Starting phenix.real_space_refine on Fri Mar 6 08:13:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwl_32869/03_2026/7wwl_32869.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwl_32869/03_2026/7wwl_32869.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwl_32869/03_2026/7wwl_32869.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwl_32869/03_2026/7wwl_32869.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwl_32869/03_2026/7wwl_32869.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwl_32869/03_2026/7wwl_32869.cif" } resolution = 3.0 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= 0.000 sd= 0.005 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 126 5.16 5 C 18859 2.51 5 N 4890 2.21 5 O 5829 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 86 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29704 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 7765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7765 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 53, 'TRANS': 940} Chain breaks: 8 Chain: "B" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "C" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7759 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 53, 'TRANS': 939} Chain breaks: 8 Chain: "H" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "L" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "M" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "J" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} Chain: "N" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 842 Classifications: {'peptide': 108} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 99} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 7.04, per 1000 atoms: 0.24 Number of scatterers: 29704 At special positions: 0 Unit cell: (134.788, 153.267, 200.008, 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 126 16.00 O 5829 8.00 N 4890 7.00 C 18859 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.31 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.17 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.63 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.75 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.17 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.53 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.05 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.05 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.12 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.10 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.17 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.52 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.05 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=1.98 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " 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 K 1 " - " NAG K 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 603 " " NAG A1407 " - " ASN A 616 " " NAG A1408 " - " ASN A 657 " " NAG A1409 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 616 " " NAG B1408 " - " ASN B 657 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 603 " " NAG C1407 " - " ASN C 616 " " NAG C1408 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG E 1 " - " ASN A 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG K 1 " - " ASN A1074 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 331 " " NAG R 1 " - " ASN B 343 " " NAG S 1 " - " ASN B 709 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 331 " " NAG Y 1 " - " ASN C 343 " " NAG Z 1 " - " ASN C 709 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1074 " " NAG d 1 " - " ASN C1098 " " NAG e 1 " - " ASN C1134 " " NAG f 1 " - " ASN B1074 " Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6836 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 60 sheets defined 19.1% alpha, 28.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.773A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A 815 " --> pdb=" O PRO A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 811 through 815' Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.774A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.573A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 3.993A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.626A pdb=" N LYS A 933 " --> pdb=" O SER A 929 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 3.694A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.603A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.009A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.245A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.578A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.849A pdb=" N THR C 572 " --> pdb=" O ILE C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.698A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 939 removed outlier: 3.590A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.221A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE H 106 " --> pdb=" O TRP H 103 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE I 106 " --> pdb=" O TRP I 103 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 107 removed outlier: 3.563A pdb=" N ILE J 106 " --> pdb=" O TRP J 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.012A pdb=" N GLY A 311 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.524A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 653 through 655 Processing sheet with id=AB2, first strand: chain 'A' and resid 664 through 667 removed outlier: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.589A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.713A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.060A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.857A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC2, first strand: chain 'B' and resid 116 through 121 removed outlier: 3.732A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 4.037A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.554A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N THR B 573 " --> pdb=" O ASP B 568 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 568 " --> pdb=" O THR B 573 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.526A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.264A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.541A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.579A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 30 removed outlier: 8.061A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.858A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AD8, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.731A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE C 128 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N PHE C 168 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL C 130 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N CYS C 166 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.908A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.525A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.851A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 5 through 6 removed outlier: 3.632A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU L 11 " --> pdb=" O LYS L 104 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 46 through 48 removed outlier: 6.666A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 5 through 6 Processing sheet with id=AF9, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU M 11 " --> pdb=" O LYS M 104 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 46 through 48 removed outlier: 6.666A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AG3, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.606A pdb=" N ALA J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 5 through 6 removed outlier: 3.632A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.574A pdb=" N LEU N 11 " --> pdb=" O LYS N 104 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 46 through 48 removed outlier: 6.665A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1038 hydrogen bonds defined for protein. 