Starting phenix.real_space_refine on Sun Jul 5 04:20:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v77_31761/07_2026/7v77_31761.map" } resolution = 3.3 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= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16089 2.51 5 N 4099 2.21 5 O 4994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s 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: 25293 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "B" Number of atoms: 8109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1038, 8109 Classifications: {'peptide': 1038} Link IDs: {'PTRANS': 53, 'TRANS': 984} Chain breaks: 7 Chain: "C" Number of atoms: 8053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8053 Classifications: {'peptide': 1032} Link IDs: {'PTRANS': 52, 'TRANS': 979} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.33, per 1000 atoms: 0.21 Number of scatterers: 25293 At special positions: 0 Unit cell: (141.9, 150.7, 198, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4994 8.00 N 4099 7.00 C 16089 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 298 " distance=2.03 Simple disulfide: pdb=" SG CYS A 333 " - pdb=" SG CYS A 358 " distance=2.03 Simple disulfide: pdb=" SG CYS A 376 " - pdb=" SG CYS A 429 " distance=2.03 Simple disulfide: pdb=" SG CYS A 388 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 485 " distance=2.03 Simple disulfide: pdb=" SG CYS A 535 " - pdb=" SG CYS A 587 " distance=2.04 Simple disulfide: pdb=" SG CYS A 659 " - pdb=" SG CYS A 668 " distance=2.03 Simple disulfide: pdb=" SG CYS A 735 " - pdb=" SG CYS A 757 " distance=2.02 Simple disulfide: pdb=" SG CYS A 740 " - pdb=" SG CYS A 746 " distance=2.03 Simple disulfide: pdb=" SG CYS A1029 " - pdb=" SG CYS A1040 " distance=2.03 Simple disulfide: pdb=" SG CYS A1079 " - pdb=" SG CYS A1123 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.02 Simple disulfide: pdb=" SG CYS B 288 " - pdb=" SG CYS B 298 " distance=2.03 Simple disulfide: pdb=" SG CYS B 333 " - pdb=" SG CYS B 358 " distance=2.03 Simple disulfide: pdb=" SG CYS B 376 " - pdb=" SG CYS B 429 " distance=2.03 Simple disulfide: pdb=" SG CYS B 388 " - pdb=" SG CYS B 522 " distance=2.03 Simple disulfide: pdb=" SG CYS B 477 " - pdb=" SG CYS B 485 " distance=2.03 Simple disulfide: pdb=" SG CYS B 535 " - pdb=" SG CYS B 587 " distance=2.04 Simple disulfide: pdb=" SG CYS B 614 " - pdb=" SG CYS B 646 " distance=2.03 Simple disulfide: pdb=" SG CYS B 659 " - pdb=" SG CYS B 668 " distance=2.02 Simple disulfide: pdb=" SG CYS B 735 " - pdb=" SG CYS B 757 " distance=2.03 Simple disulfide: pdb=" SG CYS B 740 " - pdb=" SG CYS B 746 " distance=2.03 Simple disulfide: pdb=" SG CYS B1029 " - pdb=" SG CYS B1040 " distance=2.02 Simple disulfide: pdb=" SG CYS B1079 " - pdb=" SG CYS B1123 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 288 " - pdb=" SG CYS C 298 " distance=2.03 Simple disulfide: pdb=" SG CYS C 333 " - pdb=" SG CYS C 358 " distance=2.03 Simple disulfide: pdb=" SG CYS C 376 " - pdb=" SG CYS C 429 " distance=2.03 Simple disulfide: pdb=" SG CYS C 388 " - pdb=" SG CYS C 522 " distance=2.03 Simple disulfide: pdb=" SG CYS C 477 " - pdb=" SG CYS C 485 " distance=2.03 Simple disulfide: pdb=" SG CYS C 535 " - pdb=" SG CYS C 587 " distance=2.02 Simple disulfide: pdb=" SG CYS C 659 " - pdb=" SG CYS C 668 " distance=2.03 Simple disulfide: pdb=" SG CYS C 735 " - pdb=" SG CYS C 757 " distance=2.03 Simple disulfide: pdb=" SG CYS C 740 " - pdb=" SG CYS C 746 " distance=2.03 Simple disulfide: pdb=" SG CYS C1029 " - pdb=" SG CYS C1040 " distance=2.03 Simple disulfide: pdb=" SG CYS C1079 " - pdb=" SG CYS C1123 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 234 " " NAG A2003 " - " ASN A 600 " " NAG A2004 " - " ASN A 654 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 234 " " NAG B2004 " - " ASN B 328 " " NAG B2005 " - " ASN B 600 " " NAG B2006 " - " ASN B 654 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 234 " " NAG C2005 " - " ASN C 340 " " NAG C2006 " - " ASN C 600 " " NAG C2007 " - " ASN C 654 " " NAG D 1 " - " ASN A 165 " " NAG E 1 " - " ASN A 279 " " NAG F 1 " - " ASN A 328 " " NAG G 1 " - " ASN A 340 " " NAG H 1 " - " ASN A 613 " " NAG I 1 " - " ASN A 706 " " NAG J 1 " - " ASN A 714 " " NAG K 1 " - " ASN A 798 " " NAG L 1 " - " ASN A1071 " " NAG M 1 " - " ASN A1095 " " NAG N 1 " - " ASN A1131 " " NAG O 1 " - " ASN B 165 " " NAG P 1 " - " ASN B 279 " " NAG Q 1 " - " ASN B 340 " " NAG R 1 " - " ASN B 613 " " NAG S 1 " - " ASN B 706 " " NAG T 1 " - " ASN B 714 " " NAG U 1 " - " ASN B 798 " " NAG V 1 " - " ASN B1071 " " NAG W 1 " - " ASN B1095 " " NAG X 1 " - " ASN B1131 " " NAG Y 1 " - " ASN C 279 " " NAG Z 1 " - " ASN C 328 " " NAG a 1 " - " ASN C 613 " " NAG b 1 " - " ASN C 706 " " NAG c 1 " - " ASN C 714 " " NAG d 1 " - " ASN C 798 " " NAG e 1 " - " ASN C1071 " " NAG f 1 " - " ASN C1095 " " NAG g 1 " - " ASN C1131 " Time building additional restraints: 2.47 Conformation dependent library (CDL) restraints added in 821.2 milliseconds 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5796 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 46 sheets defined 24.2% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 291 through 301 removed outlier: 3.589A pdb=" N THR A 296 " --> pdb=" O PRO A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 340 removed outlier: 3.564A pdb=" N PHE A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN A 340 " --> pdb=" O GLY A 336 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 335 through 340' Processing helix chain 'A' and resid 361 through 368 removed outlier: 4.329A pdb=" N LEU A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 385 removed outlier: 4.226A pdb=" N ASN A 385 " --> pdb=" O THR A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 419 Processing helix chain 'A' and resid 435 through 440 removed outlier: 3.510A pdb=" N SER A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 740 Processing helix chain 'A' and resid 743 through 752 removed outlier: 3.502A pdb=" N SER A 747 " --> pdb=" O SER A 743 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN A 752 " --> pdb=" O ASN A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 780 Processing helix chain 'A' and resid 813 through 823 removed outlier: 3.544A pdb=" N VAL A 823 " --> pdb=" O LEU A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 881 Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.645A pdb=" N ALA A 887 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 906 removed outlier: 4.137A pdb=" N TYR A 901 " --> pdb=" O MET A 897 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 906 " --> pdb=" O ARG A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 916 removed outlier: 3.526A pdb=" N TYR A 914 " --> pdb=" O GLN A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 938 Processing helix chain 