.00e+01 1.00e-02 8.35e+01 ... (remaining 14714 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.127: 4173 0.127 - 0.253: 31 0.253 - 0.380: 2 0.380 - 0.506: 1 0.506 - 0.633: 1 Chirality restraints: 4208 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.77 -0.63 2.00e-01 2.50e+01 1.00e+01 chirality pdb=" C1 NAG A2004 " pdb=" ND2 ASN A 654 " pdb=" C2 NAG A2004 " pdb=" O5 NAG A2004 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 4205 not shown) Planarity restraints: 4478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 983 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.12e+00 pdb=" N PRO C 984 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO C 984 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 984 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 982 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 983 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 983 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 983 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 982 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO C 983 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO C 983 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 983 " 0.022 5.00e-02 4.00e+02 ... (remaining 4475 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 857 2.71 - 3.26: 24180 3.26 - 3.81: 38167 3.81 - 4.35: 45675 4.35 - 4.90: 80180 Nonbonded interactions: 189059 Sorted by model distance: nonbonded pdb=" OG1 THR C 713 " pdb=" O GLN C1068 " model vdw 2.164 3.040 nonbonded pdb=" NH1 ARG C 400 " pdb=" O GLY C 501 " model vdw 2.205 3.120 nonbonded pdb=" O GLY B 493 " pdb=" OH TYR B 502 " model vdw 2.210 3.040 nonbonded pdb=" OG SER A 346 " pdb=" O LEU A 449 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP C 565 " pdb=" OG1 THR C 569 " model vdw 2.225 3.040 ... (remaining 189054 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 260 or resid 262 through 2004)) selection = (chain 'B' and (resid 14 through 260 or resid 262 through 618 or resid 632 throu \ gh 824 or resid 852 through 2004)) selection = (chain 'C' and (resid 14 through 618 or resid 632 through 824 or resid 852 throu \ gh 2004)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 0.020 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 23.920 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 25894 Z= 0.178 Angle : 0.626 18.400 35393 Z= 0.301 Chirality : 0.047 0.633 4208 Planarity : 0.003 0.071 4432 Dihedral : 13.702 89.887 8817 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.16), residues: 3040 helix: 1.96 (0.22), residues: 674 sheet: 0.64 (0.19), residues: 726 loop : -1.17 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 451 TYR 0.016 0.001 TYR B 502 PHE 0.021 0.001 PHE B 374 TRP 0.007 0.001 TRP C 433 HIS 0.001 0.000 HIS C1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.18 (25777) covalent geometry : angle 0.57804 / 0.29 (35082) SS BOND : bond 0.00259 / 0.16 ( 40) SS BOND : angle 2.17489 / 1.40 ( 80) hydrogen bonds : bond 0.12574 / 8.59 ( 965) hydrogen bonds : angle 5.55330 / 3.84 ( 2655) link_BETA1-4 : bond 0.00628 / 0.40 ( 31) link_BETA1-4 : angle 2.02122 / 1.32 ( 93) link_NAG-ASN : bond 0.00501 / 0.34 ( 46) link_NAG-ASN : angle 3.15867 / 2.62 ( 138) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1342 (pmm) cc_final: 0.0360 (mtt) REVERT: A 160 TYR cc_start: 0.7473 (p90) cc_final: 0.7155 (p90) REVERT: A 866 MET cc_start: 0.8165 (mtt) cc_final: 0.7861 (mtt) REVERT: B 140 PHE cc_start: 0.7754 (p90) cc_final: 0.7247 (p90) REVERT: B 947 ASP cc_start: 0.8164 (t70) cc_final: 0.7796 (t0) REVERT: B 999 GLN cc_start: 0.7759 (tt0) cc_final: 0.7511 (mt0) REVERT: C 207 HIS cc_start: 0.7614 (m90) cc_final: 0.7219 (m90) REVERT: C 450 TYR cc_start: 0.6018 (p90) cc_final: 0.5754 (p90) REVERT: C 901 TYR cc_start: 0.7397 (m-10) cc_final: 0.6651 (m-10) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1450 time to fit residues: 45.8280 Evaluate side-chains 130 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 130 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 2.