2805 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: 7.14 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6613 1.33 - 1.45: 7696 1.45 - 1.58: 15896 1.58 - 1.70: 0 1.70 - 1.83: 159 Bond restraints: 30364 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.444 0.078 1.20e-02 6.94e+03 4.26e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.068 1.59e-02 3.96e+03 1.80e+01 bond pdb=" N PRO A 589 " pdb=" CD PRO A 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.80e+01 bond pdb=" N PRO B 589 " pdb=" CD PRO B 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.532 -0.059 1.40e-02 5.10e+03 1.77e+01 ... (remaining 30359 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 40308 2.74 - 5.48: 875 5.48 - 8.22: 100 8.22 - 10.96: 2 10.96 - 13.70: 11 Bond angle restraints: 41296 Sorted by residual: angle pdb=" C PHE C 86 " pdb=" N ASN C 87 " pdb=" CA ASN C 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.73 -11.19 1.91e+00 2.74e-01 3.43e+01 angle pdb=" C PHE B 86 " pdb=" N ASN B 87 " pdb=" CA ASN B 87 " ideal model delta sigma weight residual 121.54 132.72 -11.18 1.91e+00 2.74e-01 3.43e+01 angle pdb=" N PHE B 565 " pdb=" CA PHE B 565 " pdb=" C PHE B 565 " ideal model delta sigma weight residual 108.86 116.78 -7.92 1.41e+00 5.03e-01 3.15e+01 angle pdb=" C SER C 31 " pdb=" N PHE C 32 " pdb=" CA PHE C 32 " ideal model delta sigma weight residual 122.56 115.23 7.33 1.50e+00 4.44e-01 2.39e+01 ... (remaining 41291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16409 17.93 - 35.87: 1795 35.87 - 53.80: 581 53.80 - 71.74: 154 71.74 - 89.67: 52 Dihedral angle restraints: 18991 sinusoidal: 8350 harmonic: 10641 Sorted by residual: dihedral pdb=" CB CYS I 22 " pdb=" SG CYS I 22 " pdb=" SG CYS I 96 " pdb=" CB CYS I 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.51 85.51 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS J 22 " pdb=" SG CYS J 22 " pdb=" SG CYS J 96 " pdb=" CB CYS J 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual -86.00 -171.50 85.50 1 1.00e+01 1.00e-02 8.85e+01 ... (remaining 18988 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 4835 0.329 - 0.659: 3 0.659 - 0.988: 5 0.988 - 1.318: 0 1.318 - 1.647: 1 Chirality restraints: 4844 Sorted by residual: chirality pdb=" C1 NAG f 2 " pdb=" O4 NAG f 1 " pdb=" C2 NAG f 2 " pdb=" O5 NAG f 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 chirality pdb=" C1 NAG e 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG e 1 " pdb=" O5 NAG e 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.75 -1.65 2.00e-01 2.50e+01 6.78e+01 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.64 -0.76 2.00e-01 2.50e+01 1.44e+01 ... (remaining 4841 not shown) Planarity restraints: 5304 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " 0.077 2.00e-02 2.50e+03 1.03e-01 1.33e+02 pdb=" CG ASN B 331 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " 0.018 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " -0.180 2.00e-02 2.50e+03 pdb=" C1 NAG Q 1 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 709 " -0.047 2.00e-02 2.50e+03 5.80e-02 4.20e+01 pdb=" CG ASN A 709 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 709 " -0.003 2.00e-02 2.50e+03 pdb=" ND2 ASN A 709 " 0.099 2.00e-02 2.50e+03 pdb=" C1 NAG A1409 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.053 2.00e-02 2.50e+03 5.69e-02 4.05e+01 pdb=" CG ASN C 331 " 0.020 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG X 1 " -0.068 2.00e-02 2.50e+03 ... (remaining 5301 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 228 2.51 - 3.11: 20919 3.11 - 3.70: 42180 3.70 - 4.30: 63969 4.30 - 4.90: 107487 Nonbonded interactions: 234783 Sorted by model distance: nonbonded pdb=" O VAL A 227 " pdb=" OD1 ASP A 228 " model vdw 1.911 3.040 nonbonded pdb=" OD1 ASN A 532 " pdb=" N LEU A 533 " model vdw 2.043 3.120 nonbonded pdb=" O GLY M 64 " pdb=" OG SER M 65 " model vdw 2.067 3.040 nonbonded pdb=" O ILE B 332 " pdb=" OG1 THR B 333 " model vdw 2.080 3.040 nonbonded pdb=" O THR B 523 " pdb=" O VAL B 524 " model vdw 2.090 3.040 ... (remaining 234778 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1408)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' 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' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 29.430 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 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 : 0.012 0.598 30480 Z= 0.532 Angle : 1.212 50.389 41599 Z= 0.638 Chirality : 0.072 1.647 4844 Planarity : 0.007 0.096 5256 Dihedral : 17.166 89.673 12020 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 2.30 % Allowed : 9.48 % Favored : 88.22 % Rotamer: Outliers : 9.75 % Allowed : 15.91 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -3.96 (0.11), residues: 3607 helix: -2.34 (0.16), residues: 677 sheet: -1.76 (0.15), residues: 1015 loop : -3.32 (0.11), residues: 1915 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 45 TYR 0.027 0.002 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.035 0.004 TRP H 103 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00978 (30364) covalent geometry : angle 1.01844 (41296) SS BOND : bond 0.15435 ( 45) SS BOND : angle 8.65718 ( 90) hydrogen bonds : bond 0.18155 ( 1002) hydrogen bonds : angle 7.62733 ( 2805) link_BETA1-4 : bond 0.04096 ( 23) link_BETA1-4 : angle 4.12244 ( 69) link_NAG-ASN : bond 0.02572 ( 48) link_NAG-ASN : angle 8.47801 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 312 poor density : 472 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 SER cc_start: 0.6367 (OUTLIER) cc_final: 0.6045 (m) REVERT: A 164 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4705 (OUTLIER) REVERT: A 389 ASP cc_start: 0.5828 (OUTLIER) cc_final: 0.5048 (m-30) REVERT: A 444 LYS cc_start: 0.6508 (pttt) cc_final: 0.5660 (tttp) REVERT: A 529 LYS cc_start: 0.6692 (OUTLIER) cc_final: 0.5705 (mtpt) REVERT: A 530 SER cc_start: 0.5179 (OUTLIER) cc_final: 0.4570 (t) REVERT: A 531 THR cc_start: 0.8786 (OUTLIER) cc_final: 0.8321 (p) REVERT: A 1039 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8792 (mtp180) REVERT: B 403 ARG cc_start: 0.7271 (ttp-170) cc_final: 0.6961 (ttp80) REVERT: B 554 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7324 (mp0) REVERT: B 599 THR cc_start: 0.8942 (OUTLIER) cc_final: 0.8681 (t) REVERT: B 811 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5701 (mtpp) REVERT: C 195 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8830 (ptmt) REVERT: C 324 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: C 354 ASN cc_start: 0.7076 (t0) cc_final: 0.6827 (t0) REVERT: J 51 ILE cc_start: 0.1272 (OUTLIER) cc_final: 0.0599 (tp) outliers start: 312 outliers final: 82 residues processed: 729 average time/residue: 0.5665 time to fit residues: 499.5494 Evaluate side-chains 338 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 244 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 334 ASN Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 442 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 565 PHE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 558 LYS Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 974 SER Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 334 ASN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 673 SER Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 31 ASN Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain I residue 27 PHE Chi-restraints excluded: chain J residue 31 ASN Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 8.