'A' and resid 942 through 962 removed outlier: 3.551A pdb=" N GLN A 946 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 965 No H-bonds generated for 'chain 'A' and resid 963 through 965' Processing helix chain 'A' and resid 973 through 980 removed outlier: 3.578A pdb=" N ILE A 977 " --> pdb=" O VAL A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 1030 removed outlier: 4.400A pdb=" N VAL A 988 " --> pdb=" O PRO A 984 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1143 Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 335 through 340 Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.575A pdb=" N SER B 368 " --> pdb=" O VAL B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 384 removed outlier: 3.588A pdb=" N LEU B 384 " --> pdb=" O PRO B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 407 removed outlier: 3.670A pdb=" N GLU B 403 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL B 404 " --> pdb=" O GLY B 401 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ARG B 405 " --> pdb=" O ASP B 402 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 419 Processing helix chain 'B' and resid 630 through 635 Processing helix chain 'B' and resid 743 through 752 removed outlier: 3.840A pdb=" N GLN B 752 " --> pdb=" O ASN B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 780 removed outlier: 3.644A pdb=" N GLN B 759 " --> pdb=" O SER B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 823 removed outlier: 3.704A pdb=" N VAL B 823 " --> pdb=" O LEU B 819 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 881 Processing helix chain 'B' and resid 883 through 887 Processing helix chain 'B' and resid 895 through 905 removed outlier: 4.033A pdb=" N ALA B 900 " --> pdb=" O ALA B 896 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TYR B 901 " --> pdb=" O MET B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 910 through 916 removed outlier: 3.816A pdb=" N TYR B 914 " --> pdb=" O GLN B 910 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B 915 " --> pdb=" O ASN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 916 through 938 removed outlier: 3.872A pdb=" N GLN B 932 " --> pdb=" O ILE B 928 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 962 Processing helix chain 'B' and resid 963 through 965 No H-bonds generated for 'chain 'B' and resid 963 through 965' Processing helix chain 'B' and resid 973 through 981 Processing helix chain 'B' and resid 982 through 1030 removed outlier: 4.484A pdb=" N VAL B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN B 989 " --> pdb=" O GLU B 985 " (cutoff:3.500A) Processing helix chain 'B' and resid 1113 through 1115 No H-bonds generated for 'chain 'B' and resid 1113 through 1115' Processing helix chain 'B' and resid 1137 through 1143 removed outlier: 3.865A pdb=" N GLU B1141 " --> pdb=" O PRO B1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 301 Processing helix chain 'C' and resid 335 through 340 Processing helix chain 'C' and resid 361 through 368 removed outlier: 4.074A pdb=" N LEU C 365 " --> pdb=" O ASP C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 384 Processing helix chain 'C' and resid 402 through 404 No H-bonds generated for 'chain 'C' and resid 402 through 404' Processing helix chain 'C' and resid 413 through 419 Processing helix chain 'C' and resid 734 through 740 Processing helix chain 'C' and resid 743 through 752 removed outlier: 3.595A pdb=" N SER C 747 " --> pdb=" O SER C 743 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN C 752 " --> pdb=" O ASN C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 780 removed outlier: 4.254A pdb=" N GLN C 759 " --> pdb=" O SER C 755 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU C 764 " --> pdb=" O LEU C 760 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 823 removed outlier: 3.589A pdb=" N VAL C 823 " --> pdb=" O LEU C 819 " (cutoff:3.500A) Processing helix chain 'C' and resid 863 through 881 Processing helix chain 'C' and resid 883 through 887 Processing helix chain 'C' and resid 895 through 906 removed outlier: 4.145A pdb=" N TYR C 901 " --> pdb=" O MET C 897 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ILE C 906 " --> pdb=" O ARG C 902 " (cutoff:3.500A) Processing helix chain 'C' and resid 910 through 916 removed outlier: 3.838A pdb=" N TYR C 914 " --> pdb=" O GLN C 910 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 938 Processing helix chain 'C' and resid 942 through 962 removed outlier: 3.950A pdb=" N GLN C 946 " --> pdb=" O LEU C 942 " (cutoff:3.500A) Processing helix chain 'C' and resid 963 through 965 No H-bonds generated for 'chain 'C' and resid 963 through 965' Processing helix chain 'C' and resid 973 through 979 removed outlier: 3.790A pdb=" N ILE C 977 " --> pdb=" O VAL C 973 " (cutoff:3.500A) Processing helix chain 'C' and resid 982 through 1030 removed outlier: 4.186A pdb=" N VAL C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1143 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.363A pdb=" N ASN A 61 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N TYR A 266 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.124A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP A 284 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.386A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 8.531A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.691A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.700A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 308 through 316 removed outlier: 5.230A pdb=" N ILE A 309 " --> pdb=" O THR A 596 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR A 596 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 5.553A pdb=" N GLN A 311 " --> pdb=" O VAL A 594 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL A 594 " --> pdb=" O GLN A 311 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N SER A 313 " --> pdb=" O VAL A 592 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY A 591 " --> pdb=" O GLN A 610 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 removed outlier: 3.620A pdb=" N PHE A 540 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 355 removed outlier: 3.603A pdb=" N ASN A 391 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 449 through 451 Processing sheet with id=AA9, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB1, first strand: chain 'A' and resid 570 through 573 removed outlier: 4.089A pdb=" N ALA A 572 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE B 43 " --> pdb=" O PHE A 562 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 651 through 652 removed outlier: 5.889A pdb=" N GLU A 651 " --> pdb=" O ALA A 691 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N THR A 693 " --> pdb=" O GLU A 651 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA A 669 " --> pdb=" O PRO A 662 