Starting phenix.real_space_refine on Sun Jul 5 03:30:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eaz_31047/07_2026/7eaz_31047.map" } resolution = 3.5 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= 0.043 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 105 5.16 5 C 15861 2.51 5 N 4038 2.21 5 O 4952 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 24956 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 7901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1013, 7901 Classifications: {'peptide': 1013} Link IDs: {'PTRANS': 50, 'TRANS': 962} Chain breaks: 7 Chain: "B" Number of atoms: 7964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7964 Classifications: {'peptide': 1020} Link IDs: {'PTRANS': 51, 'TRANS': 968} Chain breaks: 7 Chain: "C" Number of atoms: 7949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 7949 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 51, 'TRANS': 966} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 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: 6.17, per 1000 atoms: 0.25 Number of scatterers: 24956 At special positions: 0 Unit cell: (139.7, 143, 194.7, 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 105 16.00 O 4952 8.00 N 4038 7.00 C 15861 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 343 " " NAG A2005 " - " ASN A 603 " " NAG A2006 " - " ASN A 657 " " NAG B2002 " - " ASN B 122 " " NAG B2004 " - " ASN B 603 " " NAG B2005 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 603 " " NAG C2005 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 616 " " NAG H 1 " - " ASN A 709 " " NAG I 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 234 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 343 " " NAG R 1 " - " ASN B 616 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1074 " " NAG W 1 " - " ASN B1098 " " NAG X 1 " - " ASN B1134 " " NAG Y 1 " - " ASN C 234 " " NAG a 1 " - " ASN C 331 " " NAG b 1 " - " ASN C 343 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 709 " " NAG e 1 " - " ASN C 717 " " NAG f 1 " - " ASN C 801 " " NAG g 1 " - " ASN C1074 " " NAG h 1 " - " ASN C1098 " " NAG i 1 " - " ASN C1134 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 983.9 milliseconds 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5712 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 45 sheets defined 26.1% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.548A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.491A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.122A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.554A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 502 through 506 removed outlier: 3.680A pdb=" N TYR A 505 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 546 removed outlier: 4.162A pdb=" N LEU A 546 " --> pdb=" O PHE A 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 543 through 546' Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.360A pdb=" N GLU A 619 " --> pdb=" O ASN A 616 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 616 through 620' Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.551A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.601A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.861A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 910 removed outlier: 3.671A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 910 " --> pdb=" O PHE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.632A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.644A pdb=" N ILE A 923 " --> pdb=" O ASN A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.540A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.527A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.562A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 removed outlier: 3.756A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 removed outlier: 3.505A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.555A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.561A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 410 removed outlier: 4.186A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 635 through 639 removed outlier: 3.734A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.825A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.517A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.657A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.744A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.658A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.716A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.799A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 344 removed outlier: 3.589A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.731A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.053A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.331A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.056A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.779A