Starting phenix.real_space_refine on Sun Jul 5 22:46:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.cif" model { file = "/net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d0c_30530/07_2026/7d0c_30530.map" } 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 129 5.16 5 C 19639 2.51 5 N 5068 2.21 5 O 6130 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30966 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 7863 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7863 Classifications: {'peptide': 1006} Link IDs: {'PTRANS': 50, 'TRANS': 955} Chain breaks: 8 Chain: "B" Number of atoms: 7696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 982, 7696 Classifications: {'peptide': 982} Link IDs: {'PTRANS': 47, 'TRANS': 934} Chain breaks: 11 Chain: "C" Number of atoms: 7853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7853 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 8 Chain: "H" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "L" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1647 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "G" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1640 Classifications: {'peptide': 219} Link IDs: {'PTRANS': 11, 'TRANS': 207} Chain: "F" Number of atoms: 1647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1647 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, '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 chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 9 Chain: "B" 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 chiralities: 9 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 chiralities: 8 Time building chain proxies: 6.80, per 1000 atoms: 0.22 Number of scatterers: 30966 At special positions: 0 Unit cell: (134.788, 173.92, 236.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 129 16.00 O 6130 8.00 N 5068 7.00 C 19639 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=2.40 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.13 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.25 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.52 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=2.05 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.03 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=1.82 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.13 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=1.47 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.52 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=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 89 " distance=2.04 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 144 " - pdb=" SG CYS G 200 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 89 " distance=2.04 Simple disulfide: pdb=" SG CYS F 135 " - pdb=" SG CYS F 195 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " NAG-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 A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " 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 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 343 " " NAG E 1 " - " ASN A 717 " " NAG I 1 " - " ASN A 801 " " NAG J 1 " - " ASN A1074 " " NAG K 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN B 331 " " NAG O 1 " - " ASN B 709 " " NAG P 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 331 " " NAG U 1 " - " ASN C 343 " " NAG V 1 " - " ASN C 709 " " NAG W 1 " - " ASN C 717 " " NAG X 1 " - " ASN C 801 " " NAG Y 1 " - " ASN C1074 " " NAG Z 1 " - " ASN C1098 " " NAG a 1 " - " ASN C1134 " " NAG b 1 " - " ASN A 331 " " NAG c 1 " - " ASN B1074 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7204 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 66 sheets defined 19.0% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.815A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.865A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.631A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.772A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 removed outlier: 3.634A pdb=" N LYS A 814 " --> pdb=" O LYS A 811 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.677A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 3.693A 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: 3.648A 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: 3.682A pdb=" N ALA A1020 " --> pdb=" O ALA A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.646A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.641A 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: 3.964A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 776 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.545A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 3.602A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.846A 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: 3.720A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.704A 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: 