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 708 through 709 Processing sheet with id=AB4, first strand: chain 'A' and resid 714 through 725 removed outlier: 3.561A pdb=" N MET A1047 " --> pdb=" O VAL A1062 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N TYR A1064 " --> pdb=" O HIS A1045 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N HIS A1045 " --> pdb=" O TYR A1064 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 730 through 733 removed outlier: 4.512A pdb=" N LYS A 730 " --> pdb=" O LEU A 858 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 785 through 786 removed outlier: 5.699A pdb=" N ILE A 785 " --> pdb=" O ASN C 700 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 1117 through 1122 removed outlier: 4.835A pdb=" N ALA A1084 " --> pdb=" O SER A1120 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1091 through 1094 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 7.705A pdb=" N ASN B 61 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR B 266 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.060A pdb=" N ASP B 284 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.834A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.806A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 10.134A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 308 through 316 removed outlier: 5.623A pdb=" N ILE B 309 " --> pdb=" O THR B 596 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N THR B 596 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLN B 311 " --> pdb=" O VAL B 594 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL B 594 " --> pdb=" O GLN B 311 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLY B 591 " --> pdb=" O GLN B 610 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 322 through 325 removed outlier: 5.450A pdb=" N ASP B 571 " --> pdb=" O ILE B 584 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 572 " --> pdb=" O GLY B 563 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 351 through 355 Processing sheet with id=AC6, first strand: chain 'B' and resid 358 through 359 removed outlier: 6.434A pdb=" N CYS B 358 " --> pdb=" O CYS B 522 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 449 through 451 Processing sheet with id=AC8, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AC9, first strand: chain 'B' and resid 651 through 652 removed outlier: 6.060A pdb=" N GLU B 651 " --> pdb=" O ALA B 691 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N THR B 693 " --> pdb=" O GLU B 651 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ALA B 669 " --> pdb=" O PRO B 662 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 699 through 700 Processing sheet with id=AD2, first strand: chain 'B' and resid 714 through 725 removed outlier: 6.079A pdb=" N TYR B1064 " --> pdb=" O HIS B1045 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N HIS B1045 " --> pdb=" O TYR B1064 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 730 through 733 removed outlier: 4.481A pdb=" N LYS B 730 " --> pdb=" O LEU B 858 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1117 through 1122 removed outlier: 3.514A pdb=" N SER B1120 " --> pdb=" O ALA B1084 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ALA B1084 " --> pdb=" O SER B1120 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1091 through 1094 removed outlier: 4.763A pdb=" N GLN B1103 " --> pdb=" O GLU B1108 " (cutoff:3.500A) removed outlier: 5.575A pdb=" N GLU B1108 " --> pdb=" O GLN B1103 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 5.827A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.951A pdb=" N ASP C 284 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.319A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.669A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.920A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 307 through 316 removed outlier: 3.536A pdb=" N THR C 312 " --> pdb=" O VAL C 592 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N VAL C 592 " --> pdb=" O THR C 312 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ASN C 314 " --> pdb=" O GLY C 590 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLY C 590 " --> pdb=" O ASN C 314 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLY C 591 " --> pdb=" O GLN C 610 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 322 through 323 Processing sheet with id=AE2, first strand: chain 'C' and resid 351 through 355 Processing sheet with id=AE3, first strand: chain 'C' and resid 449 through 451 Processing sheet with id=AE4, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AE5, first strand: chain 'C' and resid 562 through 564 removed outlier: 4.051A pdb=" N ALA C 572 " --> pdb=" O GLY C 563 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 651 through 652 removed outlier: 6.308A pdb=" N GLU C 651 " --> pdb=" O ALA C 691 " (cutoff:3.500A) removed outlier: 8.752A pdb=" N THR C 693 " --> pdb=" O GLU C 651 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ALA C 669 " --> pdb=" O PRO C 662 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 708 through 725 removed outlier: 6.723A pdb=" N SER C 708 " --> pdb=" O THR C1073 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR C1073 " --> pdb=" O SER C 708 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ALA C 710 " --> pdb=" O ASN C1071 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ASN C1071 " --> pdb=" O ALA C 710 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N GLU C1069 " --> pdb=" O PRO C 712 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET C1047 " --> pdb=" O VAL C1062 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N TYR C1064 " --> pdb=" O HIS C1045 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N HIS C1045 " --> pdb=" O TYR C1064 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 730 through 733 removed outlier: 4.402A pdb=" N LYS C 730 " --> pdb=" O LEU C 858 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1117 through 1122 removed outlier: 4.113A pdb=" N ALA C1084 " --> pdb=" O SER C1120 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1091 through 1094 964 hydrogen bonds defined for protein. 2640 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: 5.70 Time building geometry restraints manager: 3.