Starting phenix.real_space_refine on Thu Nov 20 05:47:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7czu_30517/11_2025/7czu_30517.cif Found real_map, /net/cci-nas-00/data/ceres_data/7czu_30517/11_2025/7czu_30517.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7czu_30517/11_2025/7czu_30517.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7czu_30517/11_2025/7czu_30517.map" model { file = "/net/cci-nas-00/data/ceres_data/7czu_30517/11_2025/7czu_30517.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7czu_30517/11_2025/7czu_30517.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 133 5.16 5 C 19737 2.51 5 N 5090 2.21 5 O 6160 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31120 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: "J" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} Chain: "H" Number of atoms: 1710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1710 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 13, 'TRANS': 215} Chain: "K" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 11, 'TRANS': 202} 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: 7.14, per 1000 atoms: 0.23 Number of scatterers: 31120 At special positions: 0 Unit cell: (135.875, 170.659, 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 133 16.00 O 6160 8.00 N 5090 7.00 C 19737 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=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.08 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=2.06 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.05 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=2.15 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=2.03 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 J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 154 " - pdb=" SG CYS J 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.56 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 194 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.56 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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: 2.85 Conformation dependent library (CDL) restraints added in 1.1 seconds 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7252 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 64 sheets defined 19.2% alpha, 30.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.073A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.257A 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: 3.738A 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: 3.630A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.557A 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: 3.539A 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: 3.646A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.994A 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: 3.648A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.879A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.632A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 3.688A 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: 3.647A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 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: 3.965A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.544A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.010A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.706A 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: 4.372A 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: 3.675A 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: 3.583A 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: 4.256A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 removed outlier: 3.624A 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: 3.717A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.560A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.635A 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: 3.800A 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: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.553A 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: 3.816A 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: 3.536A 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 'J' and resid 201 through 203 No H-bonds generated for 'chain 'J' and resid 201 through 203' Processing helix chain 'N' and resid 121 through 128 Processing helix chain 'N' and resid 183 through 187 Processing helix chain 'H' and resid 201 through 203 No H-bonds generated for 'chain 'H' and resid 201 through 203' Processing helix chain 'K' and resid 121 through 128 Processing helix chain 'K' 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: 3.681A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.438A 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: 3.570A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A 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: 3.731A 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: 7.659A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.587A 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: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.547A 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: 6.680A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A 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: 3.543A 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: 5.865A pdb=" N TYR A 449 " --> pdb=" O PHE A 497 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N PHE A 497 " --> pdb=" O TYR A 449 " (cutoff:3.500A) removed outlier: 4.785A 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: 5.339A 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: 6.417A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 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: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.530A 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: 5.733A 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: 6.604A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.243A 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: 3.977A 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: 4.504A 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: 3.743A 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: 3.831A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.534A 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: 6.897A 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: 3.650A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.914A 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: 3.780A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.714A 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: 3.538A 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: 5.572A 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: 6.768A 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: 6.219A 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: 6.441A 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: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A 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: 6.213A 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: 5.857A 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: 6.543A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.798A 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: 6.213A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.578A 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: 8.151A 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: 