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 ASN A 604 GLN A 954 GLN A1008 GLN B 774 ASN B 898 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 911 ASN C 801 GLN C 911 ASN C 916 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.165327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.102901 restraints weight = 38211.550| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.18 r_work: 0.3170 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 25894 Z= 0.306 Angle : 0.730 14.763 35393 Z= 0.364 Chirality : 0.050 0.345 4208 Planarity : 0.004 0.052 4432 Dihedral : 4.534 26.301 3312 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.46 % Favored : 94.51 % Rotamer: Outliers : 0.78 % Allowed : 8.10 % Favored : 91.13 % 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: -0.45 (0.15), residues: 3040 helix: 1.38 (0.20), residues: 685 sheet: 0.37 (0.19), residues: 725 loop : -1.40 (0.15), residues: 1630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1036 TYR 0.027 0.002 TYR B1064 PHE 0.034 0.002 PHE C 903 TRP 0.022 0.002 TRP C 104 HIS 0.008 0.002 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00761 / 0.31 (25777) covalent geometry : angle 0.69409 / 0.35 (35082) SS BOND : bond 0.00517 / 0.31 ( 40) SS BOND : angle 2.49547 / 1.59 ( 80) hydrogen bonds : bond 0.06748 / 4.58 ( 965) hydrogen bonds : angle 5.12836 / 3.56 ( 2655) link_BETA1-4 : bond 0.00552 / 0.35 ( 31) link_BETA1-4 : angle 1.73987 / 1.16 ( 93) link_NAG-ASN : bond 0.00858 / 0.65 ( 46) link_NAG-ASN : angle 2.92539 / 2.60 ( 138) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6837 (OUTLIER) cc_final: 0.6351 (tttp) REVERT: A 153 MET cc_start: 0.1409 (pmm) cc_final: 0.0318 (mtt) REVERT: A 866 MET cc_start: 0.9049 (mtt) cc_final: 0.8821 (mtt) REVERT: B 140 PHE cc_start: 0.7919 (p90) cc_final: 0.7309 (p90) REVERT: B 756 PHE cc_start: 0.8045 (m-80) cc_final: 0.7826 (m-80) REVERT: B 999 GLN cc_start: 0.8702 (tt0) cc_final: 0.8481 (mt0) REVERT: C 434 ASN cc_start: 0.7896 (t0) cc_final: 0.7013 (t0) REVERT: C 449 LEU cc_start: 0.8768 (tp) cc_final: 0.8441 (tp) REVERT: C 450 TYR cc_start: 0.6741 (p90) cc_final: 0.6414 (p90) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.1403 time to fit residues: 37.0963 Evaluate side-chains 142 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 960 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 213 optimal weight: 2.9990 chunk 37 optimal weight: 20.0000 chunk 27 optimal weight: 4.9990 chunk 303 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 243 optimal weight: 9.9990 chunk 208 optimal weight: 7.9990 chunk 293 optimal weight: 0.5980 chunk 138 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 139 optimal weight: 40.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 801 GLN A 999 GLN B 115 GLN B 561 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 434 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.165976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.104203 restraints weight = 38284.280| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.22 r_work: 0.3162 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 25894 Z= 0.229 Angle : 0.657 12.979 35393 Z= 0.326 Chirality : 0.048 0.328 4208 Planarity : 0.004 0.049 4432 Dihedral : 4.471 25.839 3312 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.80 % Favored : 95.16 % Rotamer: Outliers : 1.92 % Allowed : 11.13 % Favored : 86.95 % 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 (0.15), residues: 3040 helix: 1.47 (0.21), residues: 681 sheet: 0.30 (0.19), residues: 715 loop : -1.45 (0.15), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1036 TYR 0.020 0.001 TYR B1064 PHE 0.024 0.002 PHE A1118 TRP 0.024 0.002 TRP C 104 HIS 0.006 