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 137 ASN A 188 ASN A 317 ASN A 422 ASN A 498 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 540 ASN A 644 GLN A 703 ASN A 762 GLN A 804 GLN A 856 ASN A 901 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 992 GLN A1010 GLN A1058 HIS B 134 GLN B 137 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 498 GLN B 540 ASN B 644 GLN B 675 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 954 GLN B 992 GLN B1054 GLN C 137 ASN C 422 ASN C 440 ASN C 542 ASN C 644 GLN C 703 ASN C 751 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 992 GLN C1010 GLN C1071 GLN C1101 HIS ** H 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 77 ASN L 37 GLN M 6 GLN Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.172640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118022 restraints weight = 46085.368| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.64 r_work: 0.3212 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 30480 Z= 0.157 Angle : 0.776 15.237 41599 Z= 0.381 Chirality : 0.051 0.712 4844 Planarity : 0.006 0.065 5256 Dihedral : 9.683 59.909 5590 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.88 % Favored : 92.87 % Rotamer: Outliers : 6.22 % Allowed : 20.38 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -2.60 (0.13), residues: 3607 helix: -0.11 (0.20), residues: 650 sheet: -1.25 (0.16), residues: 1014 loop : -2.66 (0.12), residues: 1943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 357 TYR 0.018 0.001 TYR A1067 PHE 0.028 0.002 PHE A 559 TRP 0.022 0.002 TRP I 103 HIS 0.005 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00359 (30364) covalent geometry : angle 0.74294 (41296) SS BOND : bond 0.00357 ( 45) SS BOND : angle 1.80451 ( 90) hydrogen bonds : bond 0.04555 ( 1002) hydrogen bonds : angle 5.63665 ( 2805) link_BETA1-4 : bond 0.00720 ( 23) link_BETA1-4 : angle 2.43768 ( 69) link_NAG-ASN : bond 0.00452 ( 48) link_NAG-ASN : angle 3.27282 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 268 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8299 (OUTLIER) cc_final: 0.8086 (m) REVERT: A 117 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6893 (tt) REVERT: A 190 ARG cc_start: 0.7918 (OUTLIER) cc_final: 0.7024 (mtt90) REVERT: A 444 LYS cc_start: 0.3993 (pttt) cc_final: 0.3079 (tttp) REVERT: A 449 TYR cc_start: 0.5967 (OUTLIER) cc_final: 0.4829 (t80) REVERT: A 529 LYS cc_start: 0.6668 (OUTLIER) cc_final: 0.5856 (mtpt) REVERT: A 531 THR cc_start: 0.8025 (OUTLIER) cc_final: 0.7560 (p) REVERT: A 878 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8946 (mt) REVERT: A 1038 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8347 (mptt) REVERT: B 403 ARG cc_start: 0.8011 (ttp-170) cc_final: 0.7692 (ttp80) REVERT: B 544 ASN cc_start: 0.7779 (p0) cc_final: 0.7176 (p0) REVERT: B 554 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: B 787 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7967 (mt0) REVERT: B 867 ASP cc_start: 0.8547 (p0) cc_final: 0.8118 (m-30) REVERT: B 990 GLU cc_start: 0.7387 (tt0) cc_final: 0.6908 (tm-30) REVERT: C 41 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.7019 (mmtp) REVERT: C 135 PHE cc_start: 0.6917 (m-80) cc_final: 0.6209 (m-80) REVERT: C 323 THR cc_start: 0.7560 (p) cc_final: 0.7230 (t) REVERT: C 354 ASN cc_start: 0.7225 (t0) cc_final: 0.6774 (t0) REVERT: C 368 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8570 (mp) REVERT: C 569 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7972 (mt) REVERT: C 988 GLU cc_start: 0.7904 (tp30) cc_final: 0.7652 (tm-30) REVERT: H 3 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7469 (tp-100) REVERT: H 4 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8514 (mm) REVERT: H 77 ASN cc_start: 0.6717 (m110) cc_final: 0.6429 (m-40) REVERT: H 99 ASP cc_start: 0.7996 (t70) cc_final: 0.7725 (t70) REVERT: L 101 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6011 (mp10) REVERT: I 39 GLN cc_start: 0.3225 (tt0) cc_final: 0.3003 (mp10) REVERT: I 64 VAL cc_start: 0.5257 (t) cc_final: 0.5004 (p) REVERT: J 71 SER cc_start: 0.5593 (p) cc_final: 0.5347 (m) outliers start: 199 outliers final: 83 residues processed: 432 average time/residue: 0.5537 time to fit residues: 291.0105 Evaluate side-chains 306 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 208 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 171 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 530 SER Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1126 CYS Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 4 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 10 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 283 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 349 optimal weight: 20.0000 chunk 258 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 314 optimal weight: 9.9990 chunk 92 optimal weight: 0.0870 chunk 311 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN B 207 HIS ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN B 506 GLN B1005 GLN B1106 GLN C 501 ASN C 519 HIS H 59 HIS ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.167084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113011 restraints weight = 45625.864| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.52 r_work: 0.3129 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30480 Z= 0.194 Angle : 0.749 14.430 41599 Z= 0.364 Chirality : 0.051 0.681 4844 Planarity : 0.005 0.062 5256 Dihedral : 8.483 59.917 5502 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.29 % Favored : 92.49 % Rotamer: Outliers : 6.06 % Allowed : 21.04 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % 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: -2.03 (0.13), residues: 3607 helix: 0.58 (0.21), residues: 653 sheet: -1.00 (0.16), residues: 1034 loop : -2.31 (0.12), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG M 18 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.002 PHE B 43 TRP 0.021 0.002 TRP I 103 HIS 0.005 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00460 (30364) covalent geometry : angle 0.71501 (41296) SS BOND : bond 0.00518 ( 45) SS BOND : angle 2.22689 ( 90) hydrogen bonds : bond 0.04806 ( 1002) hydrogen bonds : angle 5.40219 ( 2805) link_BETA1-4 : bond 0.00654 ( 23) link_BETA1-4 : angle 2.37529 ( 69) link_NAG-ASN : bond 0.00501 ( 48) link_NAG-ASN : angle 3.13080 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 194 poor density : 235 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7876 (m) REVERT: A 129 LYS cc_start: 0.7064 (ttmt) cc_final: 0.6528 (ttpt) REVERT: A 231 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7588 (mp) REVERT: A 237 ARG cc_start: 0.7930 (mtp85) cc_final: 0.7250 (ttp-110) REVERT: A 324 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.6846 (pm20) REVERT: A 480 CYS cc_start: 0.1609 (OUTLIER) cc_final: 0.0957 (t) REVERT: A 529 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.5919 (mtpt) REVERT: A 729 VAL cc_start: 0.9452 (OUTLIER) cc_final: 0.9203 (t) REVERT: B 331 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.6077 (m-40) REVERT: B 403 ARG cc_start: 0.7936 (ttp-170) cc_final: 0.7393 (ttp80) REVERT: B 554 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7738 (mp0) REVERT: B 571 ASP cc_start: 0.7963 (m-30) cc_final: 0.7637 (t0) REVERT: B 796 ASP cc_start: 0.7948 (p0) cc_final: 0.7724 (p0) REVERT: B 811 LYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6338 (mtpp) REVERT: B 867 ASP cc_start: 0.8356 (p0) cc_final: 0.8059 (m-30) REVERT: C 41 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7199 (mmtp) REVERT: C 122 ASN cc_start: 0.3497 (OUTLIER) cc_final: 0.2230 (m-40) REVERT: C 135 PHE cc_start: 0.6514 (m-80) cc_final: 0.6235 (m-80) REVERT: C 200 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6480 (t80) REVERT: C 368 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8551 (mp) REVERT: C 402 ILE cc_start: 0.8834 (pt) cc_final: 0.8617 (pp) REVERT: C 534 VAL cc_start: 0.8625 (OUTLIER) cc_final: 0.8347 (m) REVERT: C 697 MET cc_start: 0.9269 (ptm) cc_final: 0.9038 (ptm) REVERT: C 740 MET cc_start: 0.9074 (ttp) cc_final: 0.8861 (ttt) REVERT: C 756 TYR cc_start: 0.9293 (m-80) cc_final: 0.8930 (m-80) REVERT: C 988 GLU cc_start: 0.7965 (tp30) cc_final: 0.7610 (tp30) REVERT: C 995 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8266 (mtt-85) REVERT: H 3 GLN cc_start: 0.7506 (tp-100) cc_final: 0.7226 (tp-100) REVERT: H 19 ARG cc_start: 0.7136 (ttt-90) cc_final: 0.6223 (ttt-90) REVERT: H 67 ARG cc_start: 0.7862 (ttp-110) cc_final: 0.6979 (ttp80) REVERT: H 86 LEU cc_start: 0.5664 (mt) cc_final: 0.5392 (mp) REVERT: H 106 ILE cc_start: 0.8363 (OUTLIER) cc_final: 0.7848 (tt) REVERT: L 18 ARG cc_start: 0.7773 (mmm160) cc_final: 0.7510 (mtp-110) REVERT: L 48 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8378 (mt) REVERT: L 98 THR cc_start: 0.9070 (m) cc_final: 0.8732 (p) REVERT: J 51 ILE cc_start: -0.1447 (OUTLIER) cc_final: -0.1882 (tp) REVERT: J 106 ILE cc_start: 0.4600 (OUTLIER) cc_final: 0.4383 (mm) outliers start: 194 outliers final: 84 residues processed: 388 average time/residue: 0.5335 time to fit residues: 253.3817 Evaluate side-chains 302 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 200 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 811 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 41 LYS Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 79 LEU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 106 ILE Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 31 ASN Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain M residue 10 SER Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 154 optimal weight: 0.9980 chunk 362 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 chunk 225 optimal weight: 7.9990 chunk 311 optimal weight: 9.9990 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN A1010 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B 804 GLN B1005 GLN C 115 GLN C 498 GLN C 804 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 53 ASN J 74 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.166680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.110983 restraints weight = 45234.898| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.60 r_work: 0.3135 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.3834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 30480 Z= 0.140 Angle : 0.691 13.610 41599 Z= 0.334 Chirality : 0.048 0.584 4844 Planarity : 0.004 0.052 5256 Dihedral : 7.855 59.829 5490 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.35 % Favored : 93.48 % Rotamer: Outliers : 5.28 % Allowed : 21.76 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.13), residues: 3607 helix: 1.04 (0.21), residues: 637 sheet: -0.72 (0.16), residues: 1018 loop : -2.08 (0.12), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 18 TYR 0.017 0.001 TYR A1067 PHE 0.015 0.001 PHE C 86 TRP 0.012 0.001 TRP J 33 HIS 0.017 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00326 (30364) covalent geometry : angle 0.65869 (41296) SS BOND : bond 0.00493 ( 45) SS BOND : angle 2.08893 ( 90) hydrogen bonds : bond 0.04097 ( 1002) hydrogen bonds : angle 5.19549 ( 2805) link_BETA1-4 : bond 0.00510 ( 23) link_BETA1-4 : angle 2.14826 ( 69) link_NAG-ASN : bond 0.00488 ( 48) link_NAG-ASN : angle 2.94733 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 169 poor density : 231 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7868 (m) REVERT: A 117 LEU cc_start: 0.7293 (OUTLIER) cc_final: 0.7006 (tt) REVERT: A 129 LYS cc_start: 0.7114 (ttmt) cc_final: 0.6573 (ttpt) REVERT: A 231 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7633 (OUTLIER) REVERT: A 237 ARG cc_start: 0.7760 (mtp85) cc_final: 0.7149 (ttp-110) REVERT: A 269 TYR cc_start: 0.8013 (m-80) cc_final: 0.7715 (m-10) REVERT: A 314 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9083 (tm-30) REVERT: A 319 ARG cc_start: 0.7910 (ttp-110) cc_final: 0.7458 (mtm180) REVERT: A 324 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: A 444 LYS cc_start: 0.4538 (pttt) cc_final: 0.3567 (tmtm) REVERT: A 452 ARG cc_start: 0.6069 (OUTLIER) cc_final: 0.4535 (mtp85) REVERT: A 529 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.5943 (mtpt) REVERT: A 531 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7529 (p) REVERT: A 985 ASP cc_start: 0.6237 (p0) cc_final: 0.5541 (p0) REVERT: A 988 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7799 (mp0) REVERT: B 231 ILE cc_start: 0.7254 (mp) cc_final: 0.7042 (OUTLIER) REVERT: B 331 ASN cc_start: 0.6718 (OUTLIER) cc_final: 0.5930 (m-40) REVERT: B 403 ARG cc_start: 0.8060 (ttp-170) cc_final: 0.7783 (ttp80) REVERT: B 554 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7906 (mp0) REVERT: B 705 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8493 (t) REVERT: B 787 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.8115 (mt0) REVERT: B 867 ASP cc_start: 0.8255 (p0) cc_final: 0.7998 (m-30) REVERT: C 102 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6536 (mmt-90) REVERT: C 122 ASN cc_start: 0.3641 (OUTLIER) cc_final: 0.2769 (m-40) REVERT: C 135 PHE cc_start: 0.6186 (m-80) cc_final: 0.5814 (m-80) REVERT: C 200 TYR cc_start: 0.7060 (OUTLIER) cc_final: 0.6309 (t80) REVERT: C 368 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8491 (mp) REVERT: C 487 ASN cc_start: 0.6485 (m-40) cc_final: 0.5410 (p0) REVERT: C 493 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: C 529 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8157 (ttpt) REVERT: C 697 MET cc_start: 0.9276 (ptm) cc_final: 0.8998 (ptm) REVERT: C 740 MET cc_start: 0.9012 (ttp) cc_final: 0.8808 (ttt) REVERT: C 988 GLU cc_start: 0.7907 (tp30) cc_final: 0.7517 (tp30) REVERT: H 65 LYS cc_start: 0.7638 (pmtt) cc_final: 0.7430 (pmtt) REVERT: L 1 ASP cc_start: 0.5471 (OUTLIER) cc_final: 0.5176 (t70) REVERT: L 18 ARG cc_start: 0.7835 (mmm160) cc_final: 0.7511 (mtp-110) REVERT: L 98 THR cc_start: 0.9094 (m) cc_final: 0.8757 (p) REVERT: L 101 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: I 70 ILE cc_start: 0.1702 (OUTLIER) cc_final: 0.1345 (mt) REVERT: J 51 ILE cc_start: -0.1359 (OUTLIER) cc_final: -0.1857 (tp) REVERT: J 71 SER cc_start: 0.5947 (p) cc_final: 0.5712 (m) REVERT: J 106 ILE cc_start: 0.4867 (OUTLIER) cc_final: 0.4660 (mm) outliers start: 169 outliers final: 84 residues processed: 375 average time/residue: 0.5330 time to fit residues: 244.4663 Evaluate side-chains 306 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 201 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 236 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 508 TYR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain L residue 1 ASP Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 70 ILE Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 234 optimal weight: 9.9990 chunk 295 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 333 optimal weight: 5.9990 chunk 245 optimal weight: 0.9990 chunk 314 optimal weight: 0.0270 chunk 290 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 292 optimal weight: 1.9990 chunk 356 optimal weight: 20.0000 chunk 343 optimal weight: 7.9990 overall best weight: 1.6044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 493 GLN A1010 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 440 ASN B1005 GLN C 99 ASN C 218 GLN C 239 GLN C 751 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 ASN L 53 ASN J 74 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.165934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112575 restraints weight = 45277.212| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.71 r_work: 0.3118 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 30480 Z= 0.141 Angle : 0.677 14.553 41599 Z= 0.328 Chirality : 0.048 0.554 4844 Planarity : 0.004 0.052 5256 Dihedral : 7.500 59.978 5484 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.40 % Favored : 93.43 % Rotamer: Outliers : 5.47 % Allowed : 22.04 % Favored : 72.