3.626A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 7.064A 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: 7.366A 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: 7.133A 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: 4.758A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.835A 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: 5.667A 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: 4.498A 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: 3.542A 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: 6.231A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.535A 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: 6.591A 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: 3.591A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.591A 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: 3.565A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=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 'J' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'J' and resid 5 through 7 Processing sheet with id=AF2, first strand: chain 'J' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA J 151 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 198 " --> pdb=" O ALA J 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 153 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 196 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU J 155 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER J 194 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 157 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 192 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA J 151 " --> pdb=" O VAL J 198 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 198 " --> pdb=" O ALA J 151 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY J 153 " --> pdb=" O VAL J 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL J 196 " --> pdb=" O GLY J 153 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LEU J 155 " --> pdb=" O SER J 194 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER J 194 " --> pdb=" O LEU J 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS J 157 " --> pdb=" O LEU J 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU J 192 " --> pdb=" O LYS J 157 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 164 through 168 Processing sheet with id=AF6, first strand: chain 'N' and resid 19 through 24 Processing sheet with id=AF7, first strand: chain 'N' and resid 45 through 48 removed outlier: 6.680A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN N 38 " --> pdb=" O THR N 85 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 114 through 118 Processing sheet with id=AF9, first strand: chain 'N' and resid 153 through 154 Processing sheet with id=AG1, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 5 through 7 Processing sheet with id=AG3, first strand: chain 'H' and resid 46 through 51 removed outlier: 6.652A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 134 through 138 removed outlier: 5.007A pdb=" N ALA H 151 " --> pdb=" O VAL H 198 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL H 198 " --> pdb=" O ALA H 151 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY H 153 " --> pdb=" O VAL H 196 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL H 196 " --> pdb=" O GLY H 153 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LEU H 155 " --> pdb=" O SER H 194 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER H 194 " --> pdb=" O LEU H 155 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 157 " --> pdb=" O LEU H 192 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU H 192 " --> pdb=" O LYS H 157 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 164 through 168 Processing sheet with id=AG7, first strand: chain 'K' and resid 19 through 24 Processing sheet with id=AG8, first strand: chain 'K' and resid 45 through 48 removed outlier: 6.680A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN K 38 " --> pdb=" O THR K 85 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'K' and resid 114 through 118 Processing sheet with id=AH1, first strand: chain 'K' and resid 153 through 154 1141 hydrogen bonds defined for protein. 3063 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: 8.09 Time building geometry restraints manager: 3.72 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: 9714 1.34 - 1.46: 8218 1.46 - 1.59: 13691 1.59 - 1.72: 0 1.72 - 1.85: 168 Bond restraints: 31791 Sorted by residual: bond pdb=" N PRO K 141 " pdb=" CD PRO K 141 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.88e+01 bond pdb=" C THR C 588 " pdb=" N PRO C 589 " ideal model delta sigma weight residual 1.332 1.390 -0.058 1.34e-02 5.57e+03 1.86e+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 1.83e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.265 0.067 1.59e-02 3.96e+03 1.75e+01 bond pdb=" N PRO C 589 " pdb=" CD PRO C 589 " ideal model delta sigma weight residual 1.473 1.529 -0.056 1.40e-02 5.10e+03 1.61e+01 ... (remaining 31786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 42216 2.70 - 5.40: 929 5.40 - 8.11: 77 8.11 - 10.81: 9 10.81 - 13.51: 5 Bond angle restraints: 43236 Sorted by residual: angle pdb=" C PHE A 86 " pdb=" N ASN A 87 " pdb=" CA ASN A 87 " ideal model delta sigma weight residual 121.54 132.79 -11.25 1.91e+00 2.74e-01 3.47e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.83 -7.38 1.26e+00 6.30e-01 3.43e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.01 5.77 1.03e+00 9.43e-01 3.13e+01 angle pdb=" C LEU B 212 " pdb=" N VAL B 213 " pdb=" CA VAL B 213 " ideal model delta sigma weight residual 123.08 117.63 5.45 1.01e+00 9.80e-01 2.91e+01 angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 122.56 115.25 7.31 1.50e+00 4.44e-01 2.37e+01 ... (remaining 43231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 17139 17.92 - 35.84: 1945 35.84 - 53.76: 556 53.76 - 71.67: 193 71.67 - 89.59: 55 Dihedral angle restraints: 19888 sinusoidal: 8617 harmonic: 11271 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 12.13 80.87 1 1.00e+01 1.00e-02 8.08e+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 19.63 73.37 1 1.00e+01 1.00e-02 6.85e+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 21.06 71.94 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 19885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.329: 5108 0.329 - 0.658: 3 0.658 - 0.987: 2 0.987 - 1.316: 0 1.316 - 1.645: 2 Chirality restraints: 5115 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 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 -0.75 -1.65 2.00e-01 2.50e+01 6.77e+01 chirality pdb=" C1 NAG U 1 " pdb=" ND2 ASN C 331 " pdb=" C2 NAG U 1 " pdb=" O5 NAG U 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.38e+01 ... (remaining 5112 not shown) Planarity restraints: 5542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " -0.180 2.00e-02 2.50e+03 2.26e-01 6.41e+02 pdb=" CG ASN C 331 " 0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " 0.389 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.259 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " 0.057 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO A 527 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN C1134 " -0.022 2.00e-02 2.50e+03 3.14e-02 1.23e+01 pdb=" CG ASN C1134 " 0.010 2.00e-02 2.50e+03 pdb=" OD1 ASN C1134 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN C1134 " 0.056 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.034 2.00e-02 2.50e+03 ... (remaining 5539 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 272 2.54 - 3.13: 23438 3.13 - 3.72: 45199 3.72 - 4.31: 66501 4.31 - 4.90: 110957 Nonbonded interactions: 246367 Sorted by model distance: nonbonded pdb=" O ASP H 62 " pdb=" OG SER H 63 " model vdw 1.945 3.040 nonbonded pdb=" O ASP J 62 " pdb=" OG SER J 63 " model vdw 1.945 3.040 nonbonded pdb=" NH1 ARG C 346 " pdb=" O PHE C 347 " model vdw 1.982 3.120 nonbonded pdb=" NH1 ARG A 346 " pdb=" O PHE A 347 " model vdw 1.983 3.120 nonbonded pdb=" O ASN N 137 " pdb=" O ASN N 138 " model vdw 2.037 3.040 ... (remaining 246362 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 29.530 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 0.524 31907 Z= 0.514 Angle : 1.177 48.946 43538 Z= 0.623 Chirality : 0.071 1.645 5115 Planarity : 0.007 0.088 5494 Dihedral : 17.495 89.593 12498 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 1.13 % Allowed : 10.10 % Favored : 88.77 % Rotamer: Outliers : 11.32 % Allowed : 17.73 % Favored : 70.