Starting phenix.real_space_refine on Tue Apr 7 19:43:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d00_30523/04_2026/7d00_30523.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d00_30523/04_2026/7d00_30523.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 { model { file = "/net/cci-nas-00/data/ceres_data/7d00_30523/04_2026/7d00_30523.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d00_30523/04_2026/7d00_30523.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d00_30523/04_2026/7d00_30523.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d00_30523/04_2026/7d00_30523.map" } 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= 0.004 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 129 5.16 5 C 19603 2.51 5 N 5046 2.21 5 O 6108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30886 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "K" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "J" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1614 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain: "N" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1633 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} 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: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 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: 7.00, per 1000 atoms: 0.23 Number of scatterers: 30886 At special positions: 0 Unit cell: (134.788, 176.094, 233.705, 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 129 16.00 O 6108 8.00 N 5046 7.00 C 19603 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.30 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.29 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.29 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.17 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 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 95 " distance=2.04 Simple disulfide: pdb=" SG CYS H 142 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 95 " distance=2.04 Simple disulfide: pdb=" SG CYS J 142 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " 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 B1410 " - " NAG B1411 " " 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 I 1 " - " NAG I 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 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-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 343 " " NAG B1407 " - " ASN B 603 " " NAG B1408 " - " ASN B 616 " " NAG B1409 " - " ASN B 657 " " NAG B1410 " - " ASN B1074 " " 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 I 1 " - " ASN A1074 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 331 " " NAG P 1 " - " ASN B 709 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1098 " " NAG T 1 " - " ASN B1134 " " NAG U 1 " - " ASN C 331 " " NAG V 1 " - " ASN C 343 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 2.61 Conformation dependent library (CDL) restraints added in 1.3 seconds 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 62 sheets defined 19.5% alpha, 30.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.074A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.258A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 removed outlier: 3.624A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR A 421 " --> pdb=" O LYS A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A 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: 3.771A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A 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: 4.176A 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: 3.538A 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: 3.647A pdb=" N LEU A 821 " --> pdb=" O PHE 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: 3.574A 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: 3.625A 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: 3.647A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.878A 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: 3.648A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.678A 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 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.640A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 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: 3.966A 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: 3.638A 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: 3.544A 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: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.011A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.705A 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: 4.371A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.674A 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: 3.582A 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 364 through 370 removed outlier: 4.074A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 4.257A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.623A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.737A pdb=" N TYR C 421 " --> pdb=" O LYS C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.582A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.716A 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: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.721A 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: 3.551A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.636A 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: 3.591A 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: 3.713A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.356A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A 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: 4.220A 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: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.634A 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 28 through 32 removed outlier: 4.238A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 189 through 191 No H-bonds generated for 'chain 'H' and resid 189 through 191' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' and resid 183 through 187 Processing helix chain 'J' and resid 28 through 32 removed outlier: 4.238A pdb=" N ASN J 32 " --> pdb=" O VAL J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 189 through 191 No H-bonds generated for 'chain 'J' and resid 189 through 191' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 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: 6.440A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.682A 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: 4.437A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA5, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.730A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.475A 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: 7.210A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.679A 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=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.542A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR A 451 " --> pdb=" O TYR A 495 " (cutoff:3.500A) 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 539 through 543 removed outlier: 5.337A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.256A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A 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: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A 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=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.588A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.829A 