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.23 (25777) covalent geometry : angle 0.62152 / 0.32 (35082) SS BOND : bond 0.00443 / 0.26 ( 40) SS BOND : angle 2.29044 / 1.46 ( 80) hydrogen bonds : bond 0.06278 / 4.27 ( 965) hydrogen bonds : angle 5.00930 / 3.46 ( 2655) link_BETA1-4 : bond 0.00578 / 0.38 ( 31) link_BETA1-4 : angle 1.72301 / 1.14 ( 93) link_NAG-ASN : bond 0.00555 / 0.39 ( 46) link_NAG-ASN : angle 2.71438 / 2.43 ( 138) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 131 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6799 (OUTLIER) cc_final: 0.6250 (mtmm) REVERT: A 153 MET cc_start: 0.1382 (pmm) cc_final: 0.0285 (mtt) REVERT: A 160 TYR cc_start: 0.7563 (p90) cc_final: 0.7255 (p90) REVERT: A 560 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.6552 (mp10) REVERT: A 866 MET cc_start: 0.8858 (mtt) cc_final: 0.8599 (mtt) REVERT: B 140 PHE cc_start: 0.7976 (p90) cc_final: 0.7375 (p90) REVERT: B 897 MET cc_start: 0.8727 (mtp) cc_final: 0.8495 (mtp) REVERT: B 999 GLN cc_start: 0.8499 (tt0) cc_final: 0.8249 (mt0) REVERT: B 1103 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8542 (pm20) REVERT: C 204 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.7245 (m-80) REVERT: C 449 LEU cc_start: 0.8681 (tp) cc_final: 0.8257 (tp) REVERT: C 450 TYR cc_start: 0.6645 (p90) cc_final: 0.6374 (p90) outliers start: 52 outliers final: 27 residues processed: 176 average time/residue: 0.1391 time to fit residues: 42.1066 Evaluate side-chains 156 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1103 GLN Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1078 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 196 optimal weight: 0.4980 chunk 262 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 188 optimal weight: 4.9990 chunk 102 optimal weight: 20.0000 chunk 152 optimal weight: 2.9990 chunk 275 optimal weight: 0.2980 chunk 214 optimal weight: 5.9990 chunk 186 optimal weight: 0.8980 chunk 166 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.168972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.107781 restraints weight = 38059.807| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 3.16 r_work: 0.3237 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25894 Z= 0.121 Angle : 0.589 13.890 35393 Z= 0.289 Chirality : 0.045 0.304 4208 Planarity : 0.004 0.054 4432 Dihedral : 4.205 23.234 3312 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.24 % Favored : 95.69 % Rotamer: Outliers : 1.40 % Allowed : 12.27 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.15), residues: 3040 helix: 1.79 (0.21), residues: 667 sheet: 0.47 (0.19), residues: 712 loop : -1.35 (0.15), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1036 TYR 0.015 0.001 TYR A1064 PHE 0.017 0.001 PHE A1118 TRP 0.024 0.001 TRP C 104 HIS 0.002 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (25777) covalent geometry : angle 0.55197 / 0.28 (35082) SS BOND : bond 0.00496 / 0.26 ( 40) SS BOND : angle 2.20012 / 1.38 ( 80) hydrogen bonds : bond 0.05161 / 3.51 ( 965) hydrogen bonds : angle 4.78784 / 3.30 ( 2655) link_BETA1-4 : bond 0.00581 / 0.38 ( 31) link_BETA1-4 : angle 1.66174 / 1.11 ( 93) link_NAG-ASN : bond 0.00485 / 0.34 ( 46) link_NAG-ASN : angle 2.63687 / 2.37 ( 138) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 130 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 129 LYS cc_start: 0.6736 (OUTLIER) cc_final: 0.6243 (mtmm) REVERT: A 153 MET cc_start: 0.1364 (pmm) cc_final: 0.0229 (mtt) REVERT: A 160 TYR cc_start: 0.7536 (p90) cc_final: 0.7227 (p90) REVERT: A 560 GLN cc_start: 0.8122 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: A 866 MET cc_start: 0.8957 (mtt) cc_final: 0.8704 (mtt) REVERT: B 140 PHE cc_start: 0.7926 (p90) cc_final: 0.7299 (p90) REVERT: B 897 MET cc_start: 0.8874 (mtp) cc_final: 0.8620 (mtp) REVERT: B 947 ASP cc_start: 0.8960 (t70) cc_final: 0.8440 (t0) REVERT: B 999 GLN