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.75 (0.11), residues: 3810 helix: -2.15 (0.16), residues: 661 sheet: -1.81 (0.14), residues: 1155 loop : -3.09 (0.11), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1039 TYR 0.026 0.003 TYR B1067 PHE 0.025 0.003 PHE A 898 TRP 0.025 0.003 TRP A 104 HIS 0.010 0.002 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.01054 (31791) covalent geometry : angle 1.00034 (43236) SS BOND : bond 0.11320 ( 46) SS BOND : angle 9.19126 ( 92) hydrogen bonds : bond 0.19529 ( 1075) hydrogen bonds : angle 8.03357 ( 3063) link_BETA1-4 : bond 0.04182 ( 22) link_BETA1-4 : angle 4.32784 ( 66) link_NAG-ASN : bond 0.02773 ( 48) link_NAG-ASN : angle 7.45636 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 383 poor density : 462 time to evaluate : 1.121 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: A 153 MET cc_start: 0.4296 (mpp) cc_final: 0.2252 (mmt) REVERT: A 517 LEU cc_start: 0.4721 (OUTLIER) cc_final: 0.4477 (tt) REVERT: A 553 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6912 (m) REVERT: A 998 THR cc_start: 0.8982 (OUTLIER) cc_final: 0.8779 (m) REVERT: B 100 ILE cc_start: 0.7800 (mm) cc_final: 0.7321 (mt) REVERT: B 214 ARG cc_start: 0.1387 (OUTLIER) cc_final: 0.0988 (mtt180) REVERT: B 273 ARG cc_start: 0.7843 (mmt90) cc_final: 0.7632 (mmp-170) REVERT: B 567 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7146 (ptp90) REVERT: B 569 ILE cc_start: 0.2842 (OUTLIER) cc_final: 0.2550 (mm) REVERT: B 787 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8285 (mt0) REVERT: C 52 GLN cc_start: 0.7304 (tm-30) cc_final: 0.7017 (tt0) REVERT: C 117 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.6043 (pp) REVERT: C 168 PHE cc_start: 0.6321 (t80) cc_final: 0.6010 (t80) REVERT: C 215 ASP cc_start: 0.5178 (OUTLIER) cc_final: 0.3519 (p0) REVERT: C 787 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.8104 (mt0) REVERT: J 105 MET cc_start: 0.1519 (mtp) cc_final: 0.1150 (mtt) REVERT: J 170 SER cc_start: -0.0418 (OUTLIER) cc_final: -0.0888 (p) REVERT: N 47 LEU cc_start: 0.2515 (mt) cc_final: 0.1794 (mp) REVERT: K 28 ASP cc_start: -0.2068 (OUTLIER) cc_final: -0.3298 (t0) REVERT: K 29 ILE cc_start: 0.0487 (OUTLIER) cc_final: 0.0266 (pp) REVERT: K 50 ASP cc_start: 0.1413 (OUTLIER) cc_final: 0.1175 (p0) outliers start: 383 outliers final: 93 residues processed: 785 average time/residue: 0.1881 time to fit residues: 240.7166 Evaluate side-chains 350 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 243 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 421 TYR Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 528 LYS Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 998 THR Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 122 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 506 GLN Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 555 SER Chi-restraints excluded: chain B residue 567 ARG Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 787 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 991 VAL Chi-restraints excluded: chain B residue 1074 ASN Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1133 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 155 SER Chi-restraints excluded: chain C residue 172 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 421 TYR Chi-restraints excluded: chain C residue 438 SER 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 534 VAL Chi-restraints excluded: chain C residue 536 ASN Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 768 THR Chi-restraints excluded: chain C residue 770 ILE 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 929 SER Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1077 THR Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain J residue 170 SER Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 87 TYR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain H residue 217 SER Chi-restraints excluded: chain K residue 28 ASP Chi-restraints excluded: chain K residue 29 ILE Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 49 TYR Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 87 TYR Chi-restraints excluded: chain K residue 91 TYR Chi-restraints excluded: chain K residue 142 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 20.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 134 GLN A 137 ASN A 188 ASN A 239 GLN A 360 ASN A 422 ASN A 498 GLN A 644 GLN A 690 GLN A 703 ASN A 751 ASN A 764 ASN A 804 GLN A 856 ASN A 901 GLN A 913 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 969 ASN A 978 ASN A 992 GLN A1005 GLN A1010 GLN A1101 HIS B 99 ASN B 115 GLN B 188 ASN B 422 ASN B 487 ASN ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 ASN B 563 GLN B 564 GLN B 703 ASN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B 992 GLN B1054 GLN C 30 ASN C 66 HIS C 134 GLN C 321 GLN C 422 ASN C 440 ASN C 498 GLN C 536 ASN C 606 ASN C 641 ASN C 658 ASN C 690 GLN C 703 ASN C 784 GLN C 901 GLN C 914 ASN C 926 GLN C 992 GLN C1071 GLN C1101 HIS J 39 GLN J 57 ASN H 39 GLN H 57 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 90 GLN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.199019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.151847 restraints weight = 54314.271| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 3.01 r_work: 0.3295 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 31907 Z= 0.164 Angle : 0.797 14.375 43538 Z= 0.390 Chirality : 0.050 0.522 5115 Planarity : 0.005 0.072 5494 Dihedral : 9.634 68.991 5778 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.59 % Favored : 92.20 % Rotamer: Outliers : 5.64 % Allowed : 18.59 % Favored : 75.77 % 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: -2.45 (0.12), residues: 3810 helix: -0.00 (0.20), residues: 664 sheet: -1.05 (0.15), residues: 1104 loop : -2.61 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 237 TYR 0.032 0.002 TYR K 32 PHE 0.029 0.002 PHE C 86 TRP 0.012 0.001 TRP B 436 HIS 0.004 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00369 (31791) covalent geometry : angle 0.75952 (43236) SS BOND : bond 0.00458 ( 46) SS BOND : angle 2.22007 ( 92) hydrogen bonds : bond 0.04695 ( 1075) hydrogen bonds : angle 5.87031 ( 3063) link_BETA1-4 : bond 0.00592 ( 22) link_BETA1-4 : angle 2.44214 ( 66) link_NAG-ASN : bond 0.00504 ( 48) link_NAG-ASN : angle 3.62823 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 259 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 TYR cc_start: 0.8447 (t80) cc_final: 0.8144 (t80) REVERT: A 141 LEU cc_start: 0.4833 (OUTLIER) cc_final: 0.4615 (pt) REVERT: A 153 MET cc_start: 0.4024 (mpp) cc_final: 