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 3607 helix: 1.13 (0.21), residues: 655 sheet: -0.54 (0.16), residues: 1018 loop : -2.01 (0.12), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 18 TYR 0.018 0.001 TYR C1067 PHE 0.015 0.001 PHE B 86 TRP 0.015 0.001 TRP J 113 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00333 (30364) covalent geometry : angle 0.64660 (41296) SS BOND : bond 0.00474 ( 45) SS BOND : angle 2.08567 ( 90) hydrogen bonds : bond 0.04029 ( 1002) hydrogen bonds : angle 5.11322 ( 2805) link_BETA1-4 : bond 0.00512 ( 23) link_BETA1-4 : angle 2.11244 ( 69) link_NAG-ASN : bond 0.00455 ( 48) link_NAG-ASN : angle 2.78948 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 212 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7030 (tt) REVERT: A 129 LYS cc_start: 0.7153 (ttmt) cc_final: 0.6564 (ttmt) REVERT: A 190 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.7046 (mtt90) REVERT: A 197 ILE cc_start: 0.7967 (OUTLIER) cc_final: 0.7745 (mp) REVERT: A 198 ASP cc_start: 0.8149 (m-30) cc_final: 0.7281 (p0) REVERT: A 202 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8645 (mttm) REVERT: A 231 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7718 (OUTLIER) REVERT: A 237 ARG cc_start: 0.7753 (mtp85) cc_final: 0.7119 (ttp-110) REVERT: A 269 TYR cc_start: 0.8055 (m-80) cc_final: 0.7761 (m-10) REVERT: A 319 ARG cc_start: 0.7979 (ttp-110) cc_final: 0.7733 (mtp85) REVERT: A 324 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7052 (pm20) REVERT: A 449 TYR cc_start: 0.5816 (p90) cc_final: 0.4854 (t80) REVERT: A 452 ARG cc_start: 0.6055 (OUTLIER) cc_final: 0.4662 (mtp85) REVERT: A 480 CYS cc_start: 0.1227 (OUTLIER) cc_final: 0.0719 (t) REVERT: A 529 LYS cc_start: 0.6789 (OUTLIER) cc_final: 0.6001 (mtpt) REVERT: A 531 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7519 (p) REVERT: A 985 ASP cc_start: 0.6623 (p0) cc_final: 0.5830 (p0) REVERT: A 988 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7822 (mp0) REVERT: A 1029 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8980 (tpp) REVERT: B 200 TYR cc_start: 0.8061 (OUTLIER) cc_final: 0.7111 (m-80) REVERT: B 231 ILE cc_start: 0.7134 (mp) cc_final: 0.6898 (mp) REVERT: B 331 ASN cc_start: 0.6869 (OUTLIER) cc_final: 0.6146 (m-40) REVERT: B 403 ARG cc_start: 0.8154 (ttp-170) cc_final: 0.7791 (ttp80) REVERT: B 406 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7604 (mt-10) REVERT: B 444 LYS cc_start: 0.7089 (ptpp) cc_final: 0.6630 (ptmt) REVERT: B 554 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: B 787 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8151 (mt0) REVERT: B 867 ASP cc_start: 0.8253 (p0) cc_final: 0.8035 (m-30) REVERT: C 102 ARG cc_start: 0.6622 (OUTLIER) cc_final: 0.6222 (mmp80) REVERT: C 122 ASN cc_start: 0.3950 (OUTLIER) cc_final: 0.2754 (m-40) REVERT: C 135 PHE cc_start: 0.6239 (m-80) cc_final: 0.5992 (m-80) REVERT: C 200 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6224 (t80) REVERT: C 228 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8258 (t0) REVERT: C 324 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: C 368 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8529 (mp) REVERT: C 487 ASN cc_start: 0.6393 (m-40) cc_final: 0.5303 (p0) REVERT: C 493 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: C 529 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8168 (ttpt) REVERT: C 697 MET cc_start: 0.9310 (ptm) cc_final: 0.9033 (ptm) REVERT: C 740 MET cc_start: 0.9034 (ttp) cc_final: 0.8819 (ttt) REVERT: H 77 ASN cc_start: 0.6668 (m-40) cc_final: 0.6398 (m-40) REVERT: L 18 ARG cc_start: 0.7883 (mmm160) cc_final: 0.7663 (mtp-110) REVERT: L 24 ARG cc_start: 0.7547 (mtm110) cc_final: 0.7297 (mtp-110) REVERT: L 48 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8378 (mt) REVERT: L 98 THR cc_start: 0.9081 (m) cc_final: 0.8786 (p) REVERT: L 101 GLN cc_start: 0.7857 (OUTLIER) cc_final: 0.7077 (mp10) REVERT: I 39 GLN cc_start: 0.2857 (tt0) cc_final: 0.2357 (mp10) REVERT: J 51 ILE cc_start: -0.1424 (OUTLIER) cc_final: -0.2439 (mt) REVERT: J 106 ILE cc_start: 0.4890 (OUTLIER) cc_final: 0.4651 (mm) outliers start: 175 outliers final: 89 residues processed: 359 average time/residue: 0.5260 time to fit residues: 230.2958 Evaluate side-chains 312 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 197 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 117 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 190 ARG Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1029 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1017 GLU Chi-restraints excluded: chain C residue 1030 SER Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 93 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 7 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 7 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 75 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 256 optimal weight: 4.9990 chunk 358 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1010 GLN B 81 ASN B 218 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 440 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1106 GLN C 121 ASN ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.162858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.109131 restraints weight = 45160.163| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.47 r_work: 0.3101 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30480 Z= 0.191 Angle : 0.714 14.366 41599 Z= 0.348 Chirality : 0.050 0.558 4844 Planarity : 0.005 0.055 5256 Dihedral : 7.444 59.132 5481 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.82 % Favored : 93.01 % Rotamer: Outliers : 5.35 % Allowed : 22.51 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.37 (0.13), residues: 3607 helix: 1.17 (0.21), residues: 657 sheet: -0.49 (0.16), residues: 1012 loop : -1.95 (0.13), residues: 1938 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 87 TYR 0.019 0.001 TYR C1067 PHE 0.021 0.002 PHE B 329 TRP 0.016 0.002 TRP M 94 HIS 0.010 0.001 HIS I 59 Details of bonding type rmsd covalent geometry : bond 0.00464 (30364) covalent geometry : angle 0.68495 (41296) SS BOND : bond 0.00522 ( 45) SS BOND : angle 2.00899 ( 90) hydrogen bonds : bond 0.04677 ( 1002) hydrogen bonds : angle 5.24355 ( 2805) link_BETA1-4 : bond 0.00523 ( 23) link_BETA1-4 : angle 2.20620 ( 69) link_NAG-ASN : bond 0.00481 ( 48) link_NAG-ASN : angle 2.84140 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 235 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7193 (ttmt) cc_final: 0.6613 (ttpt) REVERT: A 161 SER cc_start: 0.7367 (OUTLIER) cc_final: 0.6829 (t) REVERT: A 198 ASP cc_start: 0.8165 (m-30) cc_final: 0.7853 (p0) REVERT: A 231 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7826 (mp) REVERT: A 237 ARG cc_start: 0.7707 (mtp85) cc_final: 0.7061 (ttp-110) REVERT: A 269 TYR cc_start: 0.8091 (m-80) cc_final: 0.7833 (m-10) REVERT: A 314 GLN cc_start: 0.9362 (OUTLIER) cc_final: 0.9090 (tm-30) REVERT: A 319 ARG cc_start: 0.8215 (ttp-110) cc_final: 0.7914 (mtp85) REVERT: A 324 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7191 (pm20) REVERT: A 449 TYR cc_start: 0.5968 (p90) cc_final: 0.4941 (t80) REVERT: A 452 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.4825 (mtp85) REVERT: A 480 CYS cc_start: 0.1491 (OUTLIER) cc_final: 0.0869 (t) REVERT: A 529 LYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6001 (mtpt) REVERT: A 531 THR cc_start: 0.7831 (OUTLIER) cc_final: 0.7562 (p) REVERT: A 534 VAL cc_start: 0.8241 (m) cc_final: 0.8018 (t) REVERT: A 985 ASP cc_start: 0.6722 (p0) cc_final: 0.6271 (p0) REVERT: A 988 GLU cc_start: 0.8415 (mm-30) cc_final: 0.8054 (mt-10) REVERT: B 331 ASN cc_start: 0.6853 (OUTLIER) cc_final: 0.6046 (m-40) REVERT: B 403 ARG cc_start: 0.8058 (ttp-170) cc_final: 0.7799 (mtm110) REVERT: B 444 LYS cc_start: 0.7378 (ptpp) cc_final: 0.6860 (ptmt) REVERT: B 452 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.8245 (mtt180) REVERT: B 705 VAL cc_start: 0.9052 (OUTLIER) cc_final: 0.8835 (t) REVERT: B 754 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9164 (mp) REVERT: B 1113 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: C 102 ARG cc_start: 0.6636 (OUTLIER) cc_final: 0.6024 (mmp80) REVERT: C 122 ASN cc_start: 0.4359 (OUTLIER) cc_final: 0.3655 (m-40) REVERT: C 200 TYR cc_start: 0.6993 (OUTLIER) cc_final: 0.6216 (t80) REVERT: C 228 ASP cc_start: 0.8653 (OUTLIER) cc_final: 0.8202 (t0) REVERT: C 324 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: C 340 GLU cc_start: 0.8637 (mp0) cc_final: 0.8299 (pm20) REVERT: C 368 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8490 (mp) REVERT: C 402 ILE cc_start: 0.8760 (pt) cc_final: 0.8483 (pp) REVERT: C 403 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7474 (ttm170) REVERT: C 487 ASN cc_start: 0.6569 (m-40) cc_final: 0.5573 (p0) REVERT: C 493 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7056 (tt0) REVERT: C 529 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8147 (ttpt) REVERT: C 697 MET cc_start: 0.9337 (ptm) cc_final: 0.9077 (ptm) REVERT: C 740 MET cc_start: 0.9072 (ttp) cc_final: 0.8841 (ttt) REVERT: C 756 TYR cc_start: 