pdb=" N GLU C 619 " --> pdb=" O ASN C 616 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 616 through 620' Processing helix chain 'C' and resid 632 through 636 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.792A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 4.224A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.584A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.797A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.586A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.546A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 removed outlier: 3.554A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.629A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.587A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.163A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE A 203 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.767A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 removed outlier: 3.930A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 323 through 326 removed outlier: 4.273A pdb=" N ASN A 540 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.269A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLY A 667 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 712 Processing sheet with id=AB3, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.728A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.686A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.609A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.448A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.728A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.563A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.719A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 323 through 328 removed outlier: 4.991A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.825A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 565 through 566 removed outlier: 6.859A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.570A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.811A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 670 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 728 removed outlier: 3.775A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1076 through 1078 removed outlier: 4.054A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.635A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 6.946A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.707A pdb=" N VAL C 47 " --> pdb=" O TYR C 279 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.569A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE C 238 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.615A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 326 through 328 removed outlier: 5.206A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 Processing sheet with id=AE3, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.371A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.738A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.849A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.849A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.549A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2460 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.14 Time building geometry restraints manager: 3.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7850 1.35 - 1.47: 6582 1.47 - 1.59: 10938 1.59 - 1.72: 0 1.72 - 1.84: 129 Bond restraints: 25499 Sorted by residual: bond pdb=" C1 NAG i 1 " pdb=" O5 NAG i 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.57e+00 bond pdb=" C1 NAG g 1 " pdb=" O5 NAG g 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.76e+00 bond pdb=" C1 NAG C2001 " pdb=" O5 NAG C2001 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG V 2 " pdb=" O5 NAG V 2 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.42e+00 bond pdb=" C1 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.18e+00 ... (remaining 25494 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 34012 2.09 - 4.18: 631 4.18 - 6.27: 46 6.27 - 8.36: 11 8.36 - 10.45: 4 Bond angle restraints: 34704 Sorted by residual: angle pdb=" CA GLY A 219 " pdb=" C GLY A 219 " pdb=" N PHE A 220 " ideal model delta sigma weight residual 114.23 117.09 -2.86 8.80e-01 1.29e+00 1.06e+01 angle pdb=" N LEU A 984 " pdb=" CA LEU A 984 " pdb=" C LEU A 984 " ideal model delta sigma weight residual 109.18 113.73 -4.55 1.42e+00 4.96e-01 1.03e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.58 -3.88 1.22e+00 6.72e-01 1.01e+01 angle pdb=" CA CYS C 649 " pdb=" CB CYS C 649 " pdb=" SG CYS C 649 " ideal model delta sigma weight residual 114.40 121.53 -7.13 2.30e+00 1.89e-01 9.62e+00 