0.1826 (mmt) REVERT: A 856 ASN cc_start: 0.8953 (OUTLIER) cc_final: 0.8727 (p0) REVERT: B 41 LYS cc_start: 0.7874 (mttm) cc_final: 0.7668 (mttm) REVERT: B 100 ILE cc_start: 0.8250 (mm) cc_final: 0.7840 (mt) REVERT: B 110 LEU cc_start: 0.6559 (mm) cc_final: 0.6330 (mm) REVERT: B 214 ARG cc_start: 0.1802 (OUTLIER) cc_final: 0.0568 (ttt180) REVERT: B 231 ILE cc_start: 0.8031 (OUTLIER) cc_final: 0.7766 (pt) REVERT: B 235 ILE cc_start: 0.6788 (mm) cc_final: 0.6272 (tp) REVERT: B 273 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7493 (mmp-170) REVERT: B 569 ILE cc_start: 0.2715 (OUTLIER) cc_final: 0.2508 (mm) REVERT: B 574 ASP cc_start: 0.7892 (m-30) cc_final: 0.7044 (t0) REVERT: B 745 ASP cc_start: 0.6760 (p0) cc_final: 0.6462 (p0) REVERT: C 52 GLN cc_start: 0.7798 (tm-30) cc_final: 0.7540 (tt0) REVERT: C 153 MET cc_start: 0.2294 (mtt) cc_final: 0.1178 (tpp) REVERT: C 168 PHE cc_start: 0.6850 (t80) cc_final: 0.6638 (t80) REVERT: C 188 ASN cc_start: 0.6918 (OUTLIER) cc_final: 0.6575 (p0) REVERT: C 213 VAL cc_start: 0.7905 (OUTLIER) cc_final: 0.7643 (m) REVERT: C 215 ASP cc_start: 0.5484 (OUTLIER) cc_final: 0.3712 (p0) REVERT: C 333 THR cc_start: 0.3856 (OUTLIER) cc_final: 0.3316 (m) REVERT: J 105 MET cc_start: 0.2119 (mtp) cc_final: 0.1778 (mtt) REVERT: J 187 SER cc_start: 0.1396 (OUTLIER) cc_final: 0.1158 (m) REVERT: N 33 LEU cc_start: 0.3190 (OUTLIER) cc_final: 0.2143 (pp) REVERT: N 114 SER cc_start: 0.3223 (OUTLIER) cc_final: 0.2940 (p) REVERT: N 116 PHE cc_start: 0.0121 (OUTLIER) cc_final: -0.0107 (m-80) REVERT: H 28 THR cc_start: 0.3684 (OUTLIER) cc_final: 0.3250 (p) outliers start: 191 outliers final: 96 residues processed: 429 average time/residue: 0.1740 time to fit residues: 126.9804 Evaluate side-chains 311 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 201 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 221 SER 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 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL 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 883 THR Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1018 ILE Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 469 SER Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE 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 1132 ILE Chi-restraints excluded: chain J residue 178 HIS Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 114 SER Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 116 PHE Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 89 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 134 optimal weight: 0.1980 chunk 108 optimal weight: 7.9990 chunk 277 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 317 optimal weight: 20.0000 chunk 358 optimal weight: 0.0020 chunk 356 optimal weight: 10.0000 chunk 122 optimal weight: 8.9990 chunk 229 optimal weight: 9.9990 overall best weight: 3.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 658 ASN A 856 ASN B 655 HIS B 913 GLN C 969 ASN C1106 GLN J 82 GLN ** J 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN N 90 GLN N 137 ASN ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.195942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.146328 restraints weight = 53772.189| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.89 r_work: 0.3240 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 31907 Z= 0.211 Angle : 0.765 15.220 43538 Z= 0.375 Chirality : 0.050 0.559 5115 Planarity : 0.005 0.066 5494 Dihedral : 8.327 59.954 5671 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.90 % Favored : 91.94 % Rotamer: Outliers : 5.38 % Allowed : 19.68 % Favored : 74.94 % 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: -1.96 (0.13), residues: 3810 helix: 0.42 (0.20), residues: 683 sheet: -0.65 (0.15), residues: 1116 loop : -2.38 (0.12), residues: 2011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 319 TYR 0.018 0.002 TYR A1067 PHE 0.021 0.002 PHE C 541 TRP 0.042 0.002 TRP A 104 HIS 0.005 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00507 (31791) covalent geometry : angle 0.72849 (43236) SS BOND : bond 0.00619 ( 46) SS BOND : angle 2.31696 ( 92) hydrogen bonds : bond 0.04853 ( 1075) hydrogen bonds : angle 5.59275 ( 3063) link_BETA1-4 : bond 0.00483 ( 22) link_BETA1-4 : angle 2.46651 ( 66) link_NAG-ASN : bond 0.00541 ( 48) link_NAG-ASN : angle 3.33947 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 182 poor density : 221 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.6742 (OUTLIER) cc_final: 0.6537 (m-30) REVERT: A 122 ASN cc_start: 0.2154 (OUTLIER) cc_final: 0.1438 (m110) REVERT: A 141 LEU cc_start: 0.4917 (OUTLIER) cc_final: 0.4678 (pt) REVERT: A 153 MET cc_start: 0.4110 (mpp) cc_final: 0.2105 (mmt) REVERT: A 309 GLU cc_start: 0.8246 (pm20) cc_final: 0.7894 (mp0) REVERT: A 347 PHE cc_start: 0.2267 (OUTLIER) cc_final: 0.0937 (m-80) REVERT: B 110 LEU cc_start: 0.6877 (mm) cc_final: 0.6651 (mm) REVERT: B 153 MET cc_start: 0.2486 (ppp) cc_final: 0.2200 (tmm) REVERT: B 214 ARG cc_start: 0.1920 (OUTLIER) cc_final: 0.0461 (mtt180) REVERT: B 231 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.7904 (pt) REVERT: B 273 ARG cc_start: 0.7848 (mmt90) cc_final: 0.7332 (mmp-170) REVERT: B 574 ASP cc_start: 0.7988 (m-30) cc_final: 0.7119 (t0) REVERT: B 814 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8044 (mtpt) REVERT: B 1143 PRO cc_start: 0.8261 (Cg_endo) cc_final: 0.7923 (Cg_exo) REVERT: C 52 GLN cc_start: 0.8009 (tm-30) cc_final: 0.7797 (tt0) REVERT: C 153 MET cc_start: 0.2255 (mtt) cc_final: 0.1171 (tpp) REVERT: C 168 PHE cc_start: 0.6858 (t80) cc_final: 0.6644 (t80) REVERT: C 188 ASN cc_start: 0.6690 (OUTLIER) cc_final: 0.6479 (p0) REVERT: C 1132 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8356 (pp) REVERT: J 105 MET cc_start: 0.2525 (mtp) cc_final: 0.2057 (mtt) REVERT: J 187 SER cc_start: 0.1274 (OUTLIER) cc_final: 0.1013 (m) REVERT: N 116 PHE cc_start: 0.0422 (OUTLIER) cc_final: 0.0075 (m-80) REVERT: N 175 LEU cc_start: 0.3598 (tt) cc_final: 0.3170 (mt) REVERT: H 28 THR cc_start: 0.2963 (OUTLIER) cc_final: 0.2591 (p) REVERT: H 34 MET cc_start: 0.0873 (mmt) cc_final: -0.1057 (mmp) REVERT: H 81 LEU cc_start: -0.2497 (OUTLIER) cc_final: -0.2757 (pp) REVERT: K 50 ASP cc_start: 0.0536 (OUTLIER) cc_final: -0.0010 (p0) REVERT: K 92 ASP cc_start: 0.2853 (OUTLIER) cc_final: 0.2025 (m-30) outliers start: 182 outliers final: 121 residues processed: 381 average time/residue: 0.1740 time to fit residues: 112.6875 Evaluate side-chains 316 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 180 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR 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 814 LYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 980 ILE Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1126 CYS Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER 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 1132 ILE Chi-restraints excluded: chain J residue 123 VAL Chi-restraints excluded: chain J residue 187 SER Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 90 GLN Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 116 PHE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 142 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 205 optimal weight: 20.0000 chunk 230 optimal weight: 9.9990 chunk 284 optimal weight: 0.8980 chunk 337 optimal weight: 7.9990 chunk 225 optimal weight: 10.0000 chunk 257 optimal weight: 4.9990 chunk 341 optimal weight: 30.0000 chunk 358 optimal weight: 0.0870 chunk 183 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 207 HIS A 955 