3.674A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.583A 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: 3.815A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.865A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (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: 3.561A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.604A 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: 3.712A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.355A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 961 " --> pdb=" O GLN C 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 977 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.220A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA C1016 " --> pdb=" O LEU C1012 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'L' and resid 80 through 84 Processing helix chain 'L' and resid 122 through 129 Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'G' and resid 191 through 193 No H-bonds generated for 'chain 'G' and resid 191 through 193' Processing helix chain 'F' and resid 80 through 84 Processing helix chain 'F' and resid 122 through 129 Processing helix chain 'F' and resid 184 through 188 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) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.569A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.856A 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: 7.660A 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: 4.588A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 319 removed outlier: 6.679A pdb=" N GLU A 309 " --> pdb=" O GLY A 601 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLY A 601 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 599 " --> pdb=" O GLY A 311 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 376 through 379 removed outlier: 3.839A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP A 398 " --> pdb=" O VAL A 512 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 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: 8.624A 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: 6.589A 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: 6.244A 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: 6.589A 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: 6.244A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.977A 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: 4.505A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.712A 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: 8.539A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.686A 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: 7.258A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.527A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.650A 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: 6.715A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.539A 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: 3.663A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.673A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC7, first strand: chain 'B' and resid 539 through 543 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.220A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.441A 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: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.696A 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: 6.168A 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: 6.542A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.696A 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: 3.619A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.799A 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: 8.152A 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: 3.579A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 6.214A 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: 3.515A 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: 7.134A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.757A pdb=" N THR C 274 " --> pdb=" O CYS C 291 " (cutoff:3.500A) removed outlier: 3.835A 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: 4.248A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.666A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.759A 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: 3.707A 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 376 through 379 removed outlier: 3.839A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASP C 398 " --> pdb=" O VAL C 512 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 454 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: 3.569A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.818A 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: 6.592A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.569A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'H' and resid 5 through 7 removed outlier: 3.502A pdb=" N SER H 21 " --> pdb=" O