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7962 1.34 - 1.46: 6376 1.46 - 1.58: 11378 1.58 - 1.70: 0 1.70 - 1.82: 138 Bond restraints: 25854 Sorted by residual: bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C1 NAG V 1 " pdb=" O5 NAG V 1 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C1 NAG O 1 " pdb=" O5 NAG O 1 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C PRO A 983 " pdb=" N PRO A 984 " ideal model delta sigma weight residual 1.334 1.372 -0.039 2.34e-02 1.83e+03 2.72e+00 bond pdb=" C1 NAG e 1 " pdb=" O5 NAG e 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.62e+00 ... (remaining 25849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 33916 1.56 - 3.12: 1126 3.12 - 4.68: 111 4.68 - 6.25: 23 6.25 - 7.81: 15 Bond angle restraints: 35191 Sorted by residual: angle pdb=" C ILE B 197 " pdb=" N ASP B 198 " pdb=" CA ASP B 198 " ideal model delta sigma weight residual 121.54 126.82 -5.28 1.91e+00 2.74e-01 7.65e+00 angle pdb=" CA CYS B 522 " pdb=" CB CYS B 522 " pdb=" SG CYS B 522 " ideal model delta sigma weight residual 114.40 120.69 -6.29 2.30e+00 1.89e-01 7.48e+00 angle pdb=" N PRO A 983 " pdb=" CA PRO A 983 " pdb=" C PRO A 983 " ideal model delta sigma weight residual 110.70 113.88 -3.18 1.22e+00 6.72e-01 6.81e+00 angle pdb=" CA CYS B 388 " pdb=" CB CYS B 388 " pdb=" SG CYS B 388 " ideal model delta sigma weight residual 114.40 120.09 -5.69 2.30e+00 1.89e-01 6.11e+00 angle pdb=" CA CYS C 131 " pdb=" CB CYS C 131 " pdb=" SG CYS C 131 " ideal model delta sigma weight residual 114.40 119.98 -5.58 2.30e+00 1.89e-01 5.89e+00 ... (remaining 35186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13369 17.95 - 35.90: 1112 35.90 - 53.84: 200 53.84 - 71.79: 42 71.79 - 89.74: 18 Dihedral angle restraints: 14741 sinusoidal: 5723 harmonic: 9018 Sorted by residual: dihedral pdb=" CB CYS C 288 " pdb=" SG CYS C 288 " pdb=" SG CYS C 298 " pdb=" CB CYS C 298 " ideal model delta sinusoidal sigma weight residual -86.00 -174.96 88.96 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 1.96 -87.96 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS C 388 " pdb=" SG CYS C 388 " pdb=" SG CYS C 522 " pdb=" CB CYS C 522 " ideal model delta sinusoidal sigma weight residual -86.00 0.63 -86.63 1 1.00e+01 1.00e-02 9.04e+01 ... (remaining 14738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 4185 0.131 - 0.263: 32 0.263 - 0.394: 0 0.394 - 0.526: 0 0.526 - 0.657: 1 Chirality restraints: 4218 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN A 328 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C1 NAG C2002 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C2002 " pdb=" O5 NAG C2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 4215 not shown) Planarity restraints: 4494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 138 " -0.050 5.00e-02 4.00e+02 7.53e-02 9.08e+00 pdb=" N PRO C 139 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 139 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 139 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 216 " -0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO A 217 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN B1071 " -0.021 2.00e-02 2.50e+03 1.95e-02 4.74e+00 pdb=" CG ASN B1071 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN B1071 " -0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN B1071 " 0.022 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " -0.021 2.00e-02 2.50e+03 ... (remaining 4491 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 376 2.64 - 3.21: 23168 3.21 - 3.77: 36542 3.77 - 4.34: 49482 4.34 - 4.90: 82466 Nonbonded interactions: 192034 Sorted by model distance: nonbonded pdb=" OD2 ASP A 575 " pdb=" OG1 THR A 578 " model vdw 2.077 3.040 nonbonded pdb=" OD2 ASP C 575 " pdb=" OG1 THR C 578 " model vdw 2.119 3.040 nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.137 3.120 nonbonded pdb=" NH1 ARG A 902 " pdb=" O LEU A1046 " model vdw 2.181 3.120 nonbonded pdb=" O GLU C 658 " pdb=" OH TYR C 692 " model vdw 2.181 3.040 ... (remaining 192029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 618 or resid 632 through 824 or resid 852 throu \ gh 2004)) selection = (chain 'C' and resid 14 through 2004) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 23.720 Find NCS groups from input model: 0.950 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:1.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 25971 Z= 0.237 Angle : 0.686 14.790 35502 Z= 0.336 Chirality : 0.048 0.657 4218 Planarity : 0.004 0.075 4447 Dihedral : 13.413 89.740 8825 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.22 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.49 (0.15), residues: 3054 helix: 1.47 (0.21), residues: 669 sheet: 0.34 (0.20), residues: 694 loop : -1.43 (0.14), residues: 1691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.017 0.001 TYR C 870 PHE 0.029 0.001 PHE C 903 TRP 0.024 0.001 TRP A 883 HIS 0.003 0.001 HIS A1061 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.24 (25854) covalent geometry : angle 0.64785 / 0.33 (35191) SS BOND : bond 0.00358 / 0.22 ( 40) SS BOND : angle 2.50748 / 1.73 ( 80) hydrogen bonds : bond 0.11876 / 8.06 ( 964) hydrogen bonds : angle 5.89398 / 4.06 ( 2640) link_BETA1-4 : bond 0.00316 / 0.18 ( 30) link_BETA1-4 : angle 1.67762 / 1.07 ( 90) link_NAG-ASN : bond 0.00310 / 0.18 ( 47) link_NAG-ASN : angle 2.88029 / 2.10 ( 141) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8287 (m-80) cc_final: 0.7927 (m-80) REVERT: A 106 PHE cc_start: 0.5534 (m-80) cc_final: 0.5332 (m-80) REVERT: A 237 ARG cc_start: 0.8158 (mtp180) cc_final: 0.7641 (ptp-170) REVERT: B 52 GLN cc_start: 0.8665 (pp30) cc_final: 0.8165 (pp30) REVERT: B 153 MET cc_start: 0.4158 (pmm) cc_final: 0.3494 (pmm) REVERT: B 433 TRP cc_start: 0.7500 (p90) cc_final: 0.7125 (p90) REVERT: B 773 LYS cc_start: 0.8792 (tmmt) cc_final: 0.8544 (tmmt) REVERT: B 852 PHE cc_start: 0.6779 (m-80) cc_final: 0.6451 (m-10) REVERT: B 855 LEU cc_start: 0.8359 (pt) cc_final: 0.7935 (mp) REVERT: B 866 MET cc_start: 0.8560 (mtm) cc_final: 0.8347 (mtt) REVERT: B 883 TRP cc_start: 0.7689 (p90) cc_final: 0.7221 (p90) REVERT: C 140 PHE cc_start: 0.7878 (p90) cc_final: 0.7624 (p90) REVERT: C 745 GLU cc_start: 0.7319 (tp30) cc_final: 0.7108 (tp30) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.1503 time to fit residues: 41.8201 Evaluate side-chains 124 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 124 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 30.0000 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.0050 chunk 183 optimal weight: 0.0470 chunk 298 optimal weight: 0.6980 overall best weight: 0.4292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 207 HIS B 239 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.202908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.136355 restraints weight = 42459.454| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 3.64 r_work: 0.3669 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25971 Z= 0.110 Angle : 0.588 13.955 35502 Z= 0.286 Chirality : 0.045 0.461 4218 Planarity : 0.004 0.051 4447 Dihedral : 4.164 22.233 3325 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 0.18 % Allowed : 5.58 % Favored : 94.24 % 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: -0.35 (0.15), residues: 3054 helix: 1.68 (0.21), residues: 669 sheet: 0.38 (0.19), residues: 706 loop : -1.37 (0.14), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 214 TYR 0.019 0.001 TYR C1064 PHE 0.025 0.001 PHE A 55 TRP 0.011 0.001 TRP A 883 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.11 (25854) covalent geometry : angle 0.55487 / 0.28 (35191) SS BOND : bond 0.00314 / 0.19 ( 40) SS BOND : angle 2.03956 / 1.39 ( 80) hydrogen bonds : bond 0.04485 / 2.97 ( 964) hydrogen bonds : angle 4.93158 / 3.40 ( 2640) link_BETA1-4 : bond 0.00432 / 0.26 ( 30) link_BETA1-4 : angle 1.26659 / 0.85 ( 90) link_NAG-ASN : bond 0.00381 / 0.25 ( 47) link_NAG-ASN : angle 2.58854 / 1.77 ( 141) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8341 (m-80) cc_final: 0.8009 (m-80) REVERT: A 200 TYR cc_start: 0.7362 (m-80) cc_final: 0.7115 (t80) REVERT: A 773 LYS cc_start: 0.8839 (tptp) cc_final: 0.8631 (tptp) REVERT: B 52 GLN cc_start: 0.8785 (pp30) cc_final: 0.8365 (pp30) REVERT: B 354 ARG cc_start: 0.7279 (mtt180) cc_final: 0.6907 (mtt180) REVERT: B 433 TRP cc_start: 0.7513 (p90) cc_final: 0.7253 (p90) REVERT: B 630 TRP cc_start: 0.7285 (m-10) cc_final: 0.6731 (m100) REVERT: B 883 TRP cc_start: 0.7827 (p90) cc_final: 0.7381 (p90) outliers start: 5 outliers final: 3 residues processed: 148 average time/residue: 0.1424 time to fit residues: 36.3381 Evaluate side-chains 123 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 120 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 566 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 897 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 292 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 216 optimal weight: 10.0000 chunk 105 optimal weight: 0.0020 chunk 178 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN A 911 ASN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN C 911 ASN C 923 GLN C1103 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4564 r_free = 0.4564 target = 0.198910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.130993 restraints weight = 42215.615| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 3.51 r_work: 0.3459 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25971 Z= 0.189 Angle : 0.625 11.531 35502 Z= 0.307 Chirality : 0.046 0.436 4218 Planarity : 0.004 0.046 4447 Dihedral : 4.310 24.512 3325 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.60 % Favored : 94.30 % Rotamer: Outliers : 1.00 % Allowed : 8.54 % Favored : 90.47 % 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: -0.50 (0.15), residues: 3054 helix: 1.47 (0.21), residues: 676 sheet: 0.26 (0.19), residues: 709 loop : -1.42 (0.15), residues: 1669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1036 TYR 0.023 0.001 TYR C1064 PHE 0.029 0.002 PHE C 238 TRP 0.018 0.001 TRP A 883 HIS 0.005 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (25854) covalent geometry : angle 0.59630 / 0.30 (35191) SS BOND : bond 0.00428 / 0.25 ( 40) SS BOND : angle 2.15781 / 1.45 ( 80) hydrogen bonds : bond 0.04892 / 3.26 ( 964) hydrogen bonds : angle 4.93722 / 3.40 ( 2640) link_BETA1-4 : bond 0.00356 / 0.21 ( 30) link_BETA1-4 : angle 1.35246 / 0.91 ( 90) link_NAG-ASN : bond 0.00455 / 0.32 ( 47) link_NAG-ASN : angle 2.43207 / 1.71 ( 141) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8507 (m-80) cc_final: 0.8143 (m-80) REVERT: A 189 LEU cc_start: 0.8020 (tt) cc_final: 0.7629 (tp) REVERT: A 200 TYR cc_start: 0.7289 (m-80) cc_final: 0.6936 (t80) REVERT: B 52 GLN cc_start: 0.8887 (pp30) cc_final: 0.8426 (pp30) REVERT: B 393 TYR cc_start: 0.7605 (m-80) cc_final: 0.7135 (m-80) REVERT: B 433 TRP cc_start: 0.7426 (p90) cc_final: 0.7140 (p90) REVERT: B 521 VAL cc_start: 0.5049 (OUTLIER) cc_final: 0.4788 (p) REVERT: B 630 TRP cc_start: 0.7358 (m-10) cc_final: 0.6801 (m100) REVERT: C 53 ASP cc_start: 0.7084 (OUTLIER) cc_final: 0.6798 (m-30) outliers start: 27 outliers final: 13 residues processed: 150 average time/residue: 0.1220 time to fit residues: 32.1102 Evaluate side-chains 128 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 113 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 978 LEU Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 521 VAL Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 751 LEU Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1111 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 38 optimal weight: 30.0000 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 72 optimal weight: 0.2980 chunk 141 optimal weight: 3.9990 chunk 274 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 209 optimal weight: 6.9990 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.199652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.134033 restraints weight = 41936.089| |-----------------------------------------------------------------------------| r_work (start): 0.3776 rms_B_bonded: 3.62 r_work: 0.3592 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25971 Z= 0.141 Angle : 0.588 11.126 35502 Z= 0.287 Chirality : 0.045 0.425 4218 Planarity : 0.004 0.046 4447 Dihedral : 4.181 24.363 3325 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.75 % Favored : 95.15 % Rotamer: Outliers : 1.18 % Allowed : 10.27 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.15), residues: 3054 helix: 1.64 (0.21), residues: 669 sheet: 0.23 (0.19), residues: 708 loop : -1.40 (0.15), residues: 1677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1036 TYR 0.020 0.001 TYR C1064 PHE 0.019 0.001 PHE B1118 TRP 0.018 0.001 TRP A 883 HIS 0.003 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (25854) covalent geometry : angle 0.55813 / 0.28 (35191) SS BOND : bond 0.00396 / 0.23 ( 40) SS BOND : angle 2.25039 / 1.48 ( 80) hydrogen bonds : bond 0.04439 / 2.94 ( 964) hydrogen bonds : angle 4.76914 / 3.29 ( 2640) link_BETA1-4 : bond 0.00362 / 0.22 ( 30) link_BETA1-4 : angle 1.30539 / 0.88 ( 90) link_NAG-ASN : bond 0.00348 / 0.22 ( 47) link_NAG-ASN : angle 2.29108 / 1.65 ( 141) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 128 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8500 (m-80) cc_final: 0.8195 (m-80) REVERT: A 189 LEU cc_start: 0.8114 (tt) cc_final: 0.7716 (tp) REVERT: A 200 TYR cc_start: 0.7304 (m-80) cc_final: 0.6963 (t80) REVERT: A 875 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7841 (tt) REVERT: B 52 GLN cc_start: 0.8881 (pp30) cc_final: 0.8392 (pp30) REVERT: B 393 TYR cc_start: 0.7682 (m-80) cc_final: 0.7273 (m-80) REVERT: B 433 TRP cc_start: 0.7617 (p90) cc_final: 0.7340 (p90) REVERT: B 578 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8184 (p) REVERT: B 630 TRP cc_start: 0.7391 (m-10) cc_final: 0.6810 (m100) REVERT: B 875 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8419 (tt) REVERT: C 53 ASP cc_start: 0.7030 (OUTLIER) cc_final: 0.6743 (m-30) outliers start: 32 outliers final: 14 residues processed: 154 average time/residue: 0.1312 time to fit residues: 34.6457 Evaluate side-chains 138 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 