ASN A1005 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 6 GLN ** H 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 124 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.195174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.145616 restraints weight = 53328.007| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.65 r_work: 0.3259 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 31907 Z= 0.148 Angle : 0.699 14.020 43538 Z= 0.339 Chirality : 0.048 0.531 5115 Planarity : 0.004 0.053 5494 Dihedral : 7.723 59.735 5660 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.93 % Favored : 92.94 % Rotamer: Outliers : 4.73 % Allowed : 20.69 % Favored : 74.59 % 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: -1.58 (0.13), residues: 3810 helix: 0.80 (0.20), residues: 679 sheet: -0.36 (0.15), residues: 1101 loop : -2.19 (0.12), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 995 TYR 0.020 0.001 TYR A1067 PHE 0.029 0.001 PHE A 86 TRP 0.019 0.001 TRP A 104 HIS 0.005 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00349 (31791) covalent geometry : angle 0.66650 (43236) SS BOND : bond 0.00442 ( 46) SS BOND : angle 2.25546 ( 92) hydrogen bonds : bond 0.04028 ( 1075) hydrogen bonds : angle 5.25552 ( 3063) link_BETA1-4 : bond 0.00563 ( 22) link_BETA1-4 : angle 2.31112 ( 66) link_NAG-ASN : bond 0.00384 ( 48) link_NAG-ASN : angle 2.92685 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 205 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.7069 (OUTLIER) cc_final: 0.6797 (m-30) REVERT: A 122 ASN cc_start: 0.1794 (OUTLIER) cc_final: 0.1574 (m110) REVERT: A 141 LEU cc_start: 0.5172 (OUTLIER) cc_final: 0.4925 (pt) REVERT: A 153 MET cc_start: 0.4223 (mpp) cc_final: 0.2069 (mmt) REVERT: A 309 GLU cc_start: 0.8520 (pm20) cc_final: 0.8094 (mp0) REVERT: A 347 PHE cc_start: 0.2184 (OUTLIER) cc_final: 0.0815 (m-80) REVERT: A 568 ASP cc_start: 0.8178 (t0) cc_final: 0.7948 (p0) REVERT: A 1136 THR cc_start: 0.9530 (OUTLIER) cc_final: 0.9327 (p) REVERT: B 118 LEU cc_start: 0.7972 (tt) cc_final: 0.7405 (mp) REVERT: B 214 ARG cc_start: 0.2612 (OUTLIER) cc_final: 0.0699 (ttt180) REVERT: B 273 ARG cc_start: 0.7979 (mmt90) cc_final: 0.7370 (mmp-170) REVERT: B 406 GLU cc_start: 0.5043 (OUTLIER) cc_final: 0.4818 (pm20) REVERT: B 574 ASP cc_start: 0.8097 (m-30) cc_final: 0.7373 (t0) REVERT: B 1143 PRO cc_start: 0.8250 (Cg_endo) cc_final: 0.7953 (Cg_exo) REVERT: C 52 GLN cc_start: 0.8125 (tm-30) cc_final: 0.7912 (tt0) REVERT: C 87 ASN cc_start: 0.7823 (t0) cc_final: 0.7594 (m-40) REVERT: C 153 MET cc_start: 0.2189 (mtt) cc_final: 0.1062 (tpp) REVERT: C 198 ASP cc_start: 0.6127 (t0) cc_final: 0.5840 (t0) REVERT: C 200 TYR cc_start: 0.7043 (m-10) cc_final: 0.6632 (m-10) REVERT: C 213 VAL cc_start: 0.7937 (OUTLIER) cc_final: 0.7686 (m) REVERT: C 336 CYS cc_start: 0.3236 (OUTLIER) cc_final: 0.3012 (t) REVERT: C 1132 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8364 (pp) REVERT: N 175 LEU cc_start: 0.3591 (tt) cc_final: 0.3136 (mt) REVERT: H 28 THR cc_start: 0.2883 (OUTLIER) cc_final: 0.2529 (p) REVERT: H 34 MET cc_start: 0.0531 (mmt) cc_final: -0.0921 (mmp) REVERT: H 81 LEU cc_start: -0.2316 (OUTLIER) cc_final: -0.2767 (pp) REVERT: K 50 ASP cc_start: 0.0829 (OUTLIER) cc_final: 0.0405 (p0) REVERT: K 92 ASP cc_start: 0.3001 (OUTLIER) cc_final: 0.2493 (m-30) outliers start: 160 outliers final: 116 residues processed: 348 average time/residue: 0.1725 time to fit residues: 104.0214 Evaluate side-chains 308 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 178 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 503 VAL 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 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 861 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain H residue 209 ILE Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 56 THR Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 37 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 88 optimal weight: 0.8980 chunk 312 optimal weight: 40.0000 chunk 318 optimal weight: 6.9990 chunk 206 optimal weight: 0.5980 chunk 359 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 193 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 144 optimal weight: 0.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 125 ASN A 655 HIS B 414 GLN N 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.196807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.147023 restraints weight = 53485.098| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.76 r_work: 0.3261 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 31907 Z= 0.140 Angle : 0.665 13.409 43538 Z= 0.322 Chirality : 0.047 0.533 5115 Planarity : 0.004 0.073 5494 Dihedral : 7.352 59.707 5656 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.35 % Favored : 92.55 % Rotamer: Outliers : 4.88 % Allowed : 20.80 % Favored : 74.32 % 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: -1.31 (0.13), residues: 3810 helix: 0.98 (0.20), residues: 684 sheet: -0.12 (0.15), residues: 1082 loop : -2.03 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 246 TYR 0.019 0.001 TYR A1067 PHE 0.024 0.001 PHE A 86 TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00330 (31791) covalent geometry : angle 0.63543 (43236) SS BOND : bond 0.00438 ( 46) SS BOND : angle 2.09712 ( 92) hydrogen bonds : bond 0.03893 ( 1075) hydrogen bonds : angle 5.07511 ( 3063) link_BETA1-4 : bond 0.00518 ( 22) link_BETA1-4 : angle 2.24342 ( 66) link_NAG-ASN : bond 0.00360 ( 48) link_NAG-ASN : angle 2.70241 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 193 time to evaluate : 1.162 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 53 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: A 122 ASN cc_start: 0.2236 (OUTLIER) cc_final: 0.1950 (m110) REVERT: A 125 ASN cc_start: 0.2176 (OUTLIER) cc_final: 0.1854 (p0) REVERT: A 153 MET cc_start: 0.4227 (mpp) cc_final: 0.1902 (mmt) REVERT: A 309 GLU cc_start: 0.8540 (pm20) cc_final: 0.8145 (mp0) REVERT: A 347 PHE cc_start: 0.2332 (OUTLIER) cc_final: 0.0984 (m-80) REVERT: A 568 ASP cc_start: 0.8315 (t0) cc_final: 0.8038 (p0) REVERT: A 740 MET cc_start: 0.8921 (ttt) cc_final: 0.8649 (ttt) REVERT: B 153 MET cc_start: 0.3698 (OUTLIER) cc_final: 0.3402 (tmm) REVERT: B 214 ARG cc_start: 0.2974 (OUTLIER) cc_final: 0.1003 (mtt180) REVERT: B 273 ARG cc_start: 0.7938 (mmt90) cc_final: 0.7209 (mmp-170) REVERT: B 574 ASP cc_start: 0.8175 (m-30) cc_final: 0.7539 (t0) REVERT: B 1045 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8675 (tptp) REVERT: B 1143 PRO cc_start: 0.8235 (Cg_endo) cc_final: 0.7918 (Cg_exo) REVERT: C 52 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7951 (tt0) REVERT: C 87 ASN cc_start: 0.7984 (t0) cc_final: 0.7629 (m-40) REVERT: C 153 MET cc_start: 0.1569 (mtt) cc_final: 0.0793 (tpp) REVERT: C 200 TYR cc_start: 0.7066 (m-10) cc_final: 0.6711 (m-10) REVERT: C 1132 ILE cc_start: 0.8814 (OUTLIER) cc_final: 0.8376 (pp) REVERT: J 189 LEU cc_start: 0.3201 (tp) cc_final: 0.2885 (mm) REVERT: N 175 LEU cc_start: 0.3932 (tt) cc_final: 0.3294 (mt) REVERT: H 34 MET cc_start: 0.0697 (mmt) cc_final: -0.0973 (mmp) REVERT: H 81 LEU cc_start: -0.2329 (OUTLIER) cc_final: -0.2725 (pp) REVERT: K 50 ASP cc_start: 0.0609 (OUTLIER) cc_final: 0.0116 (p0) REVERT: K 92 ASP cc_start: 0.3056 (OUTLIER) cc_final: 0.2800 (m-30) outliers start: 165 outliers final: 119 residues processed: 334 average time/residue: 0.1636 time to fit residues: 95.7163 Evaluate side-chains 310 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 180 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 