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 114.33 -3.63 1.22e+00 6.72e-01 8.86e+00 ... (remaining 34699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13160 17.98 - 35.96: 1106 35.96 - 53.94: 161 53.94 - 71.92: 36 71.92 - 89.90: 39 Dihedral angle restraints: 14502 sinusoidal: 5628 harmonic: 8874 Sorted by residual: dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.87 -88.87 1 1.00e+01 1.00e-02 9.41e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -169.35 83.35 1 1.00e+01 1.00e-02 8.49e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 175.53 -82.53 1 1.00e+01 1.00e-02 8.35e+01 ... (remaining 14499 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.197: 4175 0.197 - 0.394: 10 0.394 - 0.591: 2 0.591 - 0.788: 0 0.788 - 0.985: 1 Chirality restraints: 4188 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.42 -0.98 2.00e-01 2.50e+01 2.43e+01 chirality pdb=" C1 NAG Y 1 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG Y 1 " pdb=" O5 NAG Y 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.13e+00 chirality pdb=" C1 NAG A2006 " pdb=" ND2 ASN A 657 " pdb=" C2 NAG A2006 " pdb=" O5 NAG A2006 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.92e+00 ... (remaining 4185 not shown) Planarity restraints: 4423 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.035 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO A 986 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 987 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 97 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C LYS B 97 " 0.031 2.00e-02 2.50e+03 pdb=" O LYS B 97 " -0.012 2.00e-02 2.50e+03 pdb=" N SER B 98 " -0.010 2.00e-02 2.50e+03 ... (remaining 4420 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 703 2.70 - 3.25: 24013 3.25 - 3.80: 36379 3.80 - 4.35: 44833 4.35 - 4.90: 76877 Nonbonded interactions: 182805 Sorted by model distance: nonbonded pdb=" OG1 THR C 618 " pdb=" OE1 GLU C 619 " model vdw 2.146 3.040 nonbonded pdb=" O GLU A 661 " pdb=" OH TYR A 695 " model vdw 2.177 3.040 nonbonded pdb=" OG1 THR C 716 " pdb=" O GLN C1071 " model vdw 2.178 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.203 3.040 ... (remaining 182800 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 27 through 2005) selection = (chain 'B' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 2005)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 2005)) } ncs_group { reference = chain 'D' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.500 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.250 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25614 Z= 0.198 Angle : 0.740 18.440 35013 Z= 0.349 Chirality : 0.051 0.985 4188 Planarity : 0.004 0.063 4378 Dihedral : 13.836 89.897 8682 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: -1.15 (0.15), residues: 3003 helix: 1.56 (0.21), residues: 648 sheet: -0.48 (0.20), residues: 674 loop : -1.91 (0.14), residues: 1681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 102 TYR 0.013 0.001 TYR B1067 PHE 0.020 0.001 PHE A 823 TRP 0.017 0.001 TRP B 353 HIS 0.003 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.20 (25499) covalent geometry : angle 0.66739 / 0.33 (34704) SS BOND : bond 0.00324 / 0.17 ( 36) SS BOND : angle 1.78965 / 1.09 ( 72) hydrogen bonds : bond 0.13223 / 9.33 ( 909) hydrogen bonds : angle 5.66451 / 3.81 ( 2460) link_BETA1-4 : bond 0.00716 / 0.40 ( 34) link_BETA1-4 : angle 3.77372 / 3.02 ( 102) link_NAG-ASN : bond 0.00575 / 0.36 ( 45) link_NAG-ASN : angle 3.86571 / 2.40 ( 135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.7917 (mtp) cc_final: 0.7693 (mtp) REVERT: B 190 ARG cc_start: 0.6136 (mtt90) cc_final: 0.5684 (ttt180) REVERT: B 740 MET cc_start: 0.8259 (tpt) cc_final: 0.7956 (tpt) REVERT: C 342 PHE cc_start: 0.6894 (t80) cc_final: 0.6217 (t80) REVERT: C 994 ASP cc_start: 0.7743 (m-30) cc_final: 0.7533 (m-30) REVERT: C 1019 ARG cc_start: 0.8404 (tpt170) cc_final: 0.8183 (tpp-160) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1422 time to fit residues: 28.2276 Evaluate side-chains 89 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 919 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B 901 GLN B 919 ASN C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 544 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.133476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.088965 restraints weight = 56654.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.093947 restraints weight = 32036.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.094255 restraints weight = 19546.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.094639 restraints weight = 17887.