cc_start: 0.8578 (tt0) cc_final: 0.8364 (mt0) REVERT: C 449 LEU cc_start: 0.8712 (tp) cc_final: 0.8270 (tp) REVERT: C 450 TYR cc_start: 0.6673 (p90) cc_final: 0.6264 (p90) outliers start: 38 outliers final: 22 residues processed: 164 average time/residue: 0.1365 time to fit residues: 38.2191 Evaluate side-chains 148 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 91 optimal weight: 0.0770 chunk 95 optimal weight: 0.9990 chunk 158 optimal weight: 7.9990 chunk 167 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 56 optimal weight: 0.0870 chunk 196 optimal weight: 1.9990 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 999 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.170366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.109337 restraints weight = 37794.096| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.03 r_work: 0.3269 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25894 Z= 0.106 Angle : 0.561 13.306 35393 Z= 0.274 Chirality : 0.045 0.307 4208 Planarity : 0.003 0.053 4432 Dihedral : 3.981 20.664 3312 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.85 % Favored : 96.09 % Rotamer: Outliers : 1.81 % Allowed : 13.31 % Favored : 84.88 % 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: -0.11 (0.15), residues: 3040 helix: 1.90 (0.21), residues: 666 sheet: 0.61 (0.19), residues: 715 loop : -1.28 (0.15), residues: 1659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1036 TYR 0.015 0.001 TYR A1064 PHE 0.017 0.001 PHE C 238 TRP 0.030 0.001 TRP C 104 HIS 0.002 0.000 HIS B 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (25777) covalent geometry : angle 0.52466 / 0.26 (35082) SS BOND : bond 0.00332 / 0.18 ( 40) SS BOND : angle 2.25393 / 1.38 ( 80) hydrogen bonds : bond 0.04535 / 3.08 ( 965) hydrogen bonds : angle 4.60289 / 3.17 ( 2655) link_BETA1-4 : bond 0.00570 / 0.37 ( 31) link_BETA1-4 : angle 1.61711 / 1.08 ( 93) link_NAG-ASN : bond 0.00473 / 0.33 ( 46) link_NAG-ASN : angle 2.46481 / 2.25 ( 138) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 132 time to evaluate : 0.771 Fit side-chains REVERT: A 153 MET cc_start: 0.1360 (pmm) cc_final: 0.0198 (mtt) REVERT: A 160 TYR cc_start: 0.7379 (p90) cc_final: 0.6997 (p90) REVERT: A 560 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7808 (mt0) REVERT: B 140 PHE cc_start: 0.7884 (p90) cc_final: 0.7261 (p90) REVERT: B 947 ASP cc_start: 0.8883 (t70) cc_final: 0.8386 (t0) REVERT: B 999 GLN cc_start: 0.8529 (tt0) cc_final: 0.8325 (mt0) REVERT: C 207 HIS cc_start: 0.7701 (m90) cc_final: 0.7330 (m90) REVERT: C 434 ASN cc_start: 0.8263 (m-40) cc_final: 0.7566 (t0) REVERT: C 449 LEU cc_start: 0.8744 (tp) cc_final: 0.8291 (tp) REVERT: C 450 TYR cc_start: 0.6729 (p90) cc_final: 0.6028 (p90) REVERT: C 490 GLN cc_start: 0.6479 (tm-30) cc_final: 0.6130 (tm-30) outliers start: 49 outliers final: 27 residues processed: 176 average time/residue: 0.1347 time to fit residues: 40.8645 Evaluate side-chains 149 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 238 PHE Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 269 optimal weight: 1.9990 chunk 228 optimal weight: 0.5980 chunk 183 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 38 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 289 optimal weight: 3.9990 chunk 300 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 194 optimal weight: 0.6980 chunk 29 optimal weight: 20.