125 ASN Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 692 ILE 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 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 366 SER Chi-restraints excluded: chain B residue 414 GLN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 754 LEU Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain J residue 217 SER Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 97 optimal weight: 4.9990 chunk 282 optimal weight: 0.0370 chunk 154 optimal weight: 3.9990 chunk 251 optimal weight: 2.9990 chunk 360 optimal weight: 30.0000 chunk 359 optimal weight: 50.0000 chunk 17 optimal weight: 20.0000 chunk 157 optimal weight: 1.9990 chunk 305 optimal weight: 4.9990 chunk 139 optimal weight: 0.0870 chunk 341 optimal weight: 20.0000 overall best weight: 1.8242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN B 409 GLN C 556 ASN J 1 GLN N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.197278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147536 restraints weight = 53347.638| |-----------------------------------------------------------------------------| r_work (start): 0.3729 rms_B_bonded: 2.76 r_work: 0.3244 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 31907 Z= 0.137 Angle : 0.658 13.426 43538 Z= 0.319 Chirality : 0.047 0.521 5115 Planarity : 0.004 0.051 5494 Dihedral : 7.154 59.424 5650 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.82 % Favored : 93.07 % Rotamer: Outliers : 4.91 % Allowed : 20.74 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.13), residues: 3810 helix: 1.07 (0.20), residues: 691 sheet: 0.07 (0.15), residues: 1093 loop : -1.93 (0.13), residues: 2026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 246 TYR 0.018 0.001 TYR A1067 PHE 0.026 0.001 PHE A 86 TRP 0.011 0.001 TRP B 436 HIS 0.004 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00319 (31791) covalent geometry : angle 0.62805 (43236) SS BOND : bond 0.00678 ( 46) SS BOND : angle 1.95791 ( 92) hydrogen bonds : bond 0.03787 ( 1075) hydrogen bonds : angle 5.01598 ( 3063) link_BETA1-4 : bond 0.00551 ( 22) link_BETA1-4 : angle 2.22642 ( 66) link_NAG-ASN : bond 0.00382 ( 48) link_NAG-ASN : angle 2.80880 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 187 time to evaluate : 1.221 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 153 MET cc_start: 0.3912 (mpp) cc_final: 0.1674 (mmt) REVERT: A 309 GLU cc_start: 0.8517 (pm20) cc_final: 0.8142 (mp0) REVERT: A 364 ASP cc_start: 0.6317 (p0) cc_final: 0.6094 (p0) REVERT: A 568 ASP cc_start: 0.8343 (t0) cc_final: 0.8085 (p0) REVERT: A 740 MET cc_start: 0.8746 (ttt) cc_final: 0.8454 (ttt) REVERT: B 104 TRP cc_start: 0.7806 (m-90) cc_final: 0.7541 (m-90) REVERT: B 118 LEU cc_start: 0.7967 (tt) cc_final: 0.7443 (mp) REVERT: B 153 MET cc_start: 0.4235 (OUTLIER) cc_final: 0.3654 (tmm) REVERT: B 214 ARG cc_start: 0.2608 (OUTLIER) cc_final: 0.0602 (ttt180) REVERT: B 273 ARG cc_start: 0.7962 (mmt90) cc_final: 0.7252 (mmp-170) REVERT: B 574 ASP cc_start: 0.8179 (m-30) cc_final: 0.7602 (t0) REVERT: B 985 ASP cc_start: 0.7974 (p0) cc_final: 0.7385 (p0) REVERT: B 1045 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8654 (tptp) REVERT: B 1143 PRO cc_start: 0.8032 (Cg_endo) cc_final: 0.7697 (Cg_exo) REVERT: C 52 GLN cc_start: 0.8202 (tm-30) cc_final: 0.7969 (tt0) REVERT: C 87 ASN cc_start: 0.8093 (t0) cc_final: 0.7670 (m-40) REVERT: C 153 MET cc_start: 0.1146 (mtt) cc_final: 0.0679 (tpp) REVERT: C 200 TYR cc_start: 0.7055 (m-10) cc_final: 0.6714 (m-10) REVERT: C 1132 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8384 (pp) REVERT: J 1 GLN cc_start: 0.2754 (OUTLIER) cc_final: 0.2165 (pt0) REVERT: N 175 LEU cc_start: 0.3792 (tt) cc_final: 0.3185 (mt) REVERT: H 81 LEU cc_start: -0.2252 (OUTLIER) cc_final: -0.2730 (pp) REVERT: K 50 ASP cc_start: 0.0452 (OUTLIER) cc_final: -0.0005 (p0) REVERT: K 92 ASP cc_start: 0.2923 (OUTLIER) cc_final: 0.2715 (m-30) outliers start: 166 outliers final: 124 residues processed: 332 average time/residue: 0.1657 time to fit residues: 96.5887 Evaluate side-chains 307 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 175 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 772 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 931 ILE Chi-restraints excluded: chain A residue 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 153 MET Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 1 GLN Chi-restraints excluded: chain J residue 39 GLN Chi-restraints excluded: chain J residue 207 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 4 MET Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 284 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 320 optimal weight: 6.9990 chunk 311 optimal weight: 0.9990 chunk 296 optimal weight: 0.8980 chunk 346 optimal weight: 20.0000 chunk 278 optimal weight: 7.9990 chunk 187 optimal weight: 3.9990 chunk 196 optimal weight: 4.9990 chunk 192 optimal weight: 0.9980 chunk 297 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 245 HIS B 542 ASN C 556 ASN C1071 GLN N 160 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.195948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.146419 restraints weight = 53591.550| |-----------------------------------------------------------------------------| r_work (start): 0.3741 rms_B_bonded: 2.74 r_work: 0.3271 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31907 Z= 0.115 Angle : 0.644 12.470 43538 Z= 0.311 Chirality : 0.047 0.504 5115 Planarity : 0.004 0.052 5494 Dihedral : 6.904 58.255 5648 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.52 % Rotamer: Outliers : 4.11 % Allowed : 21.66 % Favored : 74.23 % 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: -0.94 (0.13), residues: 3810 helix: 1.29 (0.21), residues: 689 sheet: 0.06 (0.15), residues: 1117 loop : -1.79 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 246 TYR 0.019 0.001 TYR A1067 PHE 0.026 0.001 PHE A 377 TRP 0.012 0.001 TRP A 436 HIS 0.004 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00264 (31791) covalent geometry : angle 0.61711 (43236) SS BOND : bond 0.00422 ( 46) SS BOND : angle 1.94779 ( 92) hydrogen bonds : bond 0.03485 ( 1075) hydrogen bonds : angle 4.90527 ( 3063) link_BETA1-4 : bond 0.00552 ( 22) link_BETA1-4 : angle 2.13272 ( 66) link_NAG-ASN : bond 0.00363 ( 48) link_NAG-ASN : angle 2.55207 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 179 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3624 (mpp) cc_final: 0.1409 (mmt) REVERT: A 309 GLU cc_start: 0.8486 (pm20) cc_final: 0.8146 (mp0) REVERT: A 347 PHE cc_start: 0.2320 (OUTLIER) cc_final: 0.1046 (m-80) REVERT: A 364 ASP cc_start: 0.6371 (p0) cc_final: 0.6149 (p0) REVERT: A 403 ARG cc_start: 0.2028 (OUTLIER) cc_final: 0.1268 (mmm160) REVERT: A 740 MET cc_start: 0.8568 (ttt) cc_final: 0.8339 (ttt) REVERT: B 104 TRP cc_start: 0.7835 (m-90) cc_final: 0.7556 (m-90) REVERT: B 214 ARG cc_start: 0.2830 (OUTLIER) cc_final: 0.0737 (ttt180) REVERT: B 273 ARG cc_start: 0.7952 (mmt90) cc_final: 0.7256 (mmp-170) REVERT: B 574 ASP cc_start: 0.8155 (m-30) cc_final: 0.7654 (t0) REVERT: B 1045 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8619 (tptp) REVERT: B 1143 PRO cc_start: 0.8077 (Cg_endo) cc_final: 0.7707 (Cg_exo) REVERT: C 87 ASN cc_start: 0.8091 (t0) cc_final: 0.7672 (m-40) REVERT: C 153 MET cc_start: 0.1197 (mtt) cc_final: 0.0750 (tpp) REVERT: C 200 TYR cc_start: 0.7074 (m-10) cc_final: 0.6739 (m-10) REVERT: C 1132 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8360 (pp) REVERT: J 189 LEU cc_start: 0.3553 (tp) cc_final: 