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.094752 restraints weight = 16272.559| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 25614 Z= 0.124 Angle : 0.659 17.862 35013 Z= 0.310 Chirality : 0.046 0.606 4188 Planarity : 0.004 0.052 4378 Dihedral : 4.326 26.737 3260 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 0.41 % Allowed : 5.44 % Favored : 94.15 % 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: -0.97 (0.15), residues: 3003 helix: 1.62 (0.21), residues: 688 sheet: -0.29 (0.20), residues: 670 loop : -1.88 (0.14), residues: 1645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 34 TYR 0.016 0.001 TYR B1067 PHE 0.016 0.001 PHE A 823 TRP 0.019 0.001 TRP B 353 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (25499) covalent geometry : angle 0.60889 / 0.30 (34704) SS BOND : bond 0.00362 / 0.17 ( 36) SS BOND : angle 1.47519 / 0.89 ( 72) hydrogen bonds : bond 0.05697 / 3.77 ( 909) hydrogen bonds : angle 4.83386 / 3.27 ( 2460) link_BETA1-4 : bond 0.00705 / 0.40 ( 34) link_BETA1-4 : angle 2.63614 / 2.07 ( 102) link_NAG-ASN : bond 0.00594 / 0.37 ( 45) link_NAG-ASN : angle 3.32220 / 2.05 ( 135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 578 ASP cc_start: 0.8035 (p0) cc_final: 0.7681 (p0) REVERT: B 740 MET cc_start: 0.8155 (tpt) cc_final: 0.7889 (tpt) REVERT: C 342 PHE cc_start: 0.7005 (t80) cc_final: 0.6281 (t80) REVERT: C 994 ASP cc_start: 0.7696 (m-30) cc_final: 0.7492 (m-30) outliers start: 11 outliers final: 6 residues processed: 111 average time/residue: 0.1436 time to fit residues: 27.4601 Evaluate side-chains 90 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 697 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 126 optimal weight: 5.9990 chunk 153 optimal weight: 0.0980 chunk 299 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 289 optimal weight: 2.9990 chunk 124 optimal weight: 0.0570 chunk 84 optimal weight: 0.5980 chunk 214 optimal weight: 7.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1106 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.134606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090689 restraints weight = 55828.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.095411 restraints weight = 31689.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096049 restraints weight = 19544.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.096406 restraints weight = 17598.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096548 restraints weight = 15937.636| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25614 Z= 0.115 Angle : 0.626 20.383 35013 Z= 0.292 Chirality : 0.045 0.547 4188 Planarity : 0.004 0.048 4378 Dihedral : 4.125 25.179 3260 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.73 % Favored : 95.24 % Rotamer: Outliers : 0.71 % Allowed : 8.29 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 3003 helix: 1.84 (0.21), residues: 672 sheet: -0.18 (0.20), residues: 685 loop : -1.79 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.015 0.001 TYR B1067 PHE 0.027 0.001 PHE A 168 TRP 0.019 0.001 TRP B 353 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (25499) covalent geometry : angle 0.57908 / 0.28 (34704) SS BOND : bond 0.00290 / 0.15 ( 36) SS BOND : angle 1.34054 / 0.80 ( 72) hydrogen bonds : bond 0.05259 / 3.47 ( 909) hydrogen bonds : angle 4.59891 / 3.10 ( 2460) link_BETA1-4 : bond 0.00650 / 0.36 ( 34) link_BETA1-4 : angle 2.57528 / 2.03 ( 102) link_NAG-ASN : bond 0.00553 / 0.34 ( 45) link_NAG-ASN : angle 3.09100 / 1.91 ( 135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 578 ASP cc_start: 0.8031 (p0) cc_final: 0.7709 (p0) REVERT: B 740 MET cc_start: 0.8113 (tpt) cc_final: 0.7792 (tpt) REVERT: C 338 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8699 (t80) REVERT: C 342 PHE cc_start: 0.6963 (t80) cc_final: 0.6239 (t80) REVERT: C 918 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.6998 (mp0) outliers start: 19 outliers final: 10 residues processed: 121 average time/residue: 0.1415 time to fit residues: 29.1548 Evaluate side-chains 100 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 45 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 4 optimal weight: 0.2980 chunk 207 optimal weight: 5.9990 chunk 64 optimal weight: 4.9990 chunk 244 optimal weight: 6.9990 chunk 154 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN B 81 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 394 ASN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.132531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086868 restraints weight = 56599.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.092360 restraints weight = 32676.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093006 restraints weight = 19187.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.093649 restraints weight = 17069.