SER H 7 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AF2, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS H 95 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP H 107 " --> pdb=" O CYS H 95 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ARG H 97 " --> pdb=" O ASP H 105 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N TYR H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR H 111 " --> pdb=" O TYR H 93 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA H 141 " --> pdb=" O VAL H 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL H 188 " --> pdb=" O ALA H 141 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N GLY H 143 " --> pdb=" O VAL H 186 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 186 " --> pdb=" O GLY H 143 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N LEU H 145 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER H 184 " --> pdb=" O LEU H 145 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N LYS H 147 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU H 182 " --> pdb=" O LYS H 147 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 154 through 158 Processing sheet with id=AF7, first strand: chain 'L' and resid 5 through 6 removed outlier: 4.194A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 10 through 13 removed outlier: 7.137A pdb=" N LEU L 34 " --> pdb=" O TYR L 50 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TYR L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'L' and resid 115 through 119 Processing sheet with id=AG1, first strand: chain 'L' and resid 154 through 155 Processing sheet with id=AG2, first strand: chain 'G' and resid 5 through 7 removed outlier: 3.502A pdb=" N SER G 21 " --> pdb=" O SER G 7 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG4, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N CYS G 95 " --> pdb=" O TRP G 107 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N TRP G 107 " --> pdb=" O CYS G 95 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG G 97 " --> pdb=" O ASP G 105 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'G' and resid 57 through 59 removed outlier: 6.466A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N VAL G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N MET G 34 " --> pdb=" O VAL G 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR G 111 " --> pdb=" O TYR G 93 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'G' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 124 through 128 removed outlier: 5.008A pdb=" N ALA G 141 " --> pdb=" O VAL G 188 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL G 188 " --> pdb=" O ALA G 141 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N GLY G 143 " --> pdb=" O VAL G 186 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL G 186 " --> pdb=" O GLY G 143 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N LEU G 145 " --> pdb=" O SER G 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N SER G 184 " --> pdb=" O LEU G 145 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N LYS G 147 " --> pdb=" O LEU G 182 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU G 182 " --> pdb=" O LYS G 147 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 154 through 158 Processing sheet with id=AG9, first strand: chain 'F' and resid 5 through 6 removed outlier: 4.194A pdb=" N ASP F 71 " --> pdb=" O SER F 68 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 10 through 13 removed outlier: 7.136A pdb=" N LEU F 34 " --> pdb=" O TYR F 50 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N TYR F 50 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N TRP F 36 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 115 through 119 Processing sheet with id=AH3, first strand: chain 'F' and resid 154 through 155 1173 hydrogen bonds defined for protein. 3189 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: 6.76 Time building geometry restraints manager: 3.31 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: 9662 1.34 - 1.46: 8197 1.46 - 1.59: 13616 1.59 - 1.72: 0 1.72 - 1.85: 160 Bond restraints: 31635 Sorted by residual: bond pdb=" N PRO F 142 " pdb=" CD PRO F 142 " ideal model delta sigma weight residual 1.473 1.535 -0.062 1.40e-02 5.10e+03 1.93e+01 bond pdb=" N PRO L 142 " pdb=" CD PRO L 142 " 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 1.87e+01 bond pdb=" C HIS B1088 " pdb=" N PHE B1089 " ideal model delta sigma weight residual 1.331 1.264 0.067 1.59e-02 3.96e+03 1.77e+01 bond pdb=" N PRO C 521 " pdb=" CD PRO C 521 " ideal model delta sigma weight residual 1.473 1.530 -0.057 1.40e-02 5.10e+03 1.63e+01 ... (remaining 31630 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.70: 41907 2.70 - 5.39: 1015 5.39 - 8.09: 83 8.09 - 10.79: 9 10.79 - 13.48: 2 Bond angle restraints: 43016 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 121.54 132.87 -11.33 1.91e+00 2.74e-01 3.52e+01 angle pdb=" N GLU C 156 " pdb=" CA GLU C 156 " pdb=" C GLU C 156 " ideal model delta sigma weight residual 108.45 115.84 -7.39 1.26e+00 6.30e-01 3.44e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 119.78 114.03 5.75 1.03e+00 9.43e-01 3.12e+01 angle pdb=" N ILE C 468 " pdb=" CA ILE C 468 " pdb=" C ILE C 468 " ideal model delta sigma weight residual 113.42 107.04 6.38 1.17e+00 7.31e-01 2.98e+01 angle pdb=" N ILE A 468 " pdb=" CA ILE A 468 " pdb=" C ILE A 468 " ideal model delta sigma weight residual 113.42 107.07 6.35 1.17e+00 7.31e-01 2.95e+01 ... (remaining 43011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 15801 17.92 - 35.85: 1821 35.85 - 53.77: 487 53.77 - 71.69: 141 71.69 - 89.62: 60 Dihedral angle restraints: 18310 sinusoidal: 7103 harmonic: 11207 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 12.19 80.81 1 1.00e+01 1.00e-02 8.07e+01 dihedral pdb=" CB CYS B 391 " pdb=" SG CYS B 391 " pdb=" SG CYS B 525 " pdb=" CB CYS B 525 " ideal model delta sinusoidal sigma weight residual 93.00 19.61 73.39 1 1.00e+01 1.00e-02 6.86e+01 dihedral pdb=" CB CYS A 617 " pdb=" SG CYS A 617 " pdb=" SG CYS A 649 " pdb=" CB CYS A 649 " ideal model delta sinusoidal sigma weight residual 93.00 21.10 71.90 1 1.00e+01 1.00e-02 6.62e+01 ... (remaining 18307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.328: 5073 0.328 - 0.656: 3 0.656 - 0.984: 5 0.984 - 1.313: 0 1.313 - 1.641: 2 Chirality restraints: 5083 Sorted by residual: chirality pdb=" C1 NAG c 2 " pdb=" O4 NAG c 1 " pdb=" C2 NAG c 2 " pdb=" O5 NAG c 2 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.16e+03 chirality pdb=" C1 NAG b 2 " pdb=" O4 NAG b 1 " pdb=" C2 NAG b 2 " pdb=" O5 NAG b 2 " both_signs ideal model delta sigma weight residual False -2.40 -1.74 -0.66 2.00e-02 2.50e+03 1.09e+03 chirality pdb=" C1 NAG a 1 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG a 1 " pdb=" O5 NAG a 1 " both_signs ideal model delta sigma weight residual False -2.40 -0.76 -1.64 2.00e-01 2.50e+01 6.73e+01 ... (remaining 5080 not shown) Planarity restraints: 5510 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " -0.180 2.00e-02 2.50e+03 2.75e-01 9.45e+02 pdb=" CG ASN C 343 " 0.084 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " -0.070 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " 0.483 2.00e-02 2.50e+03 pdb=" C1 NAG U 1 " -0.317 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.097 2.00e-02 2.50e+03 1.41e-01 2.48e+02 pdb=" CG ASN A 343 " 0.043 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.246 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.163 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.017 2.00e-02 2.50e+03 4.02e-02 2.02e+01 pdb=" CG ASN A 331 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.022 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.072 2.00e-02 2.50e+03 pdb=" C1 NAG b 1 " -0.044 2.00e-02 2.50e+03 ... (remaining 5507 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 305 2.55 - 3.14: 23733 3.14 - 3.72: 46797 3.72 - 4.31: 67688 4.31 - 4.90: 110715 Nonbonded interactions: 249238 Sorted by model distance: nonbonded pdb=" O ILE A 233 " pdb=" O ASN A 234 " model vdw 1.962 3.040 nonbonded pdb=" O ASN L 138 " pdb=" O ASN L 139 " model vdw 2.038 3.040 nonbonded pdb=" O ASN F 138 " pdb=" O ASN F 139 " model vdw 2.039 3.040 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 2.116 3.120 nonbonded pdb=" O SER A 813 " pdb=" OG SER A 813 " model vdw 2.183 3.040 ... (remaining 249233 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 \ 10)) 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 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = chain 'F' selection = chain 'L' } ncs_group { reference = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.650 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 28.360 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 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 0.561 31751 Z= 0.522 Angle : 1.316 66.918 43318 Z= 0.675 Chirality : 0.073 1.641 5083 Planarity : 0.007 0.083 5462 Dihedral : 17.657 89.617 10968 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 1.37 % Allowed : 8.86 % Favored : 89.77 % Rotamer: Outliers : 10.05 % Allowed : 17.31 % Favored : 72.64 % 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: -3.67 (0.11), residues: 3792 helix: -2.16 (0.16), residues: 671 sheet: -1.54 (0.14), residues: 1067 loop : -3.12 (0.11), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1039 TYR 0.027 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/Z covalent geometry : bond 0.00960 / 0.43 (31635) covalent geometry : angle 1.02008 / 0.59 (43016) SS BOND : bond 0.15162 / 9.75 ( 46) SS BOND : angle 11.83739 / 7.59 ( 92) hydrogen bonds : bond 0.20376 / 13.39 ( 1095) hydrogen bonds : angle 8.37750 / 5.66 ( 3189) link_BETA1-4 : bond 0.05381 / 3.74 ( 22) link_BETA1-4 : angle 8.99109 / 5.33 ( 66) link_NAG-ASN : bond 0.02369 / 1.21 ( 48) link_NAG-ASN : angle 9.14459 / 6.28 