0.3202 (mm) REVERT: N 175 LEU cc_start: 0.3768 (tt) cc_final: 0.3142 (mt) REVERT: H 34 MET cc_start: 0.0700 (mmt) cc_final: -0.0967 (mmp) REVERT: H 81 LEU cc_start: -0.2412 (OUTLIER) cc_final: -0.2904 (pp) REVERT: K 50 ASP cc_start: 0.0392 (OUTLIER) cc_final: -0.0034 (p0) outliers start: 139 outliers final: 106 residues processed: 300 average time/residue: 0.1670 time to fit residues: 87.8996 Evaluate side-chains 276 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 163 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 403 ARG Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE 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 937 SER Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 977 LEU Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 94 LEU Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 170 optimal weight: 0.9980 chunk 126 optimal weight: 20.0000 chunk 373 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 208 optimal weight: 0.0170 chunk 163 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 152 optimal weight: 5.9990 chunk 65 optimal weight: 0.7980 chunk 227 optimal weight: 7.9990 chunk 367 optimal weight: 3.9990 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 542 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 556 ASN N 3 GLN K 160 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.195720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146190 restraints weight = 53043.926| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.76 r_work: 0.3241 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 31907 Z= 0.140 Angle : 0.658 12.788 43538 Z= 0.318 Chirality : 0.047 0.510 5115 Planarity : 0.004 0.062 5494 Dihedral : 6.824 59.337 5642 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.17 % Favored : 92.76 % Rotamer: Outliers : 4.08 % Allowed : 21.63 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -0.90 (0.13), residues: 3810 helix: 1.26 (0.20), residues: 697 sheet: 0.13 (0.15), residues: 1110 loop : -1.77 (0.13), residues: 2003 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 319 TYR 0.017 0.001 TYR B1067 PHE 0.038 0.001 PHE B 133 TRP 0.011 0.001 TRP B 436 HIS 0.035 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00333 (31791) covalent geometry : angle 0.62987 (43236) SS BOND : bond 0.00448 ( 46) SS BOND : angle 2.07545 ( 92) hydrogen bonds : bond 0.03750 ( 1075) hydrogen bonds : angle 4.93470 ( 3063) link_BETA1-4 : bond 0.00526 ( 22) link_BETA1-4 : angle 2.16088 ( 66) link_NAG-ASN : bond 0.00365 ( 48) link_NAG-ASN : angle 2.59614 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 169 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.3557 (mpp) cc_final: 0.1294 (mmt) REVERT: A 309 GLU cc_start: 0.8530 (pm20) cc_final: 0.8153 (mp0) REVERT: A 347 PHE cc_start: 0.2448 (OUTLIER) cc_final: 0.1213 (m-80) REVERT: A 364 ASP cc_start: 0.6412 (p0) cc_final: 0.6205 (p0) REVERT: A 988 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8464 (pt0) REVERT: B 104 TRP cc_start: 0.7743 (m-90) cc_final: 0.7474 (m-90) REVERT: B 118 LEU cc_start: 0.7827 (tt) cc_final: 0.7326 (mp) REVERT: B 214 ARG cc_start: 0.2919 (OUTLIER) cc_final: 0.0570 (ttt180) REVERT: B 273 ARG cc_start: 0.7964 (mmt90) cc_final: 0.7275 (mmp-170) REVERT: B 574 ASP cc_start: 0.8009 (m-30) cc_final: 0.7658 (t0) REVERT: B 1045 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8605 (tptp) REVERT: C 153 MET cc_start: 0.1100 (mtt) cc_final: 0.0668 (tpp) REVERT: C 200 TYR cc_start: 0.7046 (m-10) cc_final: 0.6720 (m-10) REVERT: C 1132 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8413 (pp) REVERT: N 175 LEU cc_start: 0.3715 (tt) cc_final: 0.3185 (mt) REVERT: H 81 LEU cc_start: -0.2370 (OUTLIER) cc_final: -0.2905 (pp) REVERT: K 50 ASP cc_start: 0.0359 (OUTLIER) cc_final: -0.0053 (p0) outliers start: 138 outliers final: 115 residues processed: 289 average time/residue: 0.1631 time to fit residues: 82.3330 Evaluate side-chains 284 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 163 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE 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 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 132 GLU Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1094 VAL Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 363 optimal weight: 0.6980 chunk 373 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 194 optimal weight: 0.0270 chunk 355 optimal weight: 30.0000 chunk 190 optimal weight: 5.9990 chunk 191 optimal weight: 0.6980 chunk 362 optimal weight: 20.0000 chunk 247 optimal weight: 4.9990 chunk 351 optimal weight: 30.0000 overall best weight: 2.2842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.193422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.142999 restraints weight = 52784.297| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.76 r_work: 0.3233 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3127 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 31907 Z= 0.155 Angle : 0.671 12.985 43538 Z= 0.325 Chirality : 0.047 0.518 5115 Planarity : 0.004 0.050 5494 Dihedral : 6.861 58.950 5641 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 3.81 % Allowed : 22.04 % Favored : 74.14 % 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: -0.85 (0.13), residues: 3810 helix: 1.28 (0.20), residues: 697 sheet: 0.26 (0.16), residues: 1083 loop : -1.77 (0.13), residues: 2030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 403 TYR 0.018 0.001 TYR A1067 PHE 0.026 0.001 PHE A 86 TRP 0.014 0.001 TRP B 436 HIS 0.004 0.001 HIS B 245 Details of bonding type rmsd covalent geometry : bond 0.00372 (31791) covalent geometry : angle 0.64374 (43236) SS BOND : bond 0.00446 ( 46) SS BOND : angle 2.04530 ( 92) hydrogen bonds : bond 0.03962 ( 1075) hydrogen bonds : angle 5.00940 ( 3063) link_BETA1-4 : bond 0.00473 ( 22) link_BETA1-4 : angle 2.18772 ( 66) link_NAG-ASN : bond 0.00370 ( 48) link_NAG-ASN : angle 2.58346 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 173 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7725 (p) cc_final: 0.7320 (p) REVERT: A 153 MET cc_start: 0.3384 (mpp) cc_final: 0.1500 (mmt) REVERT: A 309 GLU cc_start: 0.8477 (pm20) cc_final: 0.8129 (mp0) REVERT: A 347 PHE cc_start: 0.2582 (OUTLIER) cc_final: 0.1469 (m-80) REVERT: A 988 GLU cc_start: 0.8954 (mm-30) cc_final: 0.8583 (pt0) REVERT: B 104 TRP cc_start: 0.7756 (m-90) cc_final: 0.7496 (m-90) REVERT: B 118 LEU cc_start: 0.7783 (tt) cc_final: 0.7267 (mp) REVERT: B 214 ARG cc_start: 0.2944 (OUTLIER) cc_final: 0.0363 (ttt180) REVERT: B 273 ARG cc_start: 0.7983 (mmt90) cc_final: 0.7285 (mmp-170) REVERT: B 574 ASP cc_start: 0.8039 (m-30) cc_final: 0.7749 (t0) REVERT: B 1045 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8562 (tptp) REVERT: C 87 ASN cc_start: 0.8062 (t0) cc_final: 0.7665 (m-40) REVERT: C 153 MET cc_start: 0.0838 (mtt) cc_final: 0.0455 (tpp) REVERT: C 200 TYR cc_start: 0.7052 (m-10) cc_final: 0.6823 (m-10) REVERT: C 1132 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8394 (pp) REVERT: J 189 LEU cc_start: 0.3372 (tp) cc_final: 0.2980 (mm) REVERT: N 175 LEU cc_start: 0.3710 (tt) cc_final: 0.3189 (mt) REVERT: H 81 LEU cc_start: -0.2467 (OUTLIER) cc_final: -0.3121 (pp) REVERT: K 50 ASP cc_start: 0.0298 (OUTLIER) cc_final: -0.0104 (p0) outliers start: 129 outliers final: 112 residues processed: 285 average time/residue: 0.1653 time to fit residues: 82.4334 Evaluate side-chains 274 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 156 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 383 