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.093877 restraints weight = 15841.150| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25614 Z= 0.152 Angle : 0.646 21.237 35013 Z= 0.302 Chirality : 0.046 0.532 4188 Planarity : 0.004 0.046 4378 Dihedral : 4.164 23.126 3260 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 0.90 % Allowed : 10.69 % Favored : 88.41 % 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: -0.82 (0.15), residues: 3003 helix: 1.89 (0.21), residues: 664 sheet: -0.24 (0.20), residues: 695 loop : -1.80 (0.14), residues: 1644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 983 TYR 0.016 0.001 TYR B1067 PHE 0.022 0.001 PHE A 238 TRP 0.016 0.001 TRP B 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (25499) covalent geometry : angle 0.60143 / 0.29 (34704) SS BOND : bond 0.00299 / 0.16 ( 36) SS BOND : angle 1.39903 / 0.85 ( 72) hydrogen bonds : bond 0.05637 / 3.73 ( 909) hydrogen bonds : angle 4.60835 / 3.10 ( 2460) link_BETA1-4 : bond 0.00612 / 0.34 ( 34) link_BETA1-4 : angle 2.53902 / 2.00 ( 102) link_NAG-ASN : bond 0.00519 / 0.32 ( 45) link_NAG-ASN : angle 3.04371 / 1.89 ( 135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 95 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1132 ILE cc_start: 0.8616 (pt) cc_final: 0.8368 (pt) REVERT: B 190 ARG cc_start: 0.6236 (mtt90) cc_final: 0.5644 (ttt180) REVERT: B 578 ASP cc_start: 0.8087 (p0) cc_final: 0.7269 (p0) REVERT: B 740 MET cc_start: 0.8172 (tpt) cc_final: 0.7827 (tpt) REVERT: C 338 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8769 (t80) REVERT: C 342 PHE cc_start: 0.7050 (t80) cc_final: 0.6264 (t80) REVERT: C 918 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6975 (mp0) outliers start: 24 outliers final: 12 residues processed: 114 average time/residue: 0.1389 time to fit residues: 27.0090 Evaluate side-chains 99 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 125 optimal weight: 1.9990 chunk 223 optimal weight: 2.9990 chunk 112 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 15 optimal weight: 0.0270 chunk 232 optimal weight: 5.9990 chunk 39 optimal weight: 0.0170 chunk 259 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 83 optimal weight: 2.9990 chunk 29 optimal weight: 0.0570 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.133130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.087619 restraints weight = 56457.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.093052 restraints weight = 32555.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.093528 restraints weight = 19294.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.094271 restraints weight = 17001.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.094465 restraints weight = 15898.056| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25614 Z= 0.127 Angle : 0.628 21.609 35013 Z= 0.293 Chirality : 0.045 0.509 4188 Planarity : 0.004 0.045 4378 Dihedral : 4.073 21.749 3260 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.03 % Favored : 94.94 % Rotamer: Outliers : 1.20 % Allowed : 11.92 % Favored : 86.88 % 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: -0.73 (0.15), residues: 3003 helix: 1.93 (0.21), residues: 668 sheet: -0.13 (0.20), residues: 689 loop : -1.76 (0.14), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.015 0.001 TYR B1067 PHE 0.022 0.001 PHE B 168 TRP 0.014 0.001 TRP B 353 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (25499) covalent geometry : angle 0.58525 / 0.28 (34704) SS BOND : bond 0.00289 / 0.16 ( 36) SS BOND : angle 1.30220 / 0.79 ( 72) hydrogen bonds : bond 0.05362 / 3.54 ( 909) hydrogen bonds : angle 4.50893 / 3.04 ( 2460) link_BETA1-4 : bond 0.00634 / 0.36 ( 34) link_BETA1-4 : angle 2.48983 / 1.96 ( 102) link_NAG-ASN : bond 0.00528 / 0.32 ( 45) link_NAG-ASN : angle 2.94409 / 1.83 ( 135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 1132 ILE cc_start: 0.8588 (pt) cc_final: 0.8343 (pt) REVERT: B 190 ARG cc_start: 0.6226 (mtt90) cc_final: 0.5718 (ttt180) REVERT: B 740 MET cc_start: 0.8149 (tpt) cc_final: 0.7781 (tpt) REVERT: C 342 PHE cc_start: 0.7015 (t80) cc_final: 0.6215 (t80) REVERT: C 918 GLU cc_start: 0.7598 (OUTLIER) cc_final: 0.6872 (mp0) outliers start: 32 outliers final: 16 residues processed: 126 average time/residue: 0.1386 time to fit residues: 29.7583 Evaluate side-chains 107 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 274 optimal weight: 0.8980 chunk 214 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 163 optimal weight: 3.9990 chunk 202 optimal weight: 0.0270 chunk 159 optimal weight: 0.0370 chunk 41 optimal weight: 1.9990 chunk 145 optimal weight: 0.0980 chunk 33 optimal weight: 40.0000 chunk 132 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 GLN B 955 ASN C 134 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.134183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088673 restraints weight = 56657.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.094312 restraints weight = 32288.