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: 6.605A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.700A 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=AB6, 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=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, 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=AB9, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.538A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 9.441A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.649A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.779A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU B 117 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.573A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (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: 6.542A 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: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A 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: 6.542A 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: 6.525A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.798A 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: 4.578A 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 31 removed outlier: 8.150A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 10.527A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N CYS C 291 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 128 through 131 removed outlier: 4.247A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.543A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 448 through 454 removed outlier: 5.864A pdb=" N TYR C 449 " --> pdb=" O PHE C 497 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N PHE C 497 " --> pdb=" O TYR C 449 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N TYR C 451 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 543 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.230A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.534A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 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: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A 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: 3.590A 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: 5.817A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (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: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A 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: 3.564A 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=AE7, 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=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 45 through 51 removed outlier: 6.530A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR H 33 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA H 139 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL H 186 " --> pdb=" O ALA H 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 141 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL H 184 " --> pdb=" O GLY H 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 143 " --> pdb=" O SER H 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER H 182 " --> pdb=" O LEU H 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 145 " --> pdb=" O LEU H 180 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 180 " --> pdb=" O LYS H 145 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 152 through 156 Processing sheet with id=AF5, first strand: chain 'K' and resid 11 through 13 removed outlier: 6.507A pdb=" N LEU K 11 " --> pdb=" O GLU K 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR K 87 " --> pdb=" O TYR K 36 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 18 through 23 Processing sheet with id=AF7, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AF8, first strand: chain 'K' and resid 153 through 154 Processing sheet with id=AF9, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 45 through 51 removed outlier: 6.531A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR J 33 " --> pdb=" O GLU J 98 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'J' and resid 123 through 126 removed outlier: 5.009A pdb=" N ALA J 139 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL J 186 " --> pdb=" O ALA J 139 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 141 " --> pdb=" O VAL J 184 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL J 184 " --> pdb=" O GLY J 141 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU J 143 " --> pdb=" O SER J 182 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N SER J 182 " --> pdb=" O LEU J 143 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 145 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 180 " --> pdb=" O LYS J 145 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 152 through 156 Processing sheet with id=AG5, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.507A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR N 87 " --> pdb=" O TYR N 36 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'N' and resid 18 through 23 Processing sheet with id=AG7, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AG8, first strand: chain 'N' and resid 153 through 154 1123 hydrogen bonds defined for protein. 3045 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: 8.65 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9643 1.34 - 1.46: 8183 1.46 - 1.59: 13567 1.59 - 1.72: 0 1.72 - 1.85: 160 Bond restraints: 31553 Sorted by residual: bond pdb=" N PRO H 14 " pdb=" CD PRO H 14 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" N PRO J 14 " pdb=" CD PRO J 14 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.91e+01 bond pdb=" N PRO K 141 " pdb=" CD PRO K 141 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO N 141 " pdb=" CD PRO N 141 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 bond pdb=" N PRO A 479 " pdb=" CD PRO A 479 " ideal model delta sigma weight residual 1.473 1.533 -0.060 1.40e-02 5.10e+03 1.85e+01 ... (remaining 31548 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 41797 2.69 - 5.39: 1017 5.39 - 8.08: 79 8.08 - 10.78: 11 10.78 - 13.47: 8 Bond angle restraints: 42912 Sorted by residual: angle pdb=" N THR J 28 " pdb=" CA THR J 28 " pdb=" C THR J 28 " ideal model delta sigma weight residual 111.24 121.54 -10.30 1.38e+00 5.25e-01 5.57e+01 angle pdb=" N THR H 28 " pdb=" CA THR H 28 " pdb=" C THR H 28 " ideal model delta sigma weight residual 111.24 121.52 -10.28 1.38e+00 5.25e-01 5.55e+01 angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.77 -11.23 1.91e+00 2.74e-01 3.46e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.82 -7.37 1.26e+00 6.30e-01 3.42e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.07 5.71 1.03e+00 9.43e-01 3.08e+01 ... (remaining 42907 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 16990 17.91 - 35.82: 1941 35.82 - 53.73: 555 53.73 - 71.64: 195 71.64 - 89.55: 57 Dihedral angle restraints: 19738 sinusoidal: 8547 harmonic: 11191 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 12.15 80.85 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.61 73.39 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.17 71.83 1 1.00e+01 1.00e-02 6.61e+01 ... (remaining 19735 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5077 0.328 - 0.657: 7 0.657 - 0.985: 2 0.985 - 1.313: 0 1.313 - 1.642: 1 Chirality restraints: 5087 Sorted by residual: chirality pdb=" C1 NAG B1411 " pdb=" O4 NAG B1410 " pdb=" C2 NAG B1411 " pdb=" O5 NAG B1411 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.15e+03 