SER Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 739 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 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 772 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 206 GLN Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 152 optimal weight: 5.9990 chunk 325 optimal weight: 0.0970 chunk 313 optimal weight: 6.9990 chunk 306 optimal weight: 0.0570 chunk 207 optimal weight: 10.0000 chunk 327 optimal weight: 20.0000 chunk 236 optimal weight: 0.0670 chunk 233 optimal weight: 7.9990 chunk 13 optimal weight: 0.8980 chunk 108 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 overall best weight: 1.4236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1071 GLN B 422 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 493 GLN C 556 ASN C 779 GLN J 185 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.193688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.144321 restraints weight = 53054.015| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.77 r_work: 0.3247 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 31907 Z= 0.123 Angle : 0.644 12.515 43538 Z= 0.312 Chirality : 0.046 0.504 5115 Planarity : 0.004 0.051 5494 Dihedral : 6.639 59.023 5636 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.51 % Favored : 93.41 % Rotamer: Outliers : 3.43 % Allowed : 22.28 % Favored : 74.29 % 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: -0.69 (0.13), residues: 3810 helix: 1.48 (0.21), residues: 691 sheet: 0.36 (0.16), residues: 1069 loop : -1.68 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 319 TYR 0.024 0.001 TYR B 160 PHE 0.026 0.001 PHE B 133 TRP 0.019 0.001 TRP A 104 HIS 0.003 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00288 (31791) covalent geometry : angle 0.61934 (43236) SS BOND : bond 0.00414 ( 46) SS BOND : angle 1.80678 ( 92) hydrogen bonds : bond 0.03529 ( 1075) hydrogen bonds : angle 4.90748 ( 3063) link_BETA1-4 : bond 0.00564 ( 22) link_BETA1-4 : angle 2.12729 ( 66) link_NAG-ASN : bond 0.00364 ( 48) link_NAG-ASN : angle 2.43446 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7620 Ramachandran restraints generated. 3810 Oldfield, 0 Emsley, 3810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 166 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 THR cc_start: 0.7675 (p) cc_final: 0.7257 (p) REVERT: A 153 MET cc_start: 0.3424 (mpp) cc_final: 0.1338 (mmt) REVERT: A 309 GLU cc_start: 0.8497 (pm20) cc_final: 0.8148 (mp0) REVERT: A 347 PHE cc_start: 0.2400 (OUTLIER) cc_final: 0.1250 (m-80) REVERT: A 988 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8560 (pt0) REVERT: B 104 TRP cc_start: 0.7742 (m-90) cc_final: 0.7480 (m-90) REVERT: B 214 ARG cc_start: 0.3006 (OUTLIER) cc_final: 0.0461 (ttt180) REVERT: B 273 ARG cc_start: 0.7925 (mmt90) cc_final: 0.7236 (mmp-170) REVERT: B 1045 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8600 (tptp) REVERT: C 87 ASN cc_start: 0.8243 (t0) cc_final: 0.7679 (m-40) REVERT: C 153 MET cc_start: 0.0883 (mtt) cc_final: 0.0536 (tpp) REVERT: C 198 ASP cc_start: 0.6216 (t0) cc_final: 0.5948 (t0) REVERT: C 200 TYR cc_start: 0.7037 (m-10) cc_final: 0.6704 (m-10) REVERT: C 1132 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8406 (pp) REVERT: J 34 MET cc_start: 0.2403 (pmm) cc_final: 0.1942 (pmm) REVERT: J 189 LEU cc_start: 0.3307 (tp) cc_final: 0.2911 (mm) REVERT: N 175 LEU cc_start: 0.3837 (tt) cc_final: 0.3304 (mt) REVERT: H 81 LEU cc_start: -0.2516 (OUTLIER) cc_final: -0.3142 (pp) REVERT: K 50 ASP cc_start: 0.0411 (OUTLIER) cc_final: 0.0027 (p0) outliers start: 116 outliers final: 105 residues processed: 267 average time/residue: 0.1631 time to fit residues: 76.2581 Evaluate side-chains 266 residues out of total 3384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 155 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 53 ASP Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 114 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 231 ILE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 503 VAL Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 641 ASN Chi-restraints excluded: chain A residue 692 ILE 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 937 SER Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1017 GLU Chi-restraints excluded: chain A residue 1125 ASN Chi-restraints excluded: chain A residue 1130 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 323 THR Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 531 THR Chi-restraints excluded: chain B residue 533 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 608 VAL Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 676 THR Chi-restraints excluded: chain B residue 746 SER Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1045 LYS Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 208 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 383 SER Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 523 THR Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 590 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 975 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1004 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 149 THR Chi-restraints excluded: chain N residue 50 ASP Chi-restraints excluded: chain N residue 83 ILE Chi-restraints excluded: chain N residue 106 ILE Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 115 ASP Chi-restraints excluded: chain H residue 125 VAL Chi-restraints excluded: chain H residue 135 VAL Chi-restraints excluded: chain H residue 184 LEU Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain K residue 50 ASP Chi-restraints excluded: chain K residue 83 ILE Chi-restraints excluded: chain K residue 142 ARG Chi-restraints excluded: chain K residue 176 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 58 optimal weight: 8.9990 chunk 244 optimal weight: 4.9990 chunk 372 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 129 optimal weight: 9.9990 chunk 352 optimal weight: 6.9990 chunk 40 optimal weight: 20.0000 chunk 200 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 104 optimal weight: 0.4980 chunk 272 optimal weight: 0.8980 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 GLN B 493 GLN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.191872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.141543 restraints weight = 52809.867| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.59 r_work: 0.3218 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31907 Z= 0.199 Angle : 0.706 13.669 43538 Z= 0.343 Chirality : 0.049 0.544 5115 Planarity : 0.004 0.050 5494 Dihedral : 6.984 59.329 5636 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.74 % Favored : 92.20 % Rotamer: Outliers : 3.58 % Allowed : 22.37 % Favored : 74.05 % 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: -0.85 (0.13), residues: 3810 helix: 1.22 (0.20), residues: 692 sheet: 0.34 (0.16), residues: 1083 loop : -1.79 (0.13), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 319 TYR 0.018 0.001 TYR C 449 PHE 0.026 0.002 PHE A 86 TRP 0.045 0.002 TRP A 104 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00487 (31791) covalent geometry : angle 0.67884 (43236) SS BOND : bond 0.00481 ( 46) SS BOND : angle 2.17924 ( 92) hydrogen bonds : bond 0.04375 ( 1075) hydrogen bonds : angle 5.11429 ( 3063) link_BETA1-4 : bond 0.00556 ( 22) link_BETA1-4 : angle 2.32037 ( 66) link_NAG-ASN : bond 0.00419 ( 48) link_NAG-ASN : angle 2.64776 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9745.12 seconds wall clock time: 166 minutes 57.15 seconds (10017.15 seconds total)