106 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 45 optimal weight: 50.0000 chunk 139 optimal weight: 20.0000 chunk 259 optimal weight: 0.9990 chunk 260 optimal weight: 2.9990 chunk 137 optimal weight: 20.0000 chunk 109 optimal weight: 4.9990 chunk 197 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN B 239 GLN B 242 HIS ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 748 ASN B 898 GLN ** B 910 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4547 r_free = 0.4547 target = 0.179200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.115695 restraints weight = 40961.544| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 3.44 r_work: 0.3472 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25971 Z= 0.186 Angle : 0.621 10.900 35502 Z= 0.303 Chirality : 0.046 0.422 4218 Planarity : 0.004 0.046 4447 Dihedral : 4.269 25.576 3325 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.53 % Favored : 94.37 % Rotamer: Outliers : 1.63 % Allowed : 11.16 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.15), residues: 3054 helix: 1.59 (0.21), residues: 663 sheet: 0.20 (0.19), residues: 691 loop : -1.43 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1036 TYR 0.022 0.001 TYR C1064 PHE 0.026 0.002 PHE B1118 TRP 0.022 0.001 TRP A 883 HIS 0.005 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.19 (25854) covalent geometry : angle 0.59265 / 0.30 (35191) SS BOND : bond 0.00446 / 0.27 ( 40) SS BOND : angle 2.22075 / 1.47 ( 80) hydrogen bonds : bond 0.04797 / 3.19 ( 964) hydrogen bonds : angle 4.82419 / 3.32 ( 2640) link_BETA1-4 : bond 0.00337 / 0.20 ( 30) link_BETA1-4 : angle 1.34044 / 0.90 ( 90) link_NAG-ASN : bond 0.00382 / 0.26 ( 47) link_NAG-ASN : angle 2.32795 / 1.67 ( 141) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 125 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8556 (m-80) cc_final: 0.8220 (m-80) REVERT: A 189 LEU cc_start: 0.8075 (tt) cc_final: 0.7675 (tp) REVERT: A 200 TYR cc_start: 0.7294 (m-80) cc_final: 0.6954 (t80) REVERT: A 270 ARG cc_start: 0.6965 (ptm160) cc_final: 0.6469 (ptm160) REVERT: A 875 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.7872 (tt) REVERT: B 52 GLN cc_start: 0.8802 (pp30) cc_final: 0.8307 (pp30) REVERT: B 393 TYR cc_start: 0.7666 (m-80) cc_final: 0.7323 (m-80) REVERT: B 433 TRP cc_start: 0.7481 (p90) cc_final: 0.7153 (p90) REVERT: B 578 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8195 (p) REVERT: B 630 TRP cc_start: 0.7237 (m-10) cc_final: 0.6742 (m100) REVERT: B 875 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8468 (tt) REVERT: C 53 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.6985 (m-30) REVERT: C 561 GLN cc_start: 0.7623 (mm-40) cc_final: 0.7347 (mt0) outliers start: 44 outliers final: 27 residues processed: 164 average time/residue: 0.1272 time to fit residues: 36.4748 Evaluate side-chains 148 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 117 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 875 LEU Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 294 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 273 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 210 optimal weight: 0.9990 chunk 0 optimal weight: 50.0000 chunk 306 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN ** B 391 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.199413 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.133140 restraints weight = 41891.752| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.60 r_work: 0.3596 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25971 Z= 0.127 Angle : 0.587 10.768 35502 Z= 0.285 Chirality : 0.044 0.414 4218 Planarity : 0.003 0.046 4447 Dihedral : 4.166 31.732 3325 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 1.66 % Allowed : 12.08 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.42 (0.15), residues: 3054 helix: 1.77 (0.21), residues: 662 sheet: 0.22 (0.19), residues: 692 loop : -1.40 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 214 TYR 0.018 0.001 TYR C1064 PHE 0.018 0.001 PHE A 55 TRP 0.016 0.001 TRP A 883 HIS 0.003 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (25854) covalent geometry : angle 0.55797 / 0.28 (35191) SS BOND : bond 0.00375 / 0.21 ( 40) SS BOND : angle 2.32947 / 1.52 ( 80) hydrogen bonds : bond 0.04299 / 2.85 ( 964) hydrogen bonds : angle 4.68048 / 3.23 ( 2640) link_BETA1-4 : bond 0.00368 / 0.23 ( 30) link_BETA1-4 : angle 1.29051 / 0.87 ( 90) link_NAG-ASN : bond 0.00335 / 0.21 ( 47) link_NAG-ASN : angle 2.22561 / 1.62 ( 141) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 135 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8502 (m-80) cc_final: 0.8189 (m-80) REVERT: A 189 LEU cc_start: 0.8076 (tt) cc_final: 0.7673 (tp) REVERT: A 200 TYR cc_start: 0.7230 (m-80) cc_final: 0.6882 (t80) REVERT: A 560 GLN cc_start: 0.6341 (OUTLIER) cc_final: 0.6043 (mt0) REVERT: A 875 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7925 (tt) REVERT: B 52 GLN cc_start: 0.8838 (pp30) cc_final: 0.8338 (pp30) REVERT: B 239 GLN cc_start: 0.6713 (OUTLIER) cc_final: 0.6404 (mm110) REVERT: B 393 TYR cc_start: 0.7780 (m-80) cc_final: 0.7546 (m-80) REVERT: B 433 TRP cc_start: 0.7672 (p90) cc_final: 0.7346 (p90) REVERT: B 578 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 630 TRP cc_start: 0.7253 (m-10) cc_final: 0.6750 (m100) REVERT: C 53 ASP cc_start: 0.7056 (OUTLIER) cc_final: 0.6771 (m-30) REVERT: C 388 CYS cc_start: 0.2650 (OUTLIER) cc_final: 0.1873 (m) REVERT: C 561 GLN cc_start: 0.7541 (mm-40) cc_final: 0.7225 (mt0) REVERT: C 1089 GLU cc_start: 0.7778 (tp30) cc_final: 0.7511 (pt0) outliers start: 45 outliers final: 28 residues processed: 173 average time/residue: 0.1229 time to fit residues: 37.3007 Evaluate side-chains 159 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 560 GLN Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 578 THR Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 183 optimal weight: 1.9990 chunk 297 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 278 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 296 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 157 optimal weight: 0.7980 chunk 299 optimal weight: 0.5980 chunk 291 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN A 954 GLN B 560 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4571 r_free = 0.4571 target = 0.199154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.133357 restraints weight = 41710.078| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 3.70 r_work: 0.3592 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 25971 Z= 0.137 Angle : 0.589 10.676 35502 Z= 0.285 Chirality : 0.045 0.412 4218 Planarity : 0.003 0.046 4447 Dihedral : 4.118 27.609 3325 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.08 % Favored : 94.83 % Rotamer: Outliers : 1.88 % Allowed : 12.64 % Favored : 85.48 % 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: -0.44 (0.15), residues: 3054 helix: 1.76 (0.21), residues: 662 sheet: 0.22 (0.19), residues: 691 loop : -1.41 (0.15), residues: 1701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1036 TYR 0.019 0.001 TYR C1064 PHE 0.020 0.001 PHE B1118 TRP 0.017 0.001 TRP A 883 HIS 0.003 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (25854) covalent geometry : angle 0.56117 / 0.28 (35191) SS BOND : bond 0.00349 / 0.19 ( 40) SS BOND : angle 2.21785 / 1.45 ( 80) hydrogen bonds : bond 0.04316 / 2.86 ( 964) hydrogen bonds : angle 4.66878 / 3.22 ( 2640) link_BETA1-4 : bond 0.00364 / 0.22 ( 30) link_BETA1-4 : angle 1.28909 / 0.87 ( 90) link_NAG-ASN : bond 0.00330 / 0.21 ( 47) link_NAG-ASN : angle 2.18508 / 1.57 ( 141) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8546 (m-80) cc_final: 0.8282 (m-80) REVERT: A 189 LEU cc_start: 0.8077 (tt) cc_final: 0.7679 (tp) REVERT: A 200 TYR cc_start: 0.7221 (m-80) cc_final: 0.6938 (t80) REVERT: A 875 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.7929 (tt) REVERT: B 52 GLN cc_start: 0.8825 (pp30) cc_final: 0.8391 (pp30) REVERT: B 393 TYR cc_start: 0.7828 (m-80) cc_final: 0.7555 (m-80) REVERT: B 433 TRP cc_start: 0.7683 (p90) cc_final: 0.7312 (p90) REVERT: B 560 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.6941 (mm110) REVERT: B 630 TRP cc_start: 0.7305 (m-10) cc_final: 0.6799 (m100) REVERT: C 53 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6892 (m-30) REVERT: C 388 CYS cc_start: 0.2210 (OUTLIER) cc_final: 0.1312 (m) REVERT: C 561 GLN cc_start: 0.7730 (mm-40) cc_final: 0.7385 (mt0) REVERT: C 1089 GLU cc_start: 0.7754 (tp30) cc_final: 0.7503 (pt0) outliers start: 51 outliers final: 38 residues processed: 176 average time/residue: 0.1313 time to fit residues: 40.5178 Evaluate side-chains 171 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 129 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 11 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 269 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 185 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 305 optimal weight: 0.0970 chunk 283 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN A 954 GLN B 239 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4562 r_free = 0.4562 target = 0.180515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117671 restraints weight = 41067.800| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.46 r_work: 0.3477 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25971 Z= 0.132 Angle : 0.583 10.655 35502 Z= 0.283 Chirality : 0.045 0.408 4218 Planarity : 0.003 0.046 4447 Dihedral : 4.096 24.685 3325 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.81 % Favored : 95.09 % Rotamer: Outliers : 1.88 % Allowed : 13.19 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.15), residues: 3054 helix: 1.78 (0.21), residues: 660 sheet: 0.27 (0.19), residues: 677 loop : -1.38 (0.15), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1036 TYR 0.019 0.001 TYR C1064 PHE 0.019 0.001 PHE B1118 TRP 0.015 0.001 TRP A 883 HIS 0.003 0.001 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (25854) covalent geometry : angle 0.55721 / 0.28 (35191) SS BOND : bond 0.00355 / 0.20 ( 40) SS BOND : angle 2.09284 / 1.38 ( 80) hydrogen bonds : bond 0.04265 / 2.82 ( 964) hydrogen bonds : angle 4.63968 / 3.20 ( 2640) link_BETA1-4 : bond 0.00360 / 0.22 ( 30) link_BETA1-4 : angle 1.27866 / 0.86 ( 90) link_NAG-ASN : bond 0.00322 / 0.20 ( 47) link_NAG-ASN : angle 2.15711 / 1.55 ( 141) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 PHE cc_start: 0.8451 (m-80) cc_final: 0.8231 (m-80) REVERT: A 189 LEU cc_start: 0.8125 (tt) cc_final: 0.7702 (tp) REVERT: A 200 TYR cc_start: 0.7232 (m-80) cc_final: 0.6939 (t80) REVERT: A 875 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7926 (tt) REVERT: B 52 GLN cc_start: 0.8829 (pp30) cc_final: 0.8408 (pp30) REVERT: B 393 TYR cc_start: 0.7771 (m-80) cc_final: 0.7533 (m-80) REVERT: B 433 TRP cc_start: 0.7518 (p90) cc_final: 0.7141 (p90) REVERT: B 630 TRP cc_start: 0.7365 (m-10) cc_final: 0.6795 (m100) REVERT: C 53 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6866 (m-30) REVERT: C 388 CYS cc_start: 0.2513 (OUTLIER) cc_final: 0.1418 (m) REVERT: C 561 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7408 (mt0) REVERT: C 1089 GLU cc_start: 0.7808 (tp30) cc_final: 0.7551 (pt0) outliers start: 51 outliers final: 40 residues processed: 177 average time/residue: 0.1349 time to fit residues: 42.1039 Evaluate side-chains 172 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 129 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 817 ASP Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 897 MET Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 735 CYS Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 171 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 295 optimal weight: 1.9990 chunk 217 optimal weight: 6.9990 chunk 36 optimal weight: 50.0000 chunk 264 optimal weight: 5.9990 chunk 289 optimal weight: 0.9990 chunk 244 optimal weight: 30.0000 chunk 179 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN B 560 GLN ** B 910 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 = 0.4450 r_free = 0.4450 target = 0.178340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.111426 restraints weight = 42692.372| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 3.65 r_work: 0.3422 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25971 Z= 0.213 Angle : 0.648 10.635 35502 Z= 0.317 Chirality : 0.047 0.407 4218 Planarity : 0.004 0.045 4447 Dihedral : 4.354 25.468 3325 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.99 % Favored : 93.91 % Rotamer: Outliers : 2.00 % Allowed : 13.34 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.15), residues: 3054 helix: 1.51 (0.21), residues: 661 sheet: 0.12 (0.20), residues: 667 loop : -1.48 (0.14), residues: 1726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C1036 TYR 0.022 0.001 TYR C1064 PHE 0.031 0.002 PHE B1118 TRP 0.021 0.002 TRP A 883 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00516 / 0.21 (25854) covalent geometry : angle 0.62132 / 0.31 (35191) SS BOND : bond 0.00475 / 0.29 ( 40) SS BOND : angle 2.34126 / 1.55 ( 80) hydrogen bonds : bond 0.05036 / 3.35 ( 964) hydrogen bonds : angle 4.86959 / 3.35 ( 2640) link_BETA1-4 : bond 0.00329 / 0.20 ( 30) link_BETA1-4 : angle 1.35426 / 0.92 ( 90) link_NAG-ASN : bond 0.00320 / 0.19 ( 47) link_NAG-ASN : angle 2.29000 / 1.63 ( 141) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 127 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8050 (tt) cc_final: 0.7678 (tp) REVERT: A 875 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.7993 (tt) REVERT: B 52 GLN cc_start: 0.8843 (pp30) cc_final: 0.8257 (pp30) REVERT: B 393 TYR cc_start: 