0.9278 (m-80) cc_final: 0.8901 (m-80) REVERT: C 995 ARG cc_start: 0.8516 (mtp180) cc_final: 0.8275 (mtt-85) REVERT: H 77 ASN cc_start: 0.6596 (m-40) cc_final: 0.6314 (m-40) REVERT: H 104 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: L 18 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7780 (mtp-110) REVERT: L 48 ILE cc_start: 0.8660 (OUTLIER) cc_final: 0.8384 (mt) REVERT: L 61 ARG cc_start: 0.7125 (mtp180) cc_final: 0.6799 (ttp-110) REVERT: L 74 THR cc_start: 0.7743 (m) cc_final: 0.7503 (t) REVERT: L 98 THR cc_start: 0.9123 (m) cc_final: 0.8860 (p) REVERT: L 101 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7189 (mp10) REVERT: I 106 ILE cc_start: 0.4953 (OUTLIER) cc_final: 0.4503 (mp) REVERT: J 51 ILE cc_start: -0.1081 (OUTLIER) cc_final: -0.2052 (mt) REVERT: J 106 ILE cc_start: 0.5240 (OUTLIER) cc_final: 0.5000 (mm) outliers start: 171 outliers final: 86 residues processed: 379 average time/residue: 0.5386 time to fit residues: 249.7691 Evaluate side-chains 330 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 217 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 304 LYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 314 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 421 TYR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 960 ASN Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain L residue 101 GLN Chi-restraints excluded: chain L residue 105 VAL Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain N residue 7 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 167 optimal weight: 0.6980 chunk 233 optimal weight: 4.9990 chunk 283 optimal weight: 0.6980 chunk 211 optimal weight: 10.0000 chunk 328 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 324 optimal weight: 7.9990 chunk 214 optimal weight: 7.9990 chunk 196 optimal weight: 0.0770 chunk 97 optimal weight: 1.9990 chunk 285 optimal weight: 0.9980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1010 GLN B 81 ASN B 218 GLN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN C 188 ASN C1002 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 31 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.165019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110786 restraints weight = 45335.107| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.48 r_work: 0.3143 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.4836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30480 Z= 0.112 Angle : 0.655 13.204 41599 Z= 0.315 Chirality : 0.047 0.504 4844 Planarity : 0.004 0.049 5256 Dihedral : 6.984 58.440 5474 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.02 % Favored : 93.82 % Rotamer: Outliers : 3.91 % Allowed : 24.10 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.14), residues: 3607 helix: 1.56 (0.22), residues: 656 sheet: -0.31 (0.16), residues: 1027 loop : -1.83 (0.13), residues: 1924 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 67 TYR 0.016 0.001 TYR B1067 PHE 0.024 0.001 PHE C 133 TRP 0.013 0.001 TRP I 36 HIS 0.003 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00247 (30364) covalent geometry : angle 0.62889 (41296) SS BOND : bond 0.00398 ( 45) SS BOND : angle 1.79455 ( 90) hydrogen bonds : bond 0.03605 ( 1002) hydrogen bonds : angle 5.00168 ( 2805) link_BETA1-4 : bond 0.00494 ( 23) link_BETA1-4 : angle 1.98256 ( 69) link_NAG-ASN : bond 0.00440 ( 48) link_NAG-ASN : angle 2.57201 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 218 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7127 (ttmt) cc_final: 0.6484 (ttpt) REVERT: A 161 SER cc_start: 0.7429 (OUTLIER) cc_final: 0.6926 (t) REVERT: A 197 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7510 (mp) REVERT: A 198 ASP cc_start: 0.8188 (m-30) cc_final: 0.7891 (p0) REVERT: A 202 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8582 (mttm) REVERT: A 231 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7742 (mp) REVERT: A 237 ARG cc_start: 0.7913 (mtp85) cc_final: 0.7303 (ttp-110) REVERT: A 269 TYR cc_start: 0.8050 (m-80) cc_final: 0.7722 (m-10) REVERT: A 319 ARG cc_start: 0.8090 (ttp-110) cc_final: 0.7773 (mtp85) REVERT: A 324 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7202 (pm20) REVERT: A 449 TYR cc_start: 0.5798 (p90) cc_final: 0.4795 (t80) REVERT: A 452 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.4799 (mtp85) REVERT: A 480 CYS cc_start: 0.1289 (OUTLIER) cc_final: 0.0835 (t) REVERT: A 529 LYS cc_start: 0.6934 (OUTLIER) cc_final: 0.6007 (mtpt) REVERT: B 52 GLN cc_start: 0.8245 (tp40) cc_final: 0.7797 (tp-100) REVERT: B 200 TYR cc_start: 0.8142 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: B 280 ASN cc_start: 0.8182 (t0) cc_final: 0.7524 (t0) REVERT: B 331 ASN cc_start: 0.6805 (OUTLIER) cc_final: 0.6006 (m-40) REVERT: B 403 ARG cc_start: 0.8263 (ttp-170) cc_final: 0.8046 (mtm110) REVERT: B 444 LYS cc_start: 0.7389 (ptpp) cc_final: 0.6859 (ptmt) REVERT: B 452 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8323 (mtt180) REVERT: B 787 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8156 (mt0) REVERT: B 1113 GLN cc_start: 0.8805 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: C 95 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.8197 (p) REVERT: C 102 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5654 (mmp80) REVERT: C 135 PHE cc_start: 0.6182 (m-80) cc_final: 0.5780 (m-80) REVERT: C 200 TYR cc_start: 0.6901 (OUTLIER) cc_final: 0.6150 (t80) REVERT: C 228 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8293 (t0) REVERT: C 340 GLU cc_start: 0.8604 (mp0) cc_final: 0.8104 (pm20) REVERT: C 402 ILE cc_start: 0.8692 (pt) cc_final: 0.8440 (pp) REVERT: C 403 ARG cc_start: 0.8010 (ttp-170) cc_final: 0.7497 (ttm170) REVERT: C 487 ASN cc_start: 0.6658 (m-40) cc_final: 0.5717 (p0) REVERT: C 529 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8214 (ttpt) REVERT: C 534 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8402 (m) REVERT: C 776 LYS cc_start: 0.9127 (ttmm) cc_final: 0.8847 (tttm) REVERT: H 19 ARG cc_start: 0.8068 (mmt180) cc_final: 0.7601 (tpt90) REVERT: L 18 ARG cc_start: 0.8055 (mmm160) cc_final: 0.7821 (mtp-110) REVERT: L 74 THR cc_start: 0.7702 (m) cc_final: 0.7446 (t) REVERT: L 75 ILE cc_start: 0.7829 (mt) cc_final: 0.7629 (mt) REVERT: I 39 GLN cc_start: 0.2640 (tt0) cc_final: 0.2111 (mp-120) REVERT: J 51 ILE cc_start: -0.0964 (OUTLIER) cc_final: -0.1909 (mt) REVERT: J 67 ARG cc_start: 0.5575 (ttt-90) cc_final: 0.5125 (ttt-90) REVERT: J 106 ILE cc_start: 0.5151 (OUTLIER) cc_final: 0.4937 (mm) outliers start: 125 outliers final: 58 residues processed: 325 average time/residue: 0.5884 time to fit residues: 230.7228 Evaluate side-chains 282 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 80 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 315 optimal weight: 9.9990 chunk 261 optimal weight: 5.9990 chunk 362 optimal weight: 0.8980 chunk 305 optimal weight: 10.0000 chunk 292 optimal weight: 4.9990 chunk 31 optimal weight: 8.9990 chunk 285 optimal weight: 4.9990 chunk 301 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1010 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN L 6 GLN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.160662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106220 restraints weight = 45365.166| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.62 r_work: 0.3077 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 30480 Z= 0.216 Angle : 0.753 14.828 41599 Z= 0.365 Chirality : 0.051 0.528 4844 Planarity : 0.005 0.056 5256 Dihedral : 7.264 58.603 5469 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.07 % Favored : 92.79 % Rotamer: Outliers : 4.31 % Allowed : 24.10 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.14), residues: 3607 helix: 1.22 (0.21), residues: 657 sheet: -0.65 (0.16), residues: 1066 loop : -1.81 (0.13), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 408 TYR 0.022 0.002 TYR C1067 PHE 0.024 0.002 PHE C 133 TRP 0.024 0.002 TRP I 103 HIS 0.004 0.001 HIS H 112 Details of bonding type rmsd covalent geometry : bond 0.00525 (30364) covalent geometry : angle 0.72333 (41296) SS BOND : bond 0.00538 ( 45) SS BOND : angle 2.31424 ( 