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.094710 restraints weight = 18871.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.095326 restraints weight = 16896.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.095933 restraints weight = 15896.805| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 25614 Z= 0.110 Angle : 0.616 21.417 35013 Z= 0.286 Chirality : 0.045 0.486 4188 Planarity : 0.004 0.045 4378 Dihedral : 3.937 21.607 3260 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 1.09 % Allowed : 13.16 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.15), residues: 3003 helix: 2.02 (0.21), residues: 666 sheet: -0.02 (0.20), residues: 684 loop : -1.71 (0.14), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 408 TYR 0.015 0.001 TYR B1067 PHE 0.016 0.001 PHE A 238 TRP 0.012 0.001 TRP B 353 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (25499) covalent geometry : angle 0.57529 / 0.28 (34704) SS BOND : bond 0.00310 / 0.19 ( 36) SS BOND : angle 1.21286 / 0.71 ( 72) hydrogen bonds : bond 0.04923 / 3.25 ( 909) hydrogen bonds : angle 4.39547 / 2.97 ( 2460) link_BETA1-4 : bond 0.00647 / 0.37 ( 34) link_BETA1-4 : angle 2.43046 / 1.91 ( 102) link_NAG-ASN : bond 0.00527 / 0.32 ( 45) link_NAG-ASN : angle 2.85209 / 1.77 ( 135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 408 ARG cc_start: 0.8323 (mtm-85) cc_final: 0.7951 (mtm-85) REVERT: B 740 MET cc_start: 0.8099 (tpt) cc_final: 0.7726 (tpt) REVERT: C 342 PHE cc_start: 0.6994 (t80) cc_final: 0.6186 (t80) REVERT: C 914 ASN cc_start: 0.7237 (t0) cc_final: 0.6337 (t0) REVERT: C 918 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6414 (mp0) outliers start: 29 outliers final: 15 residues processed: 127 average time/residue: 0.1367 time to fit residues: 29.7486 Evaluate side-chains 110 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 164 optimal weight: 1.9990 chunk 285 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 276 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 111 optimal weight: 0.0170 chunk 75 optimal weight: 2.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 955 ASN C 239 GLN ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.130747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.085233 restraints weight = 56866.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.089143 restraints weight = 33079.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.091613 restraints weight = 21337.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.091822 restraints weight = 18045.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.091923 restraints weight = 15821.919| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 25614 Z= 0.228 Angle : 0.710 23.027 35013 Z= 0.339 Chirality : 0.048 0.499 4188 Planarity : 0.004 0.042 4378 Dihedral : 4.378 21.173 3260 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.66 % Favored : 93.31 % Rotamer: Outliers : 1.35 % Allowed : 13.91 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.15), residues: 3003 helix: 1.73 (0.21), residues: 667 sheet: -0.35 (0.19), residues: 703 loop : -1.87 (0.14), residues: 1633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 102 TYR 0.019 0.001 TYR A 91 PHE 0.027 0.002 PHE B1121 TRP 0.011 0.002 TRP B 353 HIS 0.007 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.23 (25499) covalent geometry : angle 0.67129 / 0.33 (34704) SS BOND : bond 0.00378 / 0.20 ( 36) SS BOND : angle 1.54806 / 0.96 ( 72) hydrogen bonds : bond 0.06571 / 4.35 ( 909) hydrogen bonds : angle 4.77894 / 3.22 ( 2460) link_BETA1-4 : bond 0.00580 / 0.33 ( 34) link_BETA1-4 : angle 2.48853 / 1.97 ( 102) link_NAG-ASN : bond 0.00507 / 0.31 ( 45) link_NAG-ASN : angle 2.99362 / 1.87 ( 135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 86 time to evaluate : 0.951 Fit side-chains revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7881 (tm-30) REVERT: B 740 MET cc_start: 0.8232 (tpt) cc_final: 0.7878 (tpt) REVERT: C 342 PHE cc_start: 0.7139 (t80) cc_final: 0.6442 (t80) REVERT: C 918 GLU cc_start: 0.7608 (OUTLIER) cc_final: 0.6930 (mp0) outliers start: 36 outliers final: 24 residues processed: 117 average time/residue: 0.1369 time to fit residues: 27.4217 Evaluate side-chains 106 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 228 optimal weight: 4.9990 chunk 124 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 chunk 140 optimal weight: 30.0000 chunk 1 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 7 optimal weight: 0.0870 chunk 0 optimal weight: 5.9990 chunk 182 optimal weight: 2.9990 overall best weight: 2.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 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 = 0.4048 r_free = 0.4048 target = 0.129849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085689 restraints weight = 57319.