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 999 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.167729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.106028 restraints weight = 38137.690| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 3.26 r_work: 0.3211 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25894 Z= 0.161 Angle : 0.596 12.464 35393 Z= 0.292 Chirality : 0.046 0.321 4208 Planarity : 0.004 0.054 4432 Dihedral : 4.097 22.433 3312 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.67 % Favored : 95.26 % Rotamer: Outliers : 1.85 % Allowed : 14.23 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3040 helix: 1.76 (0.21), residues: 674 sheet: 0.52 (0.19), residues: 714 loop : -1.29 (0.15), residues: 1652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.021 0.001 TYR C 450 PHE 0.020 0.001 PHE B1118 TRP 0.025 0.001 TRP C 104 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.16 (25777) covalent geometry : angle 0.56267 / 0.28 (35082) SS BOND : bond 0.00383 / 0.23 ( 40) SS BOND : angle 2.22074 / 1.38 ( 80) hydrogen bonds : bond 0.05215 / 3.55 ( 965) hydrogen bonds : angle 4.68776 / 3.23 ( 2655) link_BETA1-4 : bond 0.00547 / 0.35 ( 31) link_BETA1-4 : angle 1.61623 / 1.08 ( 93) link_NAG-ASN : bond 0.00432 / 0.30 ( 46) link_NAG-ASN : angle 2.45873 / 2.23 ( 138) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 127 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.1432 (pmm) cc_final: 0.0306 (mtt) REVERT: A 160 TYR cc_start: 0.7306 (p90) cc_final: 0.7022 (p90) REVERT: A 560 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.6811 (mt0) REVERT: B 140 PHE cc_start: 0.8040 (p90) cc_final: 0.7396 (p90) REVERT: B 947 ASP cc_start: 0.8744 (t70) cc_final: 0.8195 (t0) REVERT: B 999 GLN cc_start: 0.8452 (tt0) cc_final: 0.8230 (mt0) REVERT: C 434 ASN cc_start: 0.8140 (m-40) cc_final: 0.7424 (t0) outliers start: 50 outliers final: 39 residues processed: 172 average time/residue: 0.1309 time to fit residues: 39.4059 Evaluate side-chains 157 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 117 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1103 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 93 optimal weight: 0.5980 chunk 37 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 224 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 258 optimal weight: 2.9990 chunk 73 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 chunk 118 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 999 GLN ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.164542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.101868 restraints weight = 37876.058| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.17 r_work: 0.3148 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 25894 Z= 0.279 Angle : 0.705 10.828 35393 Z= 0.350 Chirality : 0.049 0.344 4208 Planarity : 0.004 0.054 4432 Dihedral : 4.578 26.356 3312 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.91 % Rotamer: Outliers : 2.26 % Allowed : 14.82 % Favored : 82.92 % 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: -0.54 (0.15), residues: 3040 helix: 1.44 (0.21), residues: 670 sheet: 0.23 (0.19), residues: 730 loop : -1.47 (0.15), residues: 1640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1036 TYR 0.024 0.002 TYR B1064 PHE 0.024 0.002 PHE A1118 TRP 0.026 0.002 TRP C 104 HIS 0.007 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00687 / 0.28 (25777) covalent geometry : angle 0.67251 / 0.34 (35082) SS BOND : bond 0.00520 / 0.31 ( 40) SS BOND : angle 2.59634 / 1.62 ( 80) hydrogen bonds : bond 0.06822 / 4.65 ( 965) hydrogen bonds : angle 5.02977 / 3.48 ( 2655) link_BETA1-4 : bond 0.00532 / 0.35 ( 31) link_BETA1-4 : angle 1.71145 / 1.13 ( 93) link_NAG-ASN : bond 0.00427 / 0.30 ( 46) link_NAG-ASN : angle 2.54048 / 2.25 ( 138) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 123 time to evaluate : 0.871 Fit side-chains REVERT: A 153 MET cc_start: 0.1534 (pmm) cc_final: 0.0284 (mtt) REVERT: A 160 TYR cc_start: 0.7204 (p90) cc_final: 0.6961 (p90) REVERT: A 560 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6558 (mt0) REVERT: B 140 PHE cc_start: 0.8026 (p90) cc_final: 0.7362 (p90) REVERT: C 449 LEU cc_start: 0.8801 (tp) cc_final: 0.8314 (tp) REVERT: C 490 GLN cc_start: 0.6672 (tm-30) cc_final: 0.5984 (tm-30) outliers start: 61 outliers final: 49 residues processed: 177 average time/residue: 