90) hydrogen bonds : bond 0.05052 ( 1002) hydrogen bonds : angle 5.29450 ( 2805) link_BETA1-4 : bond 0.00407 ( 23) link_BETA1-4 : angle 2.22032 ( 69) link_NAG-ASN : bond 0.00490 ( 48) link_NAG-ASN : angle 2.85932 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 227 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 THR cc_start: 0.8070 (t) cc_final: 0.7850 (t) REVERT: A 129 LYS cc_start: 0.7180 (ttmt) cc_final: 0.6548 (ttmt) REVERT: A 161 SER cc_start: 0.7469 (OUTLIER) cc_final: 0.6969 (t) REVERT: A 202 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8581 (mttt) REVERT: A 216 LEU cc_start: 0.5869 (OUTLIER) cc_final: 0.5667 (tt) REVERT: A 231 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7947 (mp) REVERT: A 237 ARG cc_start: 0.7922 (mtp85) cc_final: 0.7278 (ttp-110) REVERT: A 269 TYR cc_start: 0.8153 (m-80) cc_final: 0.7895 (m-10) REVERT: A 319 ARG cc_start: 0.8227 (ttp-110) cc_final: 0.7871 (mtp85) REVERT: A 324 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: A 452 ARG cc_start: 0.6024 (OUTLIER) cc_final: 0.4746 (mtp85) REVERT: A 480 CYS cc_start: 0.1449 (OUTLIER) cc_final: 0.1149 (t) REVERT: A 529 LYS cc_start: 0.7002 (OUTLIER) cc_final: 0.6054 (mtpt) REVERT: B 331 ASN cc_start: 0.6871 (OUTLIER) cc_final: 0.6094 (m-40) REVERT: B 444 LYS cc_start: 0.7444 (ptpp) cc_final: 0.6931 (ptmt) REVERT: B 452 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8309 (mtt180) REVERT: B 714 ILE cc_start: 0.9429 (OUTLIER) cc_final: 0.9204 (mm) REVERT: C 95 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8264 (p) REVERT: C 102 ARG cc_start: 0.6774 (OUTLIER) cc_final: 0.6094 (mmp80) REVERT: C 135 PHE cc_start: 0.6199 (m-80) cc_final: 0.5884 (m-80) REVERT: C 200 TYR cc_start: 0.6983 (OUTLIER) cc_final: 0.6029 (t80) REVERT: C 340 GLU cc_start: 0.8671 (mp0) cc_final: 0.8068 (pm20) REVERT: C 402 ILE cc_start: 0.8826 (pt) cc_final: 0.8533 (pp) REVERT: C 403 ARG cc_start: 0.7991 (ttp-170) cc_final: 0.7460 (ttm170) REVERT: C 487 ASN cc_start: 0.6599 (m-40) cc_final: 0.5674 (p0) REVERT: C 493 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7198 (tt0) REVERT: C 529 LYS cc_start: 0.8566 (OUTLIER) cc_final: 0.8132 (ttpt) REVERT: C 995 ARG cc_start: 0.8575 (mtp180) cc_final: 0.8314 (mtt-85) REVERT: H 11 LEU cc_start: 0.6384 (tm) cc_final: 0.5839 (mm) REVERT: H 19 ARG cc_start: 0.8207 (mmt180) cc_final: 0.7738 (tpt90) REVERT: H 77 ASN cc_start: 0.6665 (m-40) cc_final: 0.6409 (m-40) REVERT: L 18 ARG cc_start: 0.8019 (mmm160) cc_final: 0.7784 (mtp-110) REVERT: L 38 GLN cc_start: 0.8401 (tp-100) cc_final: 0.8029 (tm-30) REVERT: L 48 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8423 (mt) REVERT: L 61 ARG cc_start: 0.7727 (ptp90) cc_final: 0.7446 (ptp90) REVERT: M 4 MET cc_start: 0.2261 (tmt) cc_final: 0.1928 (tmm) REVERT: M 6 GLN cc_start: 0.1861 (OUTLIER) cc_final: 0.1645 (mt0) REVERT: M 31 ASN cc_start: 0.6348 (t0) cc_final: 0.6117 (t0) REVERT: J 51 ILE cc_start: -0.0280 (OUTLIER) cc_final: -0.1234 (mt) REVERT: J 67 ARG cc_start: 0.5798 (ttt-90) cc_final: 0.5576 (ttt-90) outliers start: 138 outliers final: 82 residues processed: 346 average time/residue: 0.5538 time to fit residues: 233.9375 Evaluate side-chains 305 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 204 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 162 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 480 CYS Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 786 LYS Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 571 ASP Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 102 ARG Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 325 SER Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain L residue 24 ARG Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 6 GLN Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Chi-restraints excluded: chain J residue 90 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 261 optimal weight: 0.9990 chunk 50 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 217 optimal weight: 0.7980 chunk 225 optimal weight: 6.9990 chunk 7 optimal weight: 30.0000 chunk 309 optimal weight: 0.0980 chunk 118 optimal weight: 10.0000 chunk 179 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 804 GLN A1010 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN ** I 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.163861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111284 restraints weight = 45063.714| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.48 r_work: 0.3133 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30480 Z= 0.113 Angle : 0.668 13.003 41599 Z= 0.322 Chirality : 0.047 0.496 4844 Planarity : 0.004 0.049 5256 Dihedral : 6.862 59.427 5465 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.66 % Favored : 94.21 % Rotamer: Outliers : 2.66 % Allowed : 25.88 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3607 helix: 1.60 (0.22), residues: 654 sheet: -0.42 (0.16), residues: 1077 loop : -1.71 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 67 TYR 0.016 0.001 TYR B1067 PHE 0.026 0.001 PHE C 133 TRP 0.014 0.001 TRP H 33 HIS 0.003 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00246 (30364) covalent geometry : angle 0.64383 (41296) SS BOND : bond 0.00378 ( 45) SS BOND : angle 1.72237 ( 90) hydrogen bonds : bond 0.03680 ( 1002) hydrogen bonds : angle 5.01978 ( 2805) link_BETA1-4 : bond 0.00515 ( 23) link_BETA1-4 : angle 1.96200 ( 69) link_NAG-ASN : bond 0.00441 ( 48) link_NAG-ASN : angle 2.54413 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 215 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7188 (ttmt) cc_final: 0.6545 (tttt) REVERT: A 161 SER cc_start: 0.7263 (OUTLIER) cc_final: 0.6791 (t) REVERT: A 198 ASP cc_start: 0.8232 (m-30) cc_final: 0.7902 (p0) REVERT: A 202 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8622 (mtpp) REVERT: A 231 ILE cc_start: 0.8030 (OUTLIER) cc_final: 0.7728 (OUTLIER) REVERT: A 237 ARG cc_start: 0.7956 (mtp85) cc_final: 0.7341 (ttp-110) REVERT: A 269 TYR cc_start: 0.8035 (m-80) cc_final: 0.7709 (m-10) REVERT: A 319 ARG cc_start: 0.8181 (ttp-110) cc_final: 0.7850 (mtp85) REVERT: A 324 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: A 449 TYR cc_start: 0.6025 (p90) cc_final: 0.4894 (t80) REVERT: A 452 ARG cc_start: 0.6132 (OUTLIER) cc_final: 0.4778 (mtp85) REVERT: A 529 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6132 (mtpt) REVERT: A 869 MET cc_start: 0.9100 (mtt) cc_final: 0.8802 (mtt) REVERT: B 52 GLN cc_start: 0.8236 (tp40) cc_final: 0.7841 (tp-100) REVERT: B 331 ASN cc_start: 0.6842 (OUTLIER) cc_final: 0.6120 (m-40) REVERT: B 444 LYS cc_start: 0.7503 (ptpp) cc_final: 0.6972 (ptmt) REVERT: B 569 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7511 (mp) REVERT: B 1113 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.8483 (mt0) REVERT: C 95 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8396 (p) REVERT: C 133 PHE cc_start: 0.7322 (m-80) cc_final: 0.7115 (m-80) REVERT: C 200 TYR cc_start: 0.6903 (OUTLIER) cc_final: 0.6142 (t80) REVERT: C 228 ASP cc_start: 0.8696 (OUTLIER) cc_final: 0.8261 (t70) REVERT: C 340 GLU cc_start: 0.8650 (mp0) cc_final: 0.8098 (pm20) REVERT: C 402 ILE cc_start: 0.8743 (pt) cc_final: 0.8449 (pp) REVERT: C 403 ARG cc_start: 0.8181 (ttp-170) cc_final: 0.7627 (ttm110) REVERT: C 487 ASN cc_start: 0.6615 (m-40) cc_final: 0.5664 (p0) REVERT: C 493 GLN cc_start: 0.7625 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: C 529 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.8251 (ttpt) REVERT: C 534 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8432 (m) REVERT: C 776 LYS cc_start: 0.9086 (ttmm) cc_final: 0.8865 (tttm) REVERT: H 11 LEU cc_start: 0.6430 (tm) cc_final: 0.5884 (mm) REVERT: H 19 ARG cc_start: 0.8156 (mmt180) cc_final: 0.7756 (tpt90) REVERT: L 18 ARG cc_start: 0.8159 (mmm160) cc_final: 0.7908 (mtp-110) REVERT: L 38 GLN cc_start: 0.8435 (tp-100) cc_final: 0.8080 (tm-30) REVERT: L 48 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8385 (mt) REVERT: L 61 ARG cc_start: 0.7691 (ptp90) cc_final: 0.7387 (ptp90) REVERT: L 82 ASP cc_start: 0.8717 (m-30) cc_final: 0.8356 (m-30) REVERT: I 39 GLN cc_start: 