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 338 poor density : 410 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.2041 (mpp) cc_final: -0.0475 (ptt) REVERT: A 517 LEU cc_start: 0.4881 (OUTLIER) cc_final: 0.4389 (tt) REVERT: A 532 ASN cc_start: 0.6729 (OUTLIER) cc_final: 0.6254 (m-40) REVERT: A 692 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8639 (mm) REVERT: A 698 SER cc_start: 0.8895 (OUTLIER) cc_final: 0.8694 (p) REVERT: A 984 LEU cc_start: 0.7316 (mt) cc_final: 0.6922 (mt) REVERT: B 284 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7767 (t) REVERT: B 569 ILE cc_start: 0.5385 (OUTLIER) cc_final: 0.4790 (mm) REVERT: C 86 PHE cc_start: 0.7734 (OUTLIER) cc_final: 0.7357 (t80) REVERT: C 555 SER cc_start: 0.7036 (OUTLIER) cc_final: 0.6373 (m) REVERT: C 902 MET cc_start: 0.8516 (tpt) cc_final: 0.8296 (mmt) REVERT: C 1050 MET cc_start: 0.8823 (ptm) cc_final: 0.8612 (ptp) REVERT: H 167 VAL cc_start: 0.2355 (t) cc_final: 0.1841 (p) REVERT: L 33 TYR cc_start: 0.5723 (m-80) cc_final: 0.5095 (m-80) REVERT: L 36 TRP cc_start: 0.1184 (m100) cc_final: 0.0790 (m100) REVERT: L 40 LYS cc_start: 0.2280 (mmtt) cc_final: 0.1830 (tptm) REVERT: L 177 SER cc_start: 0.1012 (OUTLIER) cc_final: 0.0365 (t) REVERT: G 103 TYR cc_start: 0.1044 (t80) cc_final: 0.0607 (t80) REVERT: G 160 SER cc_start: -0.2699 (OUTLIER) cc_final: -0.3165 (t) REVERT: F 1 GLU cc_start: 0.4263 (tm-30) cc_final: 0.4006 (pm20) outliers start: 338 outliers final: 75 residues processed: 703 average time/residue: 0.1886 time to fit residues: 213.9403 Evaluate side-chains 267 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 182 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 585 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 673 SER Chi-restraints excluded: chain A residue 692 ILE Chi-restraints excluded: chain A residue 698 SER Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 973 ILE Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1074 ASN Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 417 LYS Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain B residue 555 SER 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 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 1133 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 937 SER Chi-restraints excluded: chain C residue 1027 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 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain H residue 207 SER Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain G residue 160 SER Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 207 SER Chi-restraints excluded: chain F residue 115 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 40.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 49 HIS A 134 GLN A 137 ASN A 188 ASN ** A 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 690 GLN A 703 ASN A 762 GLN A 856 ASN A 901 GLN A 913 GLN A 914 ASN A 919 ASN A 926 GLN A 955 ASN A 957 GLN A 969 ASN A 992 GLN B 115 GLN B 134 GLN B 188 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 487 ASN B 540 ASN B 563 GLN B 901 GLN B 914 ASN B 919 ASN B 920 GLN B 926 GLN B1054 GLN C 49 HIS C 66 HIS ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 134 GLN C 188 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 321 GLN ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN C 641 ASN C 690 GLN C 703 ASN C 751 ASN C 784 GLN C 804 GLN C 901 GLN C 914 ASN C 926 GLN C 935 GLN C 954 GLN C 957 GLN C 969 ASN C 992 GLN C1010 GLN C1071 GLN C1101 HIS H 109 GLN H 168 HIS ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN G 32 ASN G 109 GLN G 168 HIS G 175 GLN F 39 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.157083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.099308 restraints weight = 68043.574| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.67 r_work: 0.3087 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31751 Z= 0.181 Angle : 0.824 15.078 43318 Z= 0.400 Chirality : 0.051 0.402 5083 Planarity : 0.005 0.059 5462 Dihedral : 7.847 59.886 4262 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.15 % Favored : 92.59 % Rotamer: Outliers : 4.46 % Allowed : 19.66 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.12), residues: 3792 helix: -0.15 (0.19), residues: 699 sheet: -0.95 (0.15), residues: 1062 loop : -2.60 (0.12), residues: 2031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG L 109 TYR 0.026 0.002 TYR C 365 PHE 0.024 0.002 PHE B 133 TRP 0.019 0.001 TRP G 158 HIS 0.007 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (31635) covalent geometry : angle 0.77896 / 0.39 (43016) SS BOND : bond 0.00395 / 0.23 ( 46) SS BOND : angle 1.62257 / 1.11 ( 92) hydrogen bonds : bond 0.04755 / 3.03 ( 1095) hydrogen bonds : angle 6.12506 / 4.14 ( 3189) link_BETA1-4 : bond 0.00625 / 0.33 ( 22) link_BETA1-4 : angle 2.37990 / 1.59 ( 66) link_NAG-ASN : bond 0.00990 / 0.54 ( 48) link_NAG-ASN : angle 4.31433 / 2.76 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 