0.1317 time to fit residues: 41.0053 Evaluate side-chains 169 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 119 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 309 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 550 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 720 THR Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1129 ILE Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 960 VAL Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1103 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 78 optimal weight: 0.4980 chunk 298 optimal weight: 0.9980 chunk 92 optimal weight: 0.6980 chunk 267 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 227 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 170 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 169 optimal weight: 0.7980 chunk 161 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.168395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.107251 restraints weight = 37926.874| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 3.15 r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25894 Z= 0.127 Angle : 0.595 11.085 35393 Z= 0.291 Chirality : 0.045 0.306 4208 Planarity : 0.003 0.054 4432 Dihedral : 4.190 23.503 3312 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.01 % Favored : 95.92 % Rotamer: Outliers : 1.66 % Allowed : 15.38 % Favored : 82.96 % 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: -0.31 (0.15), residues: 3040 helix: 1.71 (0.21), residues: 673 sheet: 0.37 (0.19), residues: 714 loop : -1.34 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 214 TYR 0.016 0.001 TYR A1064 PHE 0.017 0.001 PHE A1118 TRP 0.026 0.001 TRP C 104 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (25777) covalent geometry : angle 0.56324 / 0.28 (35082) SS BOND : bond 0.00337 / 0.20 ( 40) SS BOND : angle 2.11916 / 1.34 ( 80) hydrogen bonds : bond 0.05183 / 3.54 ( 965) hydrogen bonds : angle 4.74364 / 3.27 ( 2655) link_BETA1-4 : bond 0.00561 / 0.36 ( 31) link_BETA1-4 : angle 1.64153 / 1.09 ( 93) link_NAG-ASN : bond 0.00424 / 0.29 ( 46) link_NAG-ASN : angle 2.36361 / 2.14 ( 138) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 128 time to evaluate : 1.589 Fit side-chains REVERT: A 153 MET cc_start: 0.1508 (pmm) cc_final: 0.0232 (mtt) REVERT: A 160 TYR cc_start: 0.7237 (p90) cc_final: 0.7012 (p90) REVERT: A 560 GLN cc_start: 0.8147 (OUTLIER) cc_final: 0.6977 (mt0) REVERT: A 999 GLN cc_start: 0.8603 (tp40) cc_final: 0.8397 (tp40) REVERT: B 140 PHE cc_start: 0.7973 (p90) cc_final: 0.7322 (p90) REVERT: B 947 ASP cc_start: 0.9003 (t70) cc_final: 0.8436 (t0) REVERT: B 999 GLN cc_start: 0.8587 (tt0) cc_final: 0.8365 (mt0) REVERT: C 207 HIS cc_start: 0.7624 (m90) cc_final: 0.7244 (m90) REVERT: C 490 GLN cc_start: 0.6712 (tm-30) cc_final: 0.6172 (tm-30) REVERT: C 915 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.7718 (mp0) outliers start: 45 outliers final: 39 residues processed: 170 average time/residue: 0.1412 time to fit residues: 41.7690 Evaluate side-chains 163 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 122 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 578 THR Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 915 GLU Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 973 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 7 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 150 optimal weight: 0.3980 chunk 298 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 191 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 297 optimal weight: 0.2980 chunk 214 optimal weight: 0.0980 overall best weight: 0.