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.088084 restraints weight = 32891.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.089705 restraints weight = 22632.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089765 restraints weight = 22159.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.089785 restraints weight = 18870.679| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 25614 Z= 0.203 Angle : 0.696 23.440 35013 Z= 0.329 Chirality : 0.047 0.506 4188 Planarity : 0.004 0.043 4378 Dihedral : 4.411 22.708 3260 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.23 % Favored : 93.74 % Rotamer: Outliers : 1.31 % Allowed : 14.70 % Favored : 83.99 % 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: -1.05 (0.15), residues: 3003 helix: 1.67 (0.21), residues: 667 sheet: -0.42 (0.20), residues: 694 loop : -1.93 (0.14), residues: 1642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 408 TYR 0.019 0.001 TYR A 91 PHE 0.022 0.002 PHE B 92 TRP 0.012 0.001 TRP B 353 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (25499) covalent geometry : angle 0.65702 / 0.32 (34704) SS BOND : bond 0.00373 / 0.20 ( 36) SS BOND : angle 1.53509 / 0.93 ( 72) hydrogen bonds : bond 0.06431 / 4.26 ( 909) hydrogen bonds : angle 4.74853 / 3.19 ( 2460) link_BETA1-4 : bond 0.00607 / 0.35 ( 34) link_BETA1-4 : angle 2.45776 / 1.93 ( 102) link_NAG-ASN : bond 0.00497 / 0.30 ( 45) link_NAG-ASN : angle 2.97147 / 1.86 ( 135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 89 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1017 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7952 (tm-30) REVERT: A 1115 ILE cc_start: 0.8753 (OUTLIER) cc_final: 0.8545 (mt) REVERT: B 740 MET cc_start: 0.8274 (tpt) cc_final: 0.7913 (tpt) REVERT: C 66 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.5199 (p-80) REVERT: C 342 PHE cc_start: 0.7138 (t80) cc_final: 0.6426 (t80) REVERT: C 918 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6885 (mp0) outliers start: 35 outliers final: 27 residues processed: 121 average time/residue: 0.1385 time to fit residues: 28.8722 Evaluate side-chains 117 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1115 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 89 optimal weight: 0.8980 chunk 288 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 258 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 94 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 173 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 261 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 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 = 0.4042 r_free = 0.4042 target = 0.129528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083608 restraints weight = 57187.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.089004 restraints weight = 33445.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.089710 restraints weight = 19776.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.090261 restraints weight = 18125.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090542 restraints weight = 16182.229| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25614 Z= 0.196 Angle : 0.701 23.403 35013 Z= 0.333 Chirality : 0.047 0.508 4188 Planarity : 0.004 0.044 4378 Dihedral : 4.458 23.131 3260 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.46 % Favored : 93.51 % Rotamer: Outliers : 1.39 % Allowed : 14.62 % Favored : 83.99 % 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: -1.11 (0.15), residues: 3003 helix: 1.67 (0.21), residues: 667 sheet: -0.44 (0.20), residues: 689 loop : -1.99 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 408 TYR 0.017 0.001 TYR A 91 PHE 0.025 0.002 PHE B 168 TRP 0.014 0.001 TRP C 104 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (25499) covalent geometry : angle 0.66155 / 0.32 (34704) SS BOND : bond 0.00360 / 0.21 ( 36) SS BOND : angle 1.70948 / 1.18 ( 72) hydrogen bonds : bond 0.06481 / 4.30 ( 909) hydrogen bonds : angle 4.76047 / 3.20 ( 2460) link_BETA1-4 : bond 0.00604 / 0.34 ( 34) link_BETA1-4 : angle 2.43655 / 1.91 ( 102) link_NAG-ASN : bond 0.00492 / 0.30 ( 45) link_NAG-ASN : angle 2.96596 / 1.86 ( 135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 89 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 994 ASP cc_start: 0.7842 (m-30) cc_final: 0.7613 (m-30) REVERT: B 740 MET cc_start: 0.8259 (tpt) cc_final: 0.7914 (tpt) REVERT: C 66 HIS cc_start: 0.6761 (OUTLIER) cc_final: 0.5251 (p-80) REVERT: C 342 PHE cc_start: 0.7139 (t80) cc_final: 0.6416 (t80) REVERT: C 918 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.6873 (mp0) outliers start: 37 outliers final: 30 residues processed: 124 average time/residue: 0.1393 time to fit residues: 29.5418 Evaluate side-chains 116 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 253 optimal weight: 0.9980 chunk 285 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 132 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 185 optimal weight: 0.0970 chunk 228 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 162 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 chunk 177 optimal weight: 0.7980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN C 774 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.132214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086939 restraints weight = 56948.