206 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1255 (mpp) cc_final: -0.0558 (ptp) REVERT: A 195 LYS cc_start: 0.7682 (OUTLIER) cc_final: 0.7355 (mtmt) REVERT: A 532 ASN cc_start: 0.7754 (OUTLIER) cc_final: 0.6993 (m-40) REVERT: A 654 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8511 (mm-30) REVERT: A 856 ASN cc_start: 0.8630 (OUTLIER) cc_final: 0.8361 (p0) REVERT: A 878 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8969 (tt) REVERT: A 1092 GLU cc_start: 0.7940 (pp20) cc_final: 0.7723 (pp20) REVERT: B 200 TYR cc_start: 0.7205 (m-80) cc_final: 0.6959 (m-80) REVERT: B 403 ARG cc_start: 0.5235 (OUTLIER) cc_final: 0.4941 (ttm170) REVERT: B 473 TYR cc_start: 0.3578 (OUTLIER) cc_final: 0.2844 (t80) REVERT: B 569 ILE cc_start: 0.5643 (OUTLIER) cc_final: 0.5222 (mm) REVERT: B 614 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7796 (t0) REVERT: B 702 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7550 (tm-30) REVERT: B 740 MET cc_start: 0.8935 (tpp) cc_final: 0.8654 (tpp) REVERT: C 158 ARG cc_start: 0.3971 (tpt-90) cc_final: 0.2255 (mmp-170) REVERT: C 353 TRP cc_start: 0.4522 (p-90) cc_final: 0.4280 (p-90) REVERT: C 535 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8567 (mttt) REVERT: H 19 ARG cc_start: 0.4975 (tmm-80) cc_final: 0.4228 (tpt170) REVERT: H 109 GLN cc_start: 0.5292 (mm-40) cc_final: 0.5005 (pp30) REVERT: L 40 LYS cc_start: 0.3151 (mmtt) cc_final: 0.2499 (tptm) REVERT: L 108 LYS cc_start: 0.2411 (OUTLIER) cc_final: 0.1864 (tptt) REVERT: L 146 LYS cc_start: 0.3290 (mttt) cc_final: 0.2689 (tppt) REVERT: G 134 SER cc_start: -0.0868 (OUTLIER) cc_final: -0.1366 (t) outliers start: 150 outliers final: 71 residues processed: 346 average time/residue: 0.1837 time to fit residues: 106.0728 Evaluate side-chains 229 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 147 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 913 GLN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 403 ARG Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 859 THR 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 1094 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 535 LYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 778 THR Chi-restraints excluded: chain C residue 813 SER Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 976 VAL 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain F residue 176 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 193 optimal weight: 2.9990 chunk 181 optimal weight: 8.9990 chunk 247 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 351 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 240 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 275 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 755 GLN A 907 ASN B 422 ASN B 703 ASN B 913 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 ASN G 168 HIS F 138 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096089 restraints weight = 67936.819| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 3.48 r_work: 0.3056 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 31751 Z= 0.158 Angle : 0.712 12.235 43318 Z= 0.345 Chirality : 0.048 0.430 5083 Planarity : 0.005 0.070 5462 Dihedral : 6.519 59.604 4195 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.72 % Favored : 93.12 % Rotamer: Outliers : 4.49 % Allowed : 20.08 % Favored : 75.43 % 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: -1.74 (0.13), residues: 3792 helix: 0.74 (0.20), residues: 689 sheet: -0.48 (0.15), residues: 1065 loop : -2.30 (0.12), residues: 2038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 995 TYR 0.024 0.001 TYR A 365 PHE 0.023 0.002 PHE B 168 TRP 0.017 0.001 TRP F 36 HIS 0.006 0.001 HIS G 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (31635) covalent geometry : angle 0.67765 / 0.34 (43016) SS BOND : bond 0.00537 / 0.39 ( 46) SS BOND : angle 1.44221 / 0.99 ( 92) hydrogen bonds : bond 0.04355 / 2.79 ( 1095) hydrogen bonds : angle 5.61152 / 3.81 ( 3189) link_BETA1-4 : bond 0.00520 / 0.27 ( 22) link_BETA1-4 : angle 2.12817 / 1.45 ( 66) link_NAG-ASN : bond 0.00615 / 0.36 ( 48) link_NAG-ASN : angle 3.46675 / 2.19 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 168 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1097 (mpp) cc_final: -0.1640 (mmt) REVERT: A 195 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7700 (mtpt) REVERT: A 269 TYR cc_start: 0.7689 (m-10) cc_final: 0.7167 (m-10) REVERT: A 351 TYR cc_start: 0.6650 (p90) cc_final: 0.6040 (p90) REVERT: A 532 ASN cc_start: 0.7457 (OUTLIER) cc_final: 0.6684 (m-40) REVERT: A 856 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8264 (p0) REVERT: A 902 MET cc_start: 0.9040 (tpt) cc_final: 0.8790 (mmt) REVERT: A 907 ASN cc_start: 0.9156 (OUTLIER) cc_final: 0.8869 (m110) REVERT: A 988 GLU cc_start: 0.8754 (tp30) cc_final: 0.8405 (tp30) REVERT: A 1005 GLN cc_start: 0.8709 (tt0) cc_final: 0.8239 (mt0) REVERT: A 1142 GLN