chirality pdb=" C1 NAG U 2 " pdb=" O4 NAG U 1 " pdb=" C2 NAG U 2 " pdb=" O5 NAG U 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-02 2.50e+03 4.23e+02 chirality pdb=" C1 NAG b 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG b 1 " pdb=" O5 NAG b 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.74e+01 ... (remaining 5084 not shown) Planarity restraints: 5492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG U 1 " -0.151 2.00e-02 2.50e+03 1.25e-01 1.94e+02 pdb=" C7 NAG U 1 " 0.041 2.00e-02 2.50e+03 pdb=" C8 NAG U 1 " -0.112 2.00e-02 2.50e+03 pdb=" N2 NAG U 1 " 0.200 2.00e-02 2.50e+03 pdb=" O7 NAG U 1 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.062 2.00e-02 2.50e+03 7.07e-02 6.25e+01 pdb=" CG ASN A 331 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " 0.002 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.118 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.039 2.00e-02 2.50e+03 4.01e-02 2.01e+01 pdb=" CG ASN C 331 " 0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.062 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.048 2.00e-02 2.50e+03 ... (remaining 5489 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 373 2.56 - 3.15: 24472 3.15 - 3.73: 44935 3.73 - 4.32: 66002 4.32 - 4.90: 109382 Nonbonded interactions: 245164 Sorted by model distance: nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.980 3.120 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.980 3.120 nonbonded pdb=" O ASN K 137 " pdb=" O ASN K 138 " model vdw 2.039 3.040 nonbonded pdb=" O ASN N 137 " pdb=" O ASN N 138 " model vdw 2.039 3.040 nonbonded pdb=" O ALA A 522 " pdb=" OG1 THR A 523 " model vdw 2.135 3.040 ... (remaining 245159 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 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 620 or resid 641 through 939 or resid 944 through 14 \ 08)) selection = (chain 'B' and (resid 27 through 620 or resid 641 through 826 or resid 855 throu \ gh 1408)) selection = (chain 'C' and (resid 27 through 441 or resid 451 through 475 or resid 487 throu \ gh 497 or resid 503 through 826 or resid 855 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'K' 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: 2.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 31.220 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.260 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 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 : 0.011 0.270 31669 Z= 0.505 Angle : 1.205 48.946 43214 Z= 0.641 Chirality : 0.068 1.642 5087 Planarity : 0.007 0.125 5444 Dihedral : 17.548 89.555 12400 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 1.85 % Allowed : 10.25 % Favored : 87.90 % Rotamer: Outliers : 11.80 % Allowed : 18.21 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.85 (0.11), residues: 3786 helix: -2.15 (0.16), residues: 661 sheet: -1.73 (0.14), residues: 1067 loop : -3.25 (0.11), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 71 TYR 0.026 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.026 0.003 TRP A 104 HIS 0.009 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01092 (31553) covalent geometry : angle 1.03365 (42912) SS BOND : bond 0.07075 ( 46) SS BOND : angle 9.28373 ( 92) hydrogen bonds : bond 0.19394 ( 1073) hydrogen bonds : angle 7.95946 ( 3045) link_BETA1-4 : bond 0.04395 ( 22) link_BETA1-4 : angle 4.84927 ( 66) link_NAG-ASN : bond 0.03046 ( 48) link_NAG-ASN : angle 7.16006 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 396 poor density : 361 time to evaluate : 1.136 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 335 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6479 (tp) REVERT: A 389 ASP cc_start: 0.6162 (OUTLIER) cc_final: 0.5588 (p0) REVERT: A 421 TYR cc_start: 0.1276 (OUTLIER) cc_final: 0.0864 (p90) REVERT: A 517 LEU cc_start: 0.2021 (OUTLIER) cc_final: 0.1659 (pp) REVERT: A 1039 ARG cc_start: 0.9193 (OUTLIER) cc_final: 0.8933 (mtt180) REVERT: B 158 ARG cc_start: 0.6277 (OUTLIER) cc_final: 0.5255 (mmm160) REVERT: B 521 PRO cc_start: 0.7951 (Cg_exo) cc_final: 0.7588 (Cg_endo) REVERT: C 143 VAL cc_start: 0.5589 (OUTLIER) cc_final: 0.5062 (t) REVERT: C 215 ASP cc_start: 0.5494 (OUTLIER) cc_final: 0.4584 (t70) REVERT: C 389 ASP cc_start: 0.5191 (OUTLIER) cc_final: 0.4684 (m-30) REVERT: C 990 GLU cc_start: 0.7544 (tt0) cc_final: 0.7331 (tt0) REVERT: H 34 MET cc_start: 0.2233 (mmm) cc_final: 0.1245 (ptt) REVERT: H 89 ASP cc_start: 0.1696 (OUTLIER) cc_final: 0.1322 (t0) REVERT: H 100 LEU cc_start: 0.2625 (OUTLIER) cc_final: 0.2239 (mt) REVERT: H 105 TRP cc_start: 0.1113 (OUTLIER) cc_final: -0.0254 (p-90) REVERT: H 140 LEU cc_start: 0.1125 (OUTLIER) cc_final: 0.0695 (mp) REVERT: H 205 SER cc_start: -0.2483 (OUTLIER) cc_final: -0.2733 (t) REVERT: K 62 PHE cc_start: -0.1194 (OUTLIER) cc_final: -0.1672 (m-80) REVERT: K 63 SER cc_start: 0.3400 (OUTLIER) cc_final: 0.2992 (m) REVERT: J 82 MET cc_start: 0.1125 (ptp) cc_final: 0.0845 (tmm) REVERT: J 85 LEU cc_start: 0.0700 (OUTLIER) cc_final: -0.0133 (tp) REVERT: J 166 HIS cc_start: -0.1056 (OUTLIER) cc_final: -0.1494 (p-80) REVERT: N 91 LEU cc_start: 0.1586 (OUTLIER) cc_final: 0.0737 (tt) outliers start: 396 outliers final: 96 residues processed: 693 average time/residue: 0.4771 time to fit residues: 410.1320 Evaluate side-chains 273 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 158 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU 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 730 SER Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 785 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 902 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1039 ARG Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 158 ARG Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 968 SER Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1030 SER Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 693 ILE Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 205 SER Chi-restraints excluded: chain K residue 62 PHE Chi-restraints excluded: chain K residue 63 SER Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 91 LEU Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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 239 GLN A 360 ASN A 388 ASN A 422 ASN A 440 ASN A 481 ASN A 493 GLN A 498 GLN A 644 GLN A 690 GLN A 703 ASN 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 A1101 HIS B 115 GLN B 121 ASN B 164 ASN B 188 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 540 ASN B 563 GLN B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1010 GLN B1054 GLN B1142 GLN C 30 ASN C 66 HIS C 134 GLN C 321 GLN C 360 ASN C 422 ASN C 440 ASN C 481 ASN ** C 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 606 ASN C 641 ASN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 969 ASN C 992 GLN C1071 GLN C1101 HIS K 89 GLN J 81 GLN N 92 ASN Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.209301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158397 restraints weight = 46219.059| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.63 r_work: 0.3270 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31669 Z= 0.164 Angle : 0.819 14.643 43214 Z= 0.402 Chirality : 0.050 0.450 5087 Planarity : 0.005 0.047 5444 Dihedral : 9.959 72.401 5770 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.53 % Favored : 92.13 % Rotamer: Outliers : 5.99 % Allowed : 21.60 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.12), residues: 3786 helix: -0.09 (0.20), residues: 669 sheet: -1.07 (0.15), residues: 1113 loop : -2.71 (0.12), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 