0.2479 (tt0) cc_final: 0.2060 (mp-120) REVERT: I 106 ILE cc_start: 0.5302 (OUTLIER) cc_final: 0.4751 (mp) REVERT: M 4 MET cc_start: 0.2262 (tmt) cc_final: 0.2044 (tmm) REVERT: J 51 ILE cc_start: -0.0337 (OUTLIER) cc_final: -0.1316 (mt) REVERT: J 67 ARG cc_start: 0.5922 (ttt-90) cc_final: 0.5648 (ttt-90) outliers start: 85 outliers final: 53 residues processed: 288 average time/residue: 0.5902 time to fit residues: 204.6041 Evaluate side-chains 275 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 205 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 75 optimal weight: 0.8980 chunk 223 optimal weight: 10.0000 chunk 315 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 92 optimal weight: 0.7980 chunk 195 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 47 optimal weight: 0.0170 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 overall best weight: 0.7018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A 955 ASN A1010 GLN A1142 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.110554 restraints weight = 45082.714| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.49 r_work: 0.3140 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30480 Z= 0.110 Angle : 0.658 12.189 41599 Z= 0.317 Chirality : 0.047 0.469 4844 Planarity : 0.004 0.050 5256 Dihedral : 6.651 57.090 5465 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.02 % Favored : 93.85 % Rotamer: Outliers : 2.41 % Allowed : 25.95 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3607 helix: 1.78 (0.21), residues: 654 sheet: -0.27 (0.16), residues: 1112 loop : -1.70 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 408 TYR 0.018 0.001 TYR B1067 PHE 0.023 0.001 PHE C 133 TRP 0.011 0.001 TRP I 103 HIS 0.002 0.000 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00241 (30364) covalent geometry : angle 0.63449 (41296) SS BOND : bond 0.00370 ( 45) SS BOND : angle 1.59831 ( 90) hydrogen bonds : bond 0.03529 ( 1002) hydrogen bonds : angle 4.91986 ( 2805) link_BETA1-4 : bond 0.00519 ( 23) link_BETA1-4 : angle 1.91229 ( 69) link_NAG-ASN : bond 0.00416 ( 48) link_NAG-ASN : angle 2.48073 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7214 Ramachandran restraints generated. 3607 Oldfield, 0 Emsley, 3607 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 210 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 LYS cc_start: 0.7107 (ttmt) cc_final: 0.6490 (tttt) REVERT: A 197 ILE cc_start: 0.8079 (OUTLIER) cc_final: 0.7706 (mp) REVERT: A 198 ASP cc_start: 0.8207 (m-30) cc_final: 0.7888 (p0) REVERT: A 202 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8645 (mtpp) REVERT: A 231 ILE cc_start: 0.7987 (OUTLIER) cc_final: 0.7657 (mp) REVERT: A 237 ARG cc_start: 0.7877 (mtp85) cc_final: 0.7233 (ttp-110) REVERT: A 269 TYR cc_start: 0.8011 (m-80) cc_final: 0.7807 (m-80) REVERT: A 319 ARG cc_start: 0.8170 (ttp-110) cc_final: 0.7838 (mtp85) REVERT: A 324 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7201 (pm20) REVERT: A 449 TYR cc_start: 0.5990 (p90) cc_final: 0.4898 (t80) REVERT: A 452 ARG cc_start: 0.6174 (OUTLIER) cc_final: 0.4816 (mtp85) REVERT: A 529 LYS cc_start: 0.6961 (OUTLIER) cc_final: 0.6083 (mtpt) REVERT: A 869 MET cc_start: 0.9138 (mtt) cc_final: 0.8793 (mtt) REVERT: B 52 GLN cc_start: 0.8189 (tp40) cc_final: 0.7785 (tp-100) REVERT: B 331 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6125 (m-40) REVERT: B 444 LYS cc_start: 0.7629 (ptpp) cc_final: 0.7036 (ptmt) REVERT: B 1113 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8554 (mt0) REVERT: C 95 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8409 (p) REVERT: C 135 PHE cc_start: 0.6144 (m-80) cc_final: 0.5895 (m-80) REVERT: C 200 TYR cc_start: 0.6891 (OUTLIER) cc_final: 0.6204 (t80) REVERT: C 228 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.8262 (t0) REVERT: C 340 GLU cc_start: 0.8634 (mp0) cc_final: 0.8071 (pm20) REVERT: C 402 ILE cc_start: 0.8712 (pt) cc_final: 0.8423 (pp) REVERT: C 403 ARG cc_start: 0.8163 (ttp-170) cc_final: 0.7630 (ttm110) REVERT: C 487 ASN cc_start: 0.6522 (m-40) cc_final: 0.5645 (p0) REVERT: C 493 GLN cc_start: 0.7590 (OUTLIER) cc_final: 0.7219 (tt0) REVERT: C 529 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8225 (ttpt) REVERT: C 534 VAL cc_start: 0.8690 (OUTLIER) cc_final: 0.8437 (m) REVERT: C 776 LYS cc_start: 0.9117 (ttmm) cc_final: 0.8713 (ttpt) REVERT: C 1002 GLN cc_start: 0.8696 (tt0) cc_final: 0.8430 (tt0) REVERT: C 1139 ASP cc_start: 0.8745 (t0) cc_final: 0.8544 (t0) REVERT: H 11 LEU cc_start: 0.6347 (tm) cc_final: 0.5837 (mm) REVERT: H 19 ARG cc_start: 0.8072 (mmt180) cc_final: 0.7723 (tpt90) REVERT: L 18 ARG cc_start: 0.8133 (mmm160) cc_final: 0.7886 (mtp-110) REVERT: L 38 GLN cc_start: 0.8400 (tp-100) cc_final: 0.8041 (tm-30) REVERT: L 48 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8361 (mt) REVERT: L 82 ASP cc_start: 0.8700 (m-30) cc_final: 0.8461 (m-30) REVERT: I 39 GLN cc_start: 0.3095 (tt0) cc_final: 0.2527 (mp-120) REVERT: M 4 MET cc_start: 0.2254 (tmt) cc_final: 0.2025 (tmm) REVERT: J 51 ILE cc_start: -0.0515 (OUTLIER) cc_final: -0.1471 (mt) REVERT: J 67 ARG cc_start: 0.5944 (ttt-90) cc_final: 0.5677 (ttt-90) outliers start: 77 outliers final: 55 residues processed: 280 average time/residue: 0.5865 time to fit residues: 198.3497 Evaluate side-chains 273 residues out of total 3199 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 202 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 202 LYS Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 439 ASN Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 525 CYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 975 SER Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 195 LYS Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 301 CYS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 336 CYS Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1113 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 122 ASN Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 493 GLN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 529 LYS Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 48 ILE Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 88 CYS Chi-restraints excluded: chain J residue 51 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 126 optimal weight: 0.6980 chunk 282 optimal weight: 5.9990 chunk 7 optimal weight: 30.0000 chunk 194 optimal weight: 4.9990 chunk 309 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 101 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 265 optimal weight: 1.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 675 GLN A 856 ASN A1142 GLN B 81 ASN ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 74 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.163940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.111526 restraints weight = 45211.937| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.41 r_work: 0.3137 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.110 30480 Z= 0.152 Angle : 0.761 59.199 41599 Z= 0.394 Chirality : 0.049 0.776 4844 Planarity : 0.004 0.050 5256 Dihedral : 6.663 57.155 5464 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.10 % Favored : 93.73 % Rotamer: Outliers : 2.59 % Allowed : 25.88 % Favored : 71.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.17 % 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: -0.87 (0.14), residues: 3607 helix: 1.76 (0.21), residues: 654 sheet: -0.26 (0.16), residues: 1112 loop : -1.70 (0.13), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 237 TYR 0.017 0.001 TYR C1067 PHE 0.012 0.001 PHE C 133 TRP 0.011 0.001 TRP I 103 HIS 0.003 0.001 HIS C 49 Details of bonding type rmsd covalent geometry : bond 0.00335 (30364) covalent geometry : angle 0.74145 (41296) SS BOND : bond 0.00379 ( 45) SS BOND : angle 1.59431 ( 90) hydrogen bonds : bond 0.03684 ( 1002) hydrogen bonds : angle 4.91592 ( 2805) link_BETA1-4 : bond 0.00353 ( 23) link_BETA1-4 : angle 1.90771 ( 69) link_NAG-ASN : bond 0.00440 ( 48) link_NAG-ASN : angle 2.48116 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12543.70 seconds wall clock time: 213 minutes 47.14 seconds (12827.14 seconds total)