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.092532 restraints weight = 32218.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.093246 restraints weight = 18708.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093792 restraints weight = 16572.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.094054 restraints weight = 15723.057| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25614 Z= 0.116 Angle : 0.650 22.274 35013 Z= 0.305 Chirality : 0.046 0.481 4188 Planarity : 0.004 0.048 4378 Dihedral : 4.107 21.950 3260 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.09 % Favored : 94.87 % Rotamer: Outliers : 1.05 % Allowed : 15.34 % Favored : 83.61 % 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: -0.79 (0.15), residues: 3003 helix: 1.94 (0.21), residues: 658 sheet: -0.19 (0.20), residues: 676 loop : -1.78 (0.14), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 408 TYR 0.017 0.001 TYR B1067 PHE 0.016 0.001 PHE A 238 TRP 0.019 0.001 TRP C 104 HIS 0.002 0.000 HIS C1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (25499) covalent geometry : angle 0.61235 / 0.30 (34704) SS BOND : bond 0.00281 / 0.15 ( 36) SS BOND : angle 1.52198 / 1.09 ( 72) hydrogen bonds : bond 0.05221 / 3.45 ( 909) hydrogen bonds : angle 4.44710 / 2.99 ( 2460) link_BETA1-4 : bond 0.00672 / 0.39 ( 34) link_BETA1-4 : angle 2.35398 / 1.83 ( 102) link_NAG-ASN : bond 0.00519 / 0.32 ( 45) link_NAG-ASN : angle 2.78055 / 1.73 ( 135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6006 Ramachandran restraints generated. 3003 Oldfield, 0 Emsley, 3003 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 GLU cc_start: 0.8491 (pp20) cc_final: 0.8089 (pp20) REVERT: B 740 MET cc_start: 0.8080 (tpt) cc_final: 0.7795 (tpt) REVERT: C 66 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.5357 (p-80) REVERT: C 342 PHE cc_start: 0.6985 (t80) cc_final: 0.6324 (t80) REVERT: C 918 GLU cc_start: 0.7549 (OUTLIER) cc_final: 0.6761 (mp0) outliers start: 28 outliers final: 21 residues processed: 124 average time/residue: 0.1407 time to fit residues: 30.1277 Evaluate side-chains 114 residues out of total 2667 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain C residue 61 ASN Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 918 GLU Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 250 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 209 optimal weight: 0.8980 chunk 300 optimal weight: 2.9990 chunk 119 optimal weight: 3.9990 chunk 297 optimal weight: 3.9990 chunk 301 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 955 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.130244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.086661 restraints weight = 56954.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.089210 restraints weight = 32413.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.090330 restraints weight = 22844.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.090490 restraints weight = 22187.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.090632 restraints weight = 18524.759| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25614 Z= 0.171 Angle : 0.676 22.536 35013 Z= 0.319 Chirality : 0.047 0.483 4188 Planarity : 0.004 0.046 4378 Dihedral : 4.233 22.548 3260 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.16 % Favored : 93.81 % Rotamer: Outliers : 1.12 % Allowed : 15.30 % Favored : 83.58 % 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: -0.87 (0.15), residues: 3003 helix: 1.82 (0.21), residues: 674 sheet: -0.27 (0.20), residues: 690 loop : -1.85 (0.14), residues: 1639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 408 TYR 0.015 0.001 TYR B1067 PHE 0.023 0.001 PHE B 168 TRP 0.013 0.001 TRP C 104 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (25499) covalent geometry : angle 0.63968 / 0.31 (34704) SS BOND : bond 0.00318 / 0.17 ( 36) SS BOND : angle 1.58962 / 1.10 ( 72) hydrogen bonds : bond 0.05915 / 3.92 ( 909) hydrogen bonds : angle 4.58389 / 3.08 ( 2460) link_BETA1-4 : bond 0.00611 / 0.35 ( 34) link_BETA1-4 : angle 2.34448 / 1.81 ( 102) link_NAG-ASN : bond 0.00474 / 0.29 ( 45) link_NAG-ASN : angle 2.82849 / 1.77 ( 135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3913.10 seconds wall clock time: 68 minutes 50.69 seconds (4130.69 seconds total)