357 TYR 0.017 0.001 TYR A1067 PHE 0.026 0.002 PHE B 168 TRP 0.009 0.001 TRP A 436 HIS 0.006 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00371 (31553) covalent geometry : angle 0.78029 (42912) SS BOND : bond 0.00423 ( 46) SS BOND : angle 2.42584 ( 92) hydrogen bonds : bond 0.04876 ( 1073) hydrogen bonds : angle 5.91003 ( 3045) link_BETA1-4 : bond 0.00582 ( 22) link_BETA1-4 : angle 2.42291 ( 66) link_NAG-ASN : bond 0.00445 ( 48) link_NAG-ASN : angle 3.69024 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 201 poor density : 201 time to evaluate : 1.175 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: A 335 LEU cc_start: 0.6775 (OUTLIER) cc_final: 0.5740 (tm) REVERT: A 389 ASP cc_start: 0.6034 (OUTLIER) cc_final: 0.5414 (p0) REVERT: B 158 ARG cc_start: 0.6714 (mmt90) cc_final: 0.5076 (mmm160) REVERT: B 492 LEU cc_start: 0.6083 (mt) cc_final: 0.5846 (mt) REVERT: B 506 GLN cc_start: 0.6623 (mp10) cc_final: 0.6100 (pm20) REVERT: B 521 PRO cc_start: 0.8303 (Cg_exo) cc_final: 0.7852 (Cg_endo) REVERT: B 740 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8445 (ttt) REVERT: B 746 SER cc_start: 0.8235 (OUTLIER) cc_final: 0.7853 (m) REVERT: B 855 PHE cc_start: 0.7806 (OUTLIER) cc_final: 0.7591 (m-80) REVERT: B 976 VAL cc_start: 0.9299 (OUTLIER) cc_final: 0.9048 (t) REVERT: C 215 ASP cc_start: 0.5267 (OUTLIER) cc_final: 0.4198 (t70) REVERT: C 586 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7350 (m-30) REVERT: C 787 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8460 (mt0) REVERT: C 990 GLU cc_start: 0.8252 (tt0) cc_final: 0.7983 (tt0) REVERT: H 82 MET cc_start: 0.0507 (OUTLIER) cc_final: 0.0124 (mmm) REVERT: H 140 LEU cc_start: 0.0481 (OUTLIER) cc_final: 0.0137 (mp) REVERT: K 114 SER cc_start: 0.3646 (OUTLIER) cc_final: 0.2998 (m) REVERT: J 70 SER cc_start: 0.2491 (t) cc_final: 0.2145 (m) REVERT: J 85 LEU cc_start: 0.0553 (OUTLIER) cc_final: 0.0133 (tp) REVERT: J 140 LEU cc_start: 0.2661 (OUTLIER) cc_final: 0.1983 (mp) REVERT: J 166 HIS cc_start: -0.0598 (OUTLIER) cc_final: -0.0964 (m-70) REVERT: J 172 LEU cc_start: 0.3846 (OUTLIER) cc_final: 0.3574 (tt) REVERT: N 32 TYR cc_start: 0.2689 (OUTLIER) cc_final: 0.2012 (m-10) REVERT: N 49 TYR cc_start: 0.2811 (OUTLIER) cc_final: 0.1771 (t80) outliers start: 201 outliers final: 80 residues processed: 380 average time/residue: 0.4580 time to fit residues: 219.2144 Evaluate side-chains 262 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 164 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1076 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 855 PHE Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 478 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 787 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 122 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 114 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 85 LEU Chi-restraints excluded: chain J residue 95 CYS Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 199 ASN Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain N residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 272 optimal weight: 3.9990 chunk 299 optimal weight: 2.9990 chunk 162 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 222 optimal weight: 9.9990 chunk 14 optimal weight: 0.3980 chunk 318 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 856 ASN A1010 GLN A1125 ASN B 414 GLN C 487 ASN C 751 ASN C 804 GLN H 81 GLN K 137 ASN N 137 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.208720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.156838 restraints weight = 46077.245| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.71 r_work: 0.3187 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31669 Z= 0.157 Angle : 0.730 14.462 43214 Z= 0.357 Chirality : 0.049 0.430 5087 Planarity : 0.005 0.050 5444 Dihedral : 8.542 63.087 5666 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.34 % Favored : 92.42 % Rotamer: Outliers : 5.81 % Allowed : 21.33 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -1.85 (0.13), residues: 3786 helix: 0.71 (0.20), residues: 671 sheet: -0.65 (0.15), residues: 1101 loop : -2.33 (0.12), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 454 TYR 0.017 0.001 TYR C1067 PHE 0.032 0.002 PHE J 67 TRP 0.007 0.001 TRP A 436 HIS 0.005 0.001 HIS J 202 Details of bonding type rmsd covalent geometry : bond 0.00365 (31553) covalent geometry : angle 0.69932 (42912) SS BOND : bond 0.00535 ( 46) SS BOND : angle 1.78324 ( 92) hydrogen bonds : bond 0.04409 ( 1073) hydrogen bonds : angle 5.48136 ( 3045) link_BETA1-4 : bond 0.00558 ( 22) link_BETA1-4 : angle 2.33970 ( 66) link_NAG-ASN : bond 0.00434 ( 48) link_NAG-ASN : angle 3.09245 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 180 time to evaluate : 1.176 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: A 878 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8735 (tp) REVERT: B 127 VAL cc_start: 0.7576 (OUTLIER) cc_final: 0.7284 (m) REVERT: B 158 ARG cc_start: 0.6527 (mmt90) cc_final: 0.4980 (mmm160) REVERT: B 414 GLN cc_start: 0.5363 (OUTLIER) cc_final: 0.5126 (mp10) REVERT: B 440 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7263 (p0) REVERT: B 560 LEU cc_start: 0.7581 (OUTLIER) cc_final: 0.7309 (mt) REVERT: B 740 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8420 (ttt) REVERT: B 746 SER cc_start: 0.8255 (OUTLIER) cc_final: 0.7868 (m) REVERT: C 133 PHE cc_start: 0.6949 (m-80) cc_final: 0.6247 (m-80) REVERT: C 212 LEU cc_start: 0.5027 (OUTLIER) cc_final: 0.4634 (pp) REVERT: C 407 VAL cc_start: 0.3714 (OUTLIER) cc_final: 0.3339 (p) REVERT: C 988 GLU cc_start: 0.8203 (mp0) cc_final: 0.7672 (tp30) REVERT: H 34 MET cc_start: 0.1479 (OUTLIER) cc_final: 0.0442 (ttm) REVERT: H 82 MET cc_start: 0.1087 (OUTLIER) cc_final: 0.0273 (mmm) REVERT: H 140 LEU cc_start: 0.0558 (OUTLIER) cc_final: 0.0269 (mp) REVERT: J 70 SER cc_start: 0.2419 (t) cc_final: 0.1997 (m) REVERT: J 82 MET cc_start: -0.0193 (mtt) cc_final: -0.1570 (tpt) REVERT: J 102 PHE cc_start: 0.1841 (OUTLIER) cc_final: 0.1312 (m-10) REVERT: J 140 LEU cc_start: 0.2598 (OUTLIER) cc_final: 0.1846 (mp) REVERT: J 166 HIS cc_start: -0.0773 (OUTLIER) cc_final: -0.1022 (m-70) outliers start: 195 outliers final: 77 residues processed: 352 average time/residue: 0.4784 time to fit residues: 210.7974 Evaluate side-chains 242 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 150 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1050 MET 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 66 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 108 ARG Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 108 ARG Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 61 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 367 optimal weight: 40.0000 chunk 168 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 348 optimal weight: 20.0000 chunk 180 optimal weight: 5.9990 chunk 233 optimal weight: 0.2980 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 764 ASN A 856 ASN A1010 GLN B 414 GLN C 218 GLN C 957 GLN H 199 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.207627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.155490 restraints weight = 45707.562| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.65 r_work: 0.3145 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 31669 Z= 0.214 Angle : 0.756 15.002 43214 Z= 0.368 Chirality : 0.050 0.446 5087 Planarity : 0.005 0.053 5444 Dihedral : 8.232 59.854 5649 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.45 % Favored : 92.31 % Rotamer: Outliers : 5.96 % Allowed : 21.60 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.13), residues: 3786 helix: 0.85 (0.21), residues: 668 sheet: -0.52 (0.15), residues: 1087 loop : -2.18 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 454 TYR 0.018 0.001 TYR C1067 PHE 0.018 0.002 PHE K 116 TRP 0.013 0.001 TRP A 436 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00525 (31553) covalent geometry : angle 0.72438 (42912) SS BOND : bond 0.00462 ( 46) SS BOND : angle 2.13558 ( 92) hydrogen bonds : bond 0.04862 ( 1073) hydrogen bonds : angle 5.45692 ( 3045) link_BETA1-4 : bond 0.00422 ( 22) link_BETA1-4 : angle 2.36234 ( 66) link_NAG-ASN : bond 0.00445 ( 48) link_NAG-ASN : angle 3.13293 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 167 time to evaluate : 1.027 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: A 141 LEU cc_start: 0.5907 (OUTLIER) cc_final: 0.5469 (mt) REVERT: A 157 PHE cc_start: 0.6923 (t80) cc_final: 0.6584 (t80) REVERT: A 190 ARG cc_start: 0.7128 (ptp90) cc_final: 0.6841 (mtt90) REVERT: A 324 GLU cc_start: 0.7945 (tp30) cc_final: 0.7605 (tp30) REVERT: A 347 PHE cc_start: 0.1740 (OUTLIER) cc_final: 0.1392 (m-10) REVERT: A 947 LYS cc_start: 0.9238 (OUTLIER) cc_final: 0.8739 (mtmt) REVERT: B 236 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7774 (p) REVERT: B 239 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7672 (tt0) REVERT: B 314 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8235 (tt0) REVERT: B 454 ARG cc_start: 0.7643 (ttp-110) cc_final: 0.7325 (ttm110) REVERT: B 456 PHE cc_start: 0.5414 (OUTLIER) cc_final: 0.4262 (m-80) REVERT: B 508 TYR cc_start: 0.7443 (m-80) cc_final: 0.7004 (m-80) REVERT: B 740 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8341 (ttt) REVERT: B 746 SER cc_start: 0.8236 (OUTLIER) cc_final: 0.7854 (m) REVERT: C 133 PHE cc_start: 0.7403 (m-80) cc_final: 0.6274 (m-80) REVERT: C 212 LEU cc_start: 0.5066 (OUTLIER) cc_final: 0.4668 (pp) REVERT: C 553 THR cc_start: 0.7902 (OUTLIER) cc_final: 0.7702 (t) REVERT: C 988 GLU cc_start: 0.8368 (mp0) cc_final: 0.7787 (tp30) REVERT: H 34 MET cc_start: 0.1358 (ptt) cc_final: -0.0119 (tpp) REVERT: H 82 MET cc_start: 0.1196 (OUTLIER) cc_final: 0.0227 (mmm) REVERT: H 140 LEU cc_start: 0.0547 (OUTLIER) cc_final: 0.0157 (mp) REVERT: K 58 VAL cc_start: 0.3099 (OUTLIER) cc_final: 0.2730 (m) REVERT: K 176 SER cc_start: 0.1184 (OUTLIER) cc_final: 0.0919 (m) REVERT: J 82 MET cc_start: 0.0041 (mtt) cc_final: -0.1698 (tpp) REVERT: J 140 LEU cc_start: 0.2481 (OUTLIER) cc_final: 0.1952 (mp) REVERT: N 32 TYR cc_start: 0.2144 (OUTLIER) cc_final: 0.1717 (m-10) REVERT: N 55 GLN cc_start: 0.0383 (tm-30) cc_final: -0.0020 (mp10) outliers start: 200 outliers final: 105 residues processed: 343 average time/residue: 0.4558 time to fit residues: 195.6350 Evaluate side-chains 274 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 152 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 583 GLU Chi-restraints excluded: chain A residue 590 CYS 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 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1050 MET 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 A residue 1136 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 440 ASN Chi-restraints excluded: chain B residue 456 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 935 GLN Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1045 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 25 SER Chi-restraints excluded: chain J residue 99 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 76 optimal weight: 0.7980 chunk 378 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 27 optimal weight: 0.2980 chunk 187 optimal weight: 0.8980 chunk 126 optimal weight: 10.0000 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 354 optimal weight: 30.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 856 ASN A1010 GLN B 409 GLN C 957 GLN H 199 ASN J 32 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.208061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.158198 restraints weight = 45992.281| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 2.62 r_work: 0.3187 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 31669 Z= 0.153 Angle : 0.691 14.551 43214 Z= 0.336 Chirality : 0.048 0.431 5087 Planarity : 0.004 0.051 5444 Dihedral : 7.647 59.982 5633 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.87 % Favored : 92.97 % Rotamer: Outliers : 5.21 % Allowed : 22.97 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.13), residues: 3786 helix: 1.12 (0.21), residues: 667 sheet: -0.39 (0.15), residues: 1112 loop : -2.05 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 158 TYR 0.017 0.001 TYR B1067 PHE 0.017 0.001 PHE B 86 TRP 0.013 0.001 TRP J 36 HIS 0.004 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00364 (31553) covalent geometry : angle 0.66336 (42912) SS BOND : bond 0.00827 ( 46) SS BOND : angle 1.65136 ( 92) hydrogen bonds : bond 0.04080 ( 1073) hydrogen bonds : angle 5.21768 ( 3045) link_BETA1-4 : bond 0.00479 ( 22) link_BETA1-4 : angle 2.16431 ( 66) link_NAG-ASN : bond 0.00388 ( 48) link_NAG-ASN : angle 2.86941 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 175 poor density : 168 time to evaluate : 1.097 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: A 129 LYS cc_start: 0.7073 (mttt) cc_final: 0.6728 (mptt) REVERT: A 141 LEU cc_start: 0.6097 (OUTLIER) cc_final: 0.5720 (mt) REVERT: A 347 PHE cc_start: 0.1956 (OUTLIER) cc_final: 0.1558 (m-10) REVERT: A 389 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.6017 (p0) REVERT: A 646 ARG cc_start: 0.8293 (mmm160) cc_final: 0.8056 (mmm160) REVERT: A 947 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8804 (mtmt) REVERT: B 153 MET cc_start: 0.1826 (ttt) cc_final: -0.0486 (tmt) REVERT: B 160 TYR cc_start: 0.6052 (p90) cc_final: 0.5651 (p90) REVERT: B 236 THR cc_start: 0.7867 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 473 TYR cc_start: 0.3643 (OUTLIER) cc_final: 0.2967 (m-10) REVERT: B 508 TYR cc_start: 0.7415 (m-80) cc_final: 0.6909 (m-80) REVERT: B 746 SER cc_start: 0.8391 (OUTLIER) cc_final: 0.8061 (m) REVERT: C 133 PHE cc_start: 0.7270 (m-80) cc_final: 0.6274 (m-80) REVERT: C 212 LEU cc_start: 0.5096 (OUTLIER) cc_final: 0.4712 (pp) REVERT: C 988 GLU cc_start: 0.8209 (mp0) cc_final: 0.7770 (tp30) REVERT: H 12 ILE cc_start: 0.0162 (OUTLIER) cc_final: -0.0287 (pp) REVERT: H 34 MET cc_start: 0.1380 (ptt) cc_final: -0.0034 (tpp) REVERT: H 82 MET cc_start: 0.1277 (OUTLIER) cc_final: 0.0381 (mmm) REVERT: K 58 VAL cc_start: 0.2998 (OUTLIER) cc_final: 0.2698 (m) REVERT: J 82 MET cc_start: 0.0062 (mtt) cc_final: -0.1756 (tpp) REVERT: J 102 PHE cc_start: 0.1979 (OUTLIER) cc_final: 0.1064 (m-10) REVERT: J 140 LEU cc_start: 0.2390 (OUTLIER) cc_final: 0.2006 (mp) REVERT: N 32 TYR cc_start: 0.2371 (OUTLIER) cc_final: 0.1534 (m-80) outliers start: 175 outliers final: 86 residues processed: 321 average time/residue: 0.4532 time to fit residues: 182.0373 Evaluate side-chains 250 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 150 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS 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 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1050 MET 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 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 531 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 794 ILE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 275 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 187 optimal weight: 1.9990 chunk 151 optimal weight: 0.1980 chunk 257 optimal weight: 