0.7866 (m-80) cc_final: 0.7538 (m-10) REVERT: B 433 TRP cc_start: 0.7431 (p90) cc_final: 0.7055 (p90) REVERT: B 560 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7363 (mm110) REVERT: B 630 TRP cc_start: 0.7348 (m-10) cc_final: 0.6775 (m100) REVERT: C 388 CYS cc_start: 0.2604 (OUTLIER) cc_final: 0.1470 (m) REVERT: C 561 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7511 (mt0) REVERT: C 1101 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7807 (p) outliers start: 54 outliers final: 40 residues processed: 172 average time/residue: 0.1246 time to fit residues: 37.7901 Evaluate side-chains 163 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 119 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain B residue 1133 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 802 ILE Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 216 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 269 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 183 optimal weight: 0.1980 chunk 267 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 230 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN A 950 ASN ** B 910 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 = 0.4473 r_free = 0.4473 target = 0.180397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.115740 restraints weight = 42353.695| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 3.62 r_work: 0.3483 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 25971 Z= 0.117 Angle : 0.591 10.632 35502 Z= 0.286 Chirality : 0.044 0.408 4218 Planarity : 0.003 0.046 4447 Dihedral : 4.130 24.330 3325 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.32 % Favored : 95.58 % Rotamer: Outliers : 1.59 % Allowed : 13.78 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 3054 helix: 1.77 (0.21), residues: 654 sheet: 0.18 (0.19), residues: 684 loop : -1.37 (0.15), residues: 1716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 214 TYR 0.018 0.001 TYR C1064 PHE 0.019 0.001 PHE A 55 TRP 0.015 0.001 TRP C 883 HIS 0.002 0.000 HIS B1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (25854) covalent geometry : angle 0.56555 / 0.28 (35191) SS BOND : bond 0.00324 / 0.19 ( 40) SS BOND : angle 2.05543 / 1.36 ( 80) hydrogen bonds : bond 0.04239 / 2.80 ( 964) hydrogen bonds : angle 4.65672 / 3.21 ( 2640) link_BETA1-4 : bond 0.00378 / 0.23 ( 30) link_BETA1-4 : angle 1.27772 / 0.86 ( 90) link_NAG-ASN : bond 0.00338 / 0.21 ( 47) link_NAG-ASN : angle 2.13142 / 1.52 ( 141) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6108 Ramachandran restraints generated. 3054 Oldfield, 0 Emsley, 3054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 130 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 189 LEU cc_start: 0.8059 (tt) cc_final: 0.7685 (tp) REVERT: A 200 TYR cc_start: 0.7312 (m-80) cc_final: 0.7093 (t80) REVERT: A 875 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.7921 (tt) REVERT: B 52 GLN cc_start: 0.8839 (pp30) cc_final: 0.8437 (pp30) REVERT: B 393 TYR cc_start: 0.7800 (m-80) cc_final: 0.7593 (m-10) REVERT: B 433 TRP cc_start: 0.7563 (p90) cc_final: 0.7181 (p90) REVERT: B 630 TRP cc_start: 0.7419 (m-10) cc_final: 0.6853 (m100) REVERT: C 53 ASP cc_start: 0.7181 (OUTLIER) cc_final: 0.6883 (m-30) REVERT: C 388 CYS cc_start: 0.2076 (OUTLIER) cc_final: 0.0985 (m) REVERT: C 561 GLN cc_start: 0.7800 (mm-40) cc_final: 0.7428 (mt0) REVERT: C 1089 GLU cc_start: 0.7767 (tp30) cc_final: 0.7547 (pt0) outliers start: 43 outliers final: 37 residues processed: 166 average time/residue: 0.1250 time to fit residues: 36.4651 Evaluate side-chains 167 residues out of total 2706 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 788 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 875 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 991 ASP Chi-restraints excluded: chain A residue 1126 VAL Chi-restraints excluded: chain A residue 1135 TYR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 309 ILE Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 442 VAL Chi-restraints excluded: chain B residue 522 CYS Chi-restraints excluded: chain B residue 548 VAL Chi-restraints excluded: chain B residue 585 THR Chi-restraints excluded: chain B residue 587 CYS Chi-restraints excluded: chain B residue 592 VAL Chi-restraints excluded: chain B residue 646 CYS Chi-restraints excluded: chain B residue 698 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1120 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 288 CYS Chi-restraints excluded: chain C residue 388 CYS Chi-restraints excluded: chain C residue 530 LEU Chi-restraints excluded: chain C residue 537 ASN Chi-restraints excluded: chain C residue 698 VAL Chi-restraints excluded: chain C residue 782 VAL Chi-restraints excluded: chain C residue 788 THR Chi-restraints excluded: chain C residue 897 MET Chi-restraints excluded: chain C residue 1026 MET Chi-restraints excluded: chain C residue 1126 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 133 optimal weight: 5.9990 chunk 242 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 chunk 22 optimal weight: 0.9990 chunk 50 optimal weight: 0.0770 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 0.0870 chunk 20 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 41 optimal weight: 30.0000 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 771 GLN B 560 GLN ** B 910 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 = 0.4559 r_free = 0.4559 target = 0.197402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.129402 restraints weight = 41788.634| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 3.51 r_work: 0.3441 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25971 Z= 0.190 Angle : 0.633 10.623 35502 Z= 0.308 Chirality : 0.046 0.407 4218 Planarity : 0.004 0.046 4447 Dihedral : 4.270 25.118 3325 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.86 % Favored : 94.04 % Rotamer: Outliers : 1.74 % Allowed : 13.78 % Favored : 84.48 % 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: -0.58 (0.15), residues: 3054 helix: 1.59 (0.21), residues: 654 sheet: 0.14 (0.20), residues: 665 loop : -1.46 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1036 TYR 0.022 0.001 TYR C1064 PHE 0.028 0.001 PHE B1118 TRP 0.018 0.002 TRP C 883 HIS 0.004 0.001 HIS A1085 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (25854) covalent geometry : angle 0.60750 / 0.30 (35191) SS BOND : bond 0.00431 / 0.26 ( 40) SS BOND : angle 2.21180 / 1.46 ( 80) hydrogen bonds : bond 0.04799 / 3.18 ( 964) hydrogen bonds : angle 4.79967 / 3.30 ( 2640) link_BETA1-4 : bond 0.00330 / 0.20 ( 30) link_BETA1-4 : angle 1.32565 / 0.90 ( 90) link_NAG-ASN : bond 0.00308 / 0.18 ( 47) link_NAG-ASN : angle 2.21077 / 1.57 ( 141) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6007.21 seconds wall clock time: 103 minutes 49.33 seconds (6229.33 seconds total)