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.169910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109340 restraints weight = 37848.891| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.12 r_work: 0.3255 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 25894 Z= 0.110 Angle : 0.572 11.115 35393 Z= 0.280 Chirality : 0.045 0.314 4208 Planarity : 0.003 0.053 4432 Dihedral : 3.946 21.108 3312 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 1.81 % Allowed : 15.30 % Favored : 82.88 % 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: -0.13 (0.15), residues: 3040 helix: 1.90 (0.21), residues: 666 sheet: 0.54 (0.19), residues: 728 loop : -1.28 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.016 0.001 TYR A1064 PHE 0.016 0.001 PHE A1118 TRP 0.034 0.001 TRP C 104 HIS 0.002 0.000 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (25777) covalent geometry : angle 0.54401 / 0.27 (35082) SS BOND : bond 0.00303 / 0.18 ( 40) SS BOND : angle 1.95865 / 1.27 ( 80) hydrogen bonds : bond 0.04499 / 3.06 ( 965) hydrogen bonds : angle 4.57390 / 3.14 ( 2655) link_BETA1-4 : bond 0.00556 / 0.36 ( 31) link_BETA1-4 : angle 1.59374 / 1.07 ( 93) link_NAG-ASN : bond 0.00420 / 0.28 ( 46) link_NAG-ASN : angle 2.18452 / 2.06 ( 138) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 123 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.1523 (pmm) cc_final: 0.0239 (mtt) REVERT: A 160 TYR cc_start: 0.7215 (p90) cc_final: 0.6999 (p90) REVERT: A 560 GLN cc_start: 0.8083 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: A 999 GLN cc_start: 0.8529 (tp40) cc_final: 0.8322 (tp40) REVERT: A 1026 MET cc_start: 0.8733 (tpp) cc_final: 0.8354 (ttm) REVERT: B 140 PHE cc_start: 0.7911 (p90) cc_final: 0.7182 (p90) REVERT: B 947 ASP cc_start: 0.8923 (t70) cc_final: 0.8355 (t0) REVERT: B 999 GLN cc_start: 0.8554 (tt0) cc_final: 0.8297 (mt0) REVERT: C 207 HIS cc_start: 0.7635 (m90) cc_final: 0.7257 (m90) REVERT: C 490 GLN cc_start: 0.6702 (tm-30) cc_final: 0.6218 (tm-30) outliers start: 49 outliers final: 43 residues processed: 165 average time/residue: 0.1410 time to fit residues: 40.8140 Evaluate side-chains 163 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 617 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 985 GLU Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1103 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 250 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 123 optimal weight: 0.9990 chunk 300 optimal weight: 1.9990 chunk 167 optimal weight: 3.9990 chunk 254 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 234 optimal weight: 0.9990 chunk 284 optimal weight: 0.0170 chunk 32 optimal weight: 20.0000 overall best weight: 1.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.167667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.106577 restraints weight = 38279.400| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.34 r_work: 0.3191 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25894 Z= 0.154 Angle : 0.598 10.847 35393 Z= 0.293 Chirality : 0.046 0.322 4208 Planarity : 0.004 0.053 4432 Dihedral : 4.058 22.189 3312 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 1.70 % Allowed : 15.60 % Favored : 82.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.15), residues: 3040 helix: 1.76 (0.21), residues: 675 sheet: 0.46 (0.19), residues: 720 loop : -1.28 (0.15), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1036 TYR 0.017 0.001 TYR B1064 PHE 0.020 0.001 PHE C1118 TRP 0.028 0.002 TRP C 104 HIS 0.004 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.15 (25777) covalent geometry : angle 0.57111 / 0.29 (35082) SS BOND : bond 0.00363 / 0.22 ( 40) SS BOND : angle 2.06881 / 1.31 ( 80) hydrogen bonds : bond 0.05091 / 3.47 ( 965) hydrogen bonds : angle 4.65133 / 3.20 ( 2655) link_BETA1-4 : bond 0.00548 / 0.36 ( 31) link_BETA1-4 : angle 1.59031 / 1.06 ( 93) link_NAG-ASN : bond 0.00380 / 0.26 ( 46) link_NAG-ASN : angle 2.16233 / 2.03 ( 138) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6080 Ramachandran restraints generated. 