0.7980 chunk 358 optimal weight: 9.9990 chunk 200 optimal weight: 10.0000 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 804 GLN A 856 ASN A 935 GLN A1010 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 450 ASN C 957 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.207907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155664 restraints weight = 45746.493| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.62 r_work: 0.3152 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 31669 Z= 0.155 Angle : 0.691 14.548 43214 Z= 0.333 Chirality : 0.048 0.442 5087 Planarity : 0.004 0.050 5444 Dihedral : 7.312 59.986 5623 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.95 % Favored : 92.89 % Rotamer: Outliers : 4.53 % Allowed : 24.02 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.13), residues: 3786 helix: 1.23 (0.21), residues: 669 sheet: -0.25 (0.15), residues: 1088 loop : -1.99 (0.13), residues: 2029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 454 TYR 0.017 0.001 TYR C1067 PHE 0.025 0.002 PHE B 168 TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS J 202 Details of bonding type rmsd covalent geometry : bond 0.00373 (31553) covalent geometry : angle 0.66469 (42912) SS BOND : bond 0.00405 ( 46) SS BOND : angle 1.58084 ( 92) hydrogen bonds : bond 0.04099 ( 1073) hydrogen bonds : angle 5.16201 ( 3045) link_BETA1-4 : bond 0.00439 ( 22) link_BETA1-4 : angle 2.15470 ( 66) link_NAG-ASN : bond 0.00394 ( 48) link_NAG-ASN : angle 2.82836 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 158 time to evaluate : 1.070 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: A 129 LYS cc_start: 0.7045 (mttt) cc_final: 0.6650 (mptt) REVERT: A 141 LEU cc_start: 0.6077 (OUTLIER) cc_final: 0.5617 (mp) REVERT: A 157 PHE cc_start: 0.6848 (t80) cc_final: 0.6602 (t80) REVERT: A 324 GLU cc_start: 0.6991 (tp30) cc_final: 0.6712 (tm-30) REVERT: A 347 PHE cc_start: 0.1798 (OUTLIER) cc_final: 0.1380 (m-10) REVERT: A 646 ARG cc_start: 0.8402 (mmm160) cc_final: 0.8055 (mmm160) REVERT: A 947 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8724 (mtmt) REVERT: B 153 MET cc_start: 0.2217 (ttt) cc_final: -0.0508 (tmt) REVERT: B 160 TYR cc_start: 0.6016 (p90) cc_final: 0.5631 (p90) REVERT: B 378 LYS cc_start: 0.7806 (ttpt) cc_final: 0.7504 (ptmm) REVERT: B 454 ARG cc_start: 0.7290 (ttm110) cc_final: 0.6206 (ttp-110) REVERT: B 473 TYR cc_start: 0.3883 (OUTLIER) cc_final: 0.3240 (m-10) REVERT: B 508 TYR cc_start: 0.7302 (m-80) cc_final: 0.6716 (m-80) REVERT: B 746 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7932 (m) REVERT: C 128 ILE cc_start: 0.7685 (mp) cc_final: 0.7485 (mp) REVERT: C 133 PHE cc_start: 0.7388 (m-80) cc_final: 0.6245 (m-80) REVERT: C 212 LEU cc_start: 0.5120 (OUTLIER) cc_final: 0.4826 (pp) REVERT: C 226 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7227 (mp) REVERT: C 614 ASP cc_start: 0.8047 (p0) cc_final: 0.7714 (p0) REVERT: C 988 GLU cc_start: 0.8429 (mp0) cc_final: 0.7843 (tp30) REVERT: H 12 ILE cc_start: 0.0221 (OUTLIER) cc_final: -0.0221 (pp) REVERT: H 34 MET cc_start: 0.1082 (ptt) cc_final: -0.0253 (tpp) REVERT: H 82 MET cc_start: 0.1805 (OUTLIER) cc_final: 0.0109 (mmm) REVERT: K 58 VAL cc_start: 0.2873 (OUTLIER) cc_final: 0.2595 (m) REVERT: J 82 MET cc_start: -0.0165 (mtt) cc_final: -0.1840 (tpp) REVERT: J 102 PHE cc_start: 0.1764 (OUTLIER) cc_final: 0.1160 (m-10) REVERT: J 140 LEU cc_start: 0.2537 (OUTLIER) cc_final: 0.2129 (mp) REVERT: N 32 TYR cc_start: 0.2017 (OUTLIER) cc_final: 0.1433 (m-80) outliers start: 152 outliers final: 99 residues processed: 295 average time/residue: 0.4482 time to fit residues: 166.8217 Evaluate side-chains 256 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 144 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS 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 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1005 GLN Chi-restraints excluded: chain A residue 1050 MET 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 A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 969 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 172 LEU Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 205 SER Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 142 ARG Chi-restraints excluded: chain N residue 154 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 60 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 301 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 353 optimal weight: 10.0000 chunk 195 optimal weight: 0.0870 chunk 131 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 450 ASN A1010 GLN C 87 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.208405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.157945 restraints weight = 45820.373| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 2.56 r_work: 0.3191 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31669 Z= 0.120 Angle : 0.665 14.068 43214 Z= 0.320 Chirality : 0.047 0.442 5087 Planarity : 0.004 0.049 5444 Dihedral : 7.044 59.898 5621 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.42 % Favored : 93.45 % Rotamer: Outliers : 3.90 % Allowed : 24.73 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.13), residues: 3786 helix: 1.51 (0.21), residues: 662 sheet: -0.11 (0.15), residues: 1085 loop : -1.92 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 454 TYR 0.017 0.001 TYR B1067 PHE 0.019 0.001 PHE B 456 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS J 202 Details of bonding type rmsd covalent geometry : bond 0.00274 (31553) covalent geometry : angle 0.63941 (42912) SS BOND : bond 0.00357 ( 46) SS BOND : angle 1.63339 ( 92) hydrogen bonds : bond 0.03685 ( 1073) hydrogen bonds : angle 5.04950 ( 3045) link_BETA1-4 : bond 0.00512 ( 22) link_BETA1-4 : angle 2.01717 ( 66) link_NAG-ASN : bond 0.00392 ( 48) link_NAG-ASN : angle 2.67311 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 150 time to evaluate : 0.982 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: A 129 LYS cc_start: 0.7157 (mttt) cc_final: 0.6804 (mptt) REVERT: A 141 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5790 (mp) REVERT: A 157 PHE cc_start: 0.6862 (t80) cc_final: 0.6629 (t80) REVERT: A 324 GLU cc_start: 0.7198 (tp30) cc_final: 0.6975 (tm-30) REVERT: A 347 PHE cc_start: 0.1456 (OUTLIER) cc_final: 0.1040 (m-10) REVERT: A 389 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6533 (p0) REVERT: A 646 ARG cc_start: 0.8591 (mmm160) cc_final: 0.8199 (mmm160) REVERT: A 947 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8972 (mtmt) REVERT: A 985 ASP cc_start: 0.7788 (p0) cc_final: 0.7539 (p0) REVERT: B 127 VAL cc_start: 0.7532 (OUTLIER) cc_final: 0.7214 (m) REVERT: B 153 MET cc_start: 0.2042 (ttt) cc_final: -0.0439 (tmt) REVERT: B 160 TYR cc_start: 0.6062 (p90) cc_final: 0.5658 (p90) REVERT: B 378 LYS cc_start: 0.7822 (ttpt) cc_final: 0.7567 (ptmm) REVERT: B 473 TYR cc_start: 0.3880 (OUTLIER) cc_final: 0.3258 (m-10) REVERT: B 508 TYR cc_start: 0.7415 (m-80) cc_final: 0.6849 (m-80) REVERT: B 746 SER cc_start: 0.8191 (OUTLIER) cc_final: 0.7857 (m) REVERT: C 128 ILE cc_start: 0.7840 (mp) cc_final: 0.7625 (mp) REVERT: C 133 PHE cc_start: 0.7411 (m-80) cc_final: 0.6231 (m-80) REVERT: C 212 LEU cc_start: 0.5192 (OUTLIER) cc_final: 0.4892 (pp) REVERT: C 614 ASP cc_start: 0.8260 (p0) cc_final: 0.7941 (p0) REVERT: C 988 GLU cc_start: 0.8654 (mp0) cc_final: 0.7919 (tp30) REVERT: H 12 ILE cc_start: -0.0263 (OUTLIER) cc_final: -0.0609 (pp) REVERT: H 82 MET cc_start: 0.2272 (OUTLIER) cc_final: 0.0601 (mmm) REVERT: K 58 VAL cc_start: 0.2770 (OUTLIER) cc_final: 0.2515 (m) REVERT: J 82 MET cc_start: -0.0679 (mtt) cc_final: -0.2028 (tpp) REVERT: J 102 PHE cc_start: 0.1635 (OUTLIER) cc_final: 0.1238 (m-10) REVERT: J 140 LEU cc_start: 0.3069 (OUTLIER) cc_final: 0.2698 (mp) REVERT: N 32 TYR cc_start: 0.1951 (OUTLIER) cc_final: 0.1368 (m-80) REVERT: N 89 GLN cc_start: -0.0945 (OUTLIER) cc_final: -0.1335 (tt0) outliers start: 131 outliers final: 83 residues processed: 271 average time/residue: 0.4435 time to fit residues: 151.7453 Evaluate side-chains 237 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 139 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 389 ASP Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1050 MET 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 A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 195 THR Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 68 optimal weight: 0.0270 chunk 31 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 162 optimal weight: 0.5980 chunk 199 optimal weight: 4.9990 chunk 335 optimal weight: 40.0000 chunk 101 optimal weight: 5.9990 chunk 154 optimal weight: 4.9990 chunk 146 optimal weight: 0.4980 chunk 156 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.6242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 856 ASN A1010 GLN C 87 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN H 32 ASN N 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.204700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.154059 restraints weight = 45788.386| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.79 r_work: 0.3137 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 31669 Z= 0.144 Angle : 0.674 14.314 43214 Z= 0.325 Chirality : 0.048 0.457 5087 Planarity : 0.004 0.050 5444 Dihedral : 6.973 59.833 5619 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.00 % Favored : 92.87 % Rotamer: Outliers : 3.99 % Allowed : 24.91 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3786 helix: 1.49 (0.21), residues: 666 sheet: -0.05 (0.15), residues: 1095 loop : -1.87 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 454 TYR 0.017 0.001 TYR B1067 PHE 0.036 0.002 PHE A 86 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00343 (31553) covalent geometry : angle 0.64898 (42912) SS BOND : bond 0.00376 ( 46) SS BOND : angle 1.66608 ( 92) hydrogen bonds : bond 0.03940 ( 1073) hydrogen bonds : angle 5.10186 ( 3045) link_BETA1-4 : bond 0.00485 ( 22) link_BETA1-4 : angle 2.03087 ( 66) link_NAG-ASN : bond 0.00373 ( 48) link_NAG-ASN : angle 2.69610 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 144 time to evaluate : 0.994 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: A 141 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5797 (mp) REVERT: A 347 PHE cc_start: 0.1809 (OUTLIER) cc_final: 0.1242 (m-10) REVERT: A 646 ARG cc_start: 0.8427 (mmm160) cc_final: 0.8047 (mmm160) REVERT: A 947 LYS cc_start: 0.9229 (OUTLIER) cc_final: 0.8742 (mtmt) REVERT: A 985 ASP cc_start: 0.7630 (p0) cc_final: 0.7421 (p0) REVERT: B 153 MET cc_start: 0.2359 (ttt) cc_final: -0.0172 (tmt) REVERT: B 160 TYR cc_start: 0.6079 (p90) cc_final: 0.5743 (p90) REVERT: B 378 LYS cc_start: 0.7764 (ttpt) cc_final: 0.7508 (ptmm) REVERT: B 473 TYR cc_start: 0.3800 (OUTLIER) cc_final: 0.3183 (m-10) REVERT: B 508 TYR cc_start: 0.7419 (m-80) cc_final: 0.6873 (m-80) REVERT: B 746 SER cc_start: 0.8163 (OUTLIER) cc_final: 0.7867 (m) REVERT: C 133 PHE cc_start: 0.7467 (m-80) cc_final: 0.6229 (m-80) REVERT: C 614 ASP cc_start: 0.8114 (p0) cc_final: 0.7813 (p0) REVERT: C 988 GLU cc_start: 0.8431 (mp0) cc_final: 0.7823 (tp30) REVERT: H 12 ILE cc_start: 0.0165 (OUTLIER) cc_final: -0.0287 (pp) REVERT: H 34 MET cc_start: 0.1861 (ptp) cc_final: -0.0527 (tpp) REVERT: H 82 MET cc_start: 0.1803 (OUTLIER) cc_final: 0.0274 (mmm) REVERT: H 195 THR cc_start: 0.2828 (OUTLIER) cc_final: 0.2474 (p) REVERT: K 58 VAL cc_start: 0.3057 (OUTLIER) cc_final: 0.2747 (m) REVERT: J 82 MET cc_start: -0.0091 (mtt) cc_final: -0.1915 (tpp) REVERT: J 102 PHE cc_start: 0.1621 (OUTLIER) cc_final: 0.1140 (m-10) REVERT: J 140 LEU cc_start: 0.2951 (OUTLIER) cc_final: 0.2641 (mp) REVERT: N 32 TYR cc_start: 0.1986 (OUTLIER) cc_final: 0.1478 (m-80) outliers start: 134 outliers final: 91 residues processed: 265 average time/residue: 0.4380 time to fit residues: 146.9137 Evaluate side-chains 242 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 139 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 590 CYS 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 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1050 MET 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 A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 105 TRP Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain J residue 17 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 46 LEU Chi-restraints excluded: chain N residue 49 TYR Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 178 optimal weight: 1.9990 chunk 357 optimal weight: 9.9990 chunk 255 optimal weight: 1.9990 chunk 182 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 217 optimal weight: 1.9990 chunk 274 optimal weight: 2.9990 chunk 282 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 856 ASN A1010 GLN C 87 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.206015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.155760 restraints weight = 45470.533| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.75 r_work: 0.3163 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 31669 Z= 0.141 Angle : 0.670 14.109 43214 Z= 0.322 Chirality : 0.047 0.466 5087 Planarity : 0.004 0.049 5444 Dihedral : 6.866 59.849 5619 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.60 % Favored : 93.24 % Rotamer: Outliers : 3.67 % Allowed : 25.12 % Favored : 71.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.13), residues: 3786 helix: 1.55 (0.21), residues: 666 sheet: 0.03 (0.15), residues: 1095 loop : -1.79 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 454 TYR 0.019 0.001 TYR A 170 PHE 0.033 0.001 PHE A 86 TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00334 (31553) covalent geometry : angle 0.64425 (42912) SS BOND : bond 0.00393 ( 46) SS BOND : angle 1.70118 ( 92) hydrogen bonds : bond 0.03826 ( 1073) hydrogen bonds : angle 5.03695 ( 3045) link_BETA1-4 : bond 0.00474 ( 22) link_BETA1-4 : angle 1.96672 ( 66) link_NAG-ASN : bond 0.00462 ( 48) link_NAG-ASN : angle 2.68614 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 139 time to evaluate : 1.071 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 347 PHE cc_start: 0.2160 (OUTLIER) cc_final: 0.1546 (m-10) REVERT: A 646 ARG cc_start: 0.8398 (mmm160) cc_final: 0.8011 (mmm160) REVERT: A 947 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8741 (mtmt) REVERT: B 153 MET cc_start: 0.2491 (ttt) cc_final: -0.0057 (tmt) REVERT: B 236 THR cc_start: 0.7816 (OUTLIER) cc_final: 0.7599 (p) REVERT: B 473 TYR cc_start: 0.3784 (OUTLIER) cc_final: 0.3188 (m-10) REVERT: B 508 TYR cc_start: 0.7446 (m-80) cc_final: 0.6953 (m-80) REVERT: B 746 SER cc_start: 0.8160 (OUTLIER) cc_final: 0.7865 (m) REVERT: C 614 ASP cc_start: 0.8037 (p0) cc_final: 0.7744 (p0) REVERT: C 988 GLU cc_start: 0.8476 (mp0) cc_final: 0.7864 (tp30) REVERT: H 12 ILE cc_start: 0.0009 (OUTLIER) cc_final: -0.0357 (pp) REVERT: H 82 MET cc_start: 0.1778 (OUTLIER) cc_final: 0.0256 (mmm) REVERT: H 195 THR cc_start: 0.2664 (OUTLIER) cc_final: 0.2290 (p) REVERT: K 58 VAL cc_start: 0.3074 (OUTLIER) cc_final: 0.2763 (m) REVERT: J 28 THR cc_start: 0.1700 (t) cc_final: 0.0871 (p) REVERT: J 82 MET cc_start: -0.0014 (mtt) cc_final: -0.1877 (tpp) REVERT: J 102 PHE cc_start: 0.1682 (OUTLIER) cc_final: 0.1389 (m-10) REVERT: J 140 LEU cc_start: 0.2890 (OUTLIER) cc_final: 0.2649 (mp) REVERT: N 32 TYR cc_start: 0.2310 (OUTLIER) cc_final: 0.1835 (m-80) REVERT: N 89 GLN cc_start: -0.0243 (OUTLIER) cc_final: -0.0774 (tm-30) outliers start: 123 outliers final: 85 residues processed: 250 average time/residue: 0.4499 time to fit residues: 141.7305 Evaluate side-chains 231 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 133 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1050 MET 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 A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 354 ASN Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP 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 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 206 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 377 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 188 optimal weight: 0.9990 chunk 296 optimal weight: 4.9990 chunk 248 optimal weight: 7.9990 chunk 97 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 856 ASN A1010 GLN B 532 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN J 157 ASN N 89 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.201979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.152942 restraints weight = 45511.159| |-----------------------------------------------------------------------------| r_work (start): 0.3857 rms_B_bonded: 2.64 r_work: 0.3171 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 31669 Z= 0.206 Angle : 0.720 15.069 43214 Z= 0.348 Chirality : 0.050 0.485 5087 Planarity : 0.004 0.051 5444 Dihedral : 7.102 59.973 5615 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.21 % Favored : 92.63 % Rotamer: Outliers : 3.40 % Allowed : 25.66 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.13), residues: 3786 helix: 1.35 (0.21), residues: 666 sheet: 0.03 (0.15), residues: 1089 loop : -1.86 (0.13), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 454 TYR 0.018 0.001 TYR C1067 PHE 0.036 0.002 PHE A 86 TRP 0.013 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00509 (31553) covalent geometry : angle 0.69290 (42912) SS BOND : bond 0.00489 ( 46) SS BOND : angle 1.85591 ( 92) hydrogen bonds : bond 0.04549 ( 1073) hydrogen bonds : angle 5.18684 ( 3045) link_BETA1-4 : bond 0.00386 ( 22) link_BETA1-4 : angle 2.10380 ( 66) link_NAG-ASN : bond 0.00416 ( 48) link_NAG-ASN : angle 2.88546 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7572 Ramachandran restraints generated. 3786 Oldfield, 0 Emsley, 3786 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 152 time to evaluate : 1.060 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 347 PHE cc_start: 0.2411 (OUTLIER) cc_final: 0.1945 (m-10) REVERT: A 355 ARG cc_start: 0.1784 (OUTLIER) cc_final: 0.0702 (tpt-90) REVERT: A 646 ARG cc_start: 0.8388 (mmm160) cc_final: 0.7987 (mmm160) REVERT: A 947 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.8748 (mtmt) REVERT: B 153 MET cc_start: 0.2677 (ttt) cc_final: 0.0127 (tmt) REVERT: B 236 THR cc_start: 0.7857 (OUTLIER) cc_final: 0.7626 (p) REVERT: B 473 TYR cc_start: 0.3700 (OUTLIER) cc_final: 0.3025 (m-10) REVERT: B 508 TYR cc_start: 0.7471 (m-80) cc_final: 0.7065 (m-80) REVERT: B 746 SER cc_start: 0.8247 (OUTLIER) cc_final: 0.7981 (m) REVERT: C 614 ASP cc_start: 0.8108 (p0) cc_final: 0.7819 (p0) REVERT: C 988 GLU cc_start: 0.8421 (mp0) cc_final: 0.7886 (tp30) REVERT: H 12 ILE cc_start: 0.0116 (OUTLIER) cc_final: -0.0351 (pp) REVERT: H 34 MET cc_start: 0.1965 (ptp) cc_final: -0.0195 (tpp) REVERT: H 82 MET cc_start: 0.1868 (OUTLIER) cc_final: 0.0180 (mmm) REVERT: H 195 THR cc_start: 0.2585 (OUTLIER) cc_final: 0.2198 (p) REVERT: K 58 VAL cc_start: 0.3101 (p) cc_final: 0.2757 (m) REVERT: K 133 VAL cc_start: 0.0652 (t) cc_final: 0.0388 (m) REVERT: J 102 PHE cc_start: 0.1633 (OUTLIER) cc_final: 0.1113 (m-10) REVERT: J 140 LEU cc_start: 0.2885 (OUTLIER) cc_final: 0.2671 (mp) REVERT: N 32 TYR cc_start: 0.2226 (OUTLIER) cc_final: 0.1925 (m-80) REVERT: N 89 GLN cc_start: 0.0525 (OUTLIER) cc_final: -0.0226 (tm130) outliers start: 114 outliers final: 91 residues processed: 255 average time/residue: 0.4594 time to fit residues: 148.2464 Evaluate side-chains 236 residues out of total 3356 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 132 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 116 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 590 CYS 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 747 THR Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 947 LYS Chi-restraints excluded: chain A residue 1050 MET 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 A residue 1136 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 371 SER Chi-restraints excluded: chain B residue 373 SER Chi-restraints excluded: chain B residue 375 SER Chi-restraints excluded: chain B residue 399 SER Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 492 LEU Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 808 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 399 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1005 GLN Chi-restraints excluded: chain C residue 1038 LYS Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1116 THR Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 85 LEU Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 117 SER Chi-restraints excluded: chain H residue 195 THR Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 109 THR Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 102 PHE Chi-restraints excluded: chain J residue 105 TRP Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 144 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 197 ILE Chi-restraints excluded: chain J residue 209 VAL Chi-restraints excluded: chain N residue 15 VAL Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 142 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 156 optimal weight: 2.9990 chunk 39 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 262 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 369 optimal weight: 10.0000 chunk 129 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 856 ASN A1010 GLN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN J 157 ASN N 89 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.204238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.153087 restraints weight = 45742.865| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.63 r_work: 0.3166 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 31669 Z= 0.132 Angle : 0.674 14.116 43214 Z= 0.325 Chirality : 0.047 0.467 5087 Planarity : 0.004 0.049 5444 Dihedral : 6.918 59.997 5615 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.44 % Favored : 93.40 % Rotamer: Outliers : 3.13 % Allowed : 26.16 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.13), residues: 3786 helix: 1.51 (0.21), residues: 666 sheet: 0.11 (0.15), residues: 1090 loop : -1.80 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 454 TYR 0.020 0.001 TYR A 170 PHE 0.036 0.001 PHE A 86 TRP 0.033 0.001 TRP K 148 HIS 0.002 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00307 (31553) covalent geometry : angle 0.65013 (42912) SS BOND : bond 0.00408 ( 46) SS BOND : angle 1.54383 ( 92) hydrogen bonds : bond 0.03840 ( 1073) hydrogen bonds : angle 5.07471 ( 3045) link_BETA1-4 : bond 0.00485 ( 22) link_BETA1-4 : angle 1.95226 ( 66) link_NAG-ASN : bond 0.00408 ( 48) link_NAG-ASN : angle 2.67194 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9722.64 seconds wall clock time: 166 minutes 16.35 seconds (9976.35 seconds total)