3040 Oldfield, 0 Emsley, 3040 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 119 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1606 (pmm) cc_final: 0.0317 (mtt) REVERT: A 160 TYR cc_start: 0.7182 (p90) cc_final: 0.6979 (p90) REVERT: A 560 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6941 (mt0) REVERT: A 999 GLN cc_start: 0.8371 (tp40) cc_final: 0.8128 (tp40) REVERT: B 140 PHE cc_start: 0.7981 (p90) cc_final: 0.7260 (p90) REVERT: B 947 ASP cc_start: 0.8786 (t70) cc_final: 0.8207 (t0) REVERT: B 999 GLN cc_start: 0.8429 (tt0) cc_final: 0.8139 (mt0) REVERT: C 490 GLN cc_start: 0.6612 (tm-30) cc_final: 0.6107 (tm-30) outliers start: 46 outliers final: 43 residues processed: 160 average time/residue: 0.1423 time to fit residues: 39.8800 Evaluate side-chains 161 residues out of total 2705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 522 CYS Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 693 THR Chi-restraints excluded: chain A residue 698 VAL Chi-restraints excluded: chain A residue 702 VAL Chi-restraints excluded: chain A residue 783 LYS Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1103 GLN Chi-restraints excluded: chain A residue 1133 THR Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 315 PHE Chi-restraints excluded: chain B residue 379 VAL Chi-restraints excluded: chain B residue 509 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 596 THR Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 756 PHE Chi-restraints excluded: chain B residue 823 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 976 ASP Chi-restraints excluded: chain B residue 1078 ILE Chi-restraints excluded: chain B residue 1102 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 508 VAL Chi-restraints excluded: chain C residue 514 LEU Chi-restraints excluded: chain C residue 531 VAL Chi-restraints excluded: chain C residue 548 VAL Chi-restraints excluded: chain C residue 585 THR Chi-restraints excluded: chain C residue 592 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 956 LEU Chi-restraints excluded: chain C residue 973 VAL Chi-restraints excluded: chain C residue 1078 ILE Chi-restraints excluded: chain C residue 1103 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 308 random chunks: chunk 103 optimal weight: 0.9990 chunk 305 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 chunk 84 optimal weight: 0.3980 chunk 170 optimal weight: 0.8980 chunk 266 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 254 optimal weight: 0.0970 chunk 155 optimal weight: 1.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.168339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.110062 restraints weight = 38053.332| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 3.30 r_work: 0.3217 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25894 Z= 0.128 Angle : 0.579 10.861 35393 Z= 0.284 Chirality : 0.045 0.313 4208 Planarity : 0.003 0.051 4432 Dihedral : 3.989 21.829 3312 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.34 % Favored : 95.59 % Rotamer: Outliers : 1.63 % Allowed : 15.71 % Favored : 82.66 % 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: -0.16 (0.15), residues: 3040 helix: 1.80 (0.21), residues: 675 sheet: 0.50 (0.19), residues: 718 loop : -1.26 (0.15), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 354 TYR 0.016 0.001 TYR A1064 PHE 0.017 0.001 PHE A1118 TRP 0.028 0.001 TRP C 104 HIS 0.003 0.001 HIS C1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (25777) covalent geometry : angle 0.55301 / 0.28 (35082) SS BOND : bond 0.00323 / 0.19 ( 40) SS BOND : angle 1.98583 / 1.26 ( 80) hydrogen bonds : bond 0.04835 / 3.29 ( 965) hydrogen bonds : angle 4.60694 / 3.16 ( 2655) link_BETA1-4 : bond 0.00554 / 0.36 ( 31) link_BETA1-4 : angle 1.58368 / 1.06 ( 93) link_NAG-ASN : bond 0.00387 / 0.26 ( 46) link_NAG-ASN : angle 2.09550 / 2.00 ( 138) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7412.02 seconds wall clock time: 127 minutes 28.37 seconds (7648.37 seconds total)