cc_start: 0.8946 (tm-30) cc_final: 0.8714 (tm-30) REVERT: B 335 LEU cc_start: 0.5536 (OUTLIER) cc_final: 0.5329 (tt) REVERT: B 473 TYR cc_start: 0.3489 (OUTLIER) cc_final: 0.2623 (t80) REVERT: B 569 ILE cc_start: 0.5818 (OUTLIER) cc_final: 0.5437 (mm) REVERT: B 614 ASP cc_start: 0.8561 (OUTLIER) cc_final: 0.7856 (t0) REVERT: B 740 MET cc_start: 0.8951 (tpp) cc_final: 0.8701 (tpp) REVERT: B 780 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8341 (mm-30) REVERT: B 884 SER cc_start: 0.9664 (OUTLIER) cc_final: 0.9362 (p) REVERT: B 976 VAL cc_start: 0.8992 (OUTLIER) cc_final: 0.8561 (p) REVERT: C 86 PHE cc_start: 0.6343 (OUTLIER) cc_final: 0.5884 (t80) REVERT: C 133 PHE cc_start: 0.6313 (m-80) cc_final: 0.6004 (m-80) REVERT: C 158 ARG cc_start: 0.3903 (tpt-90) cc_final: 0.1787 (mmp80) REVERT: C 233 ILE cc_start: 0.6874 (tp) cc_final: 0.6366 (tt) REVERT: C 558 LYS cc_start: 0.7919 (OUTLIER) cc_final: 0.7551 (mmmt) REVERT: C 902 MET cc_start: 0.9082 (tpt) cc_final: 0.8879 (mmt) REVERT: H 19 ARG cc_start: 0.5284 (tmm-80) cc_final: 0.4552 (tpt170) REVERT: H 69 ILE cc_start: 0.1666 (pt) cc_final: 0.1292 (tt) REVERT: H 109 GLN cc_start: 0.5242 (mm-40) cc_final: 0.5006 (pp30) REVERT: L 36 TRP cc_start: 0.1838 (m100) cc_final: 0.1575 (m100) REVERT: L 40 LYS cc_start: 0.2852 (mmtt) cc_final: 0.2051 (tptm) REVERT: L 108 LYS cc_start: 0.2191 (OUTLIER) cc_final: 0.1699 (tptt) REVERT: G 134 SER cc_start: -0.1081 (OUTLIER) cc_final: -0.1626 (t) REVERT: F 138 ASN cc_start: 0.1325 (OUTLIER) cc_final: 0.1075 (t0) outliers start: 151 outliers final: 82 residues processed: 311 average time/residue: 0.1688 time to fit residues: 88.5987 Evaluate side-chains 240 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 143 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LYS Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 518 LEU Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 539 VAL Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 614 ASP Chi-restraints excluded: chain B residue 692 ILE 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 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 558 LYS Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 32 ASN Chi-restraints excluded: chain G residue 124 SER Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Chi-restraints excluded: chain F residue 138 ASN Chi-restraints excluded: chain F residue 176 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 208 optimal weight: 20.0000 chunk 356 optimal weight: 0.0000 chunk 271 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 282 optimal weight: 6.9990 chunk 138 optimal weight: 0.5980 chunk 113 optimal weight: 0.0060 chunk 239 optimal weight: 20.0000 chunk 37 optimal weight: 8.9990 chunk 374 optimal weight: 6.9990 chunk 266 optimal weight: 0.9990 overall best weight: 0.9204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 856 ASN A 907 ASN A 957 GLN A1106 GLN B 414 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN H 175 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 HIS F 38 GLN F 138 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.155715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.097375 restraints weight = 68260.676| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 3.50 r_work: 0.3076 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31751 Z= 0.116 Angle : 0.666 11.303 43318 Z= 0.321 Chirality : 0.046 0.469 5083 Planarity : 0.004 0.052 5462 Dihedral : 6.006 59.997 4189 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.46 % Favored : 93.38 % Rotamer: Outliers : 3.81 % Allowed : 20.85 % Favored : 75.34 % 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: -1.38 (0.13), residues: 3792 helix: 1.29 (0.21), residues: 673 sheet: -0.27 (0.15), residues: 1077 loop : -2.14 (0.12), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.021 0.001 TYR A 365 PHE 0.016 0.001 PHE C 92 TRP 0.009 0.001 TRP F 36 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (31635) covalent geometry : angle 0.63716 / 0.31 (43016) SS BOND : bond 0.00350 / 0.24 ( 46) SS BOND : angle 1.40931 / 0.98 ( 92) hydrogen bonds : bond 0.03648 / 2.33 ( 1095) hydrogen bonds : angle 5.35792 / 3.63 ( 3189) link_BETA1-4 : bond 0.00477 / 0.26 ( 22) link_BETA1-4 : angle 1.97180 / 1.36 ( 66) link_NAG-ASN : bond 0.00495 / 0.30 ( 48) link_NAG-ASN : angle 3.04995 / 1.92 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 165 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1450 (mpp) cc_final: -0.1476 (mmt) REVERT: A 269 TYR cc_start: 0.7502 (m-10) cc_final: 0.6923 (m-10) REVERT: A 532 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.6685 (m-40) REVERT: A 856 ASN cc_start: 0.8694 (OUTLIER) cc_final: 0.8376 (p0) REVERT: A 1005 GLN cc_start: 0.8698 (tt0) cc_final: 0.8362 (mt0) REVERT: A 1142 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8691 (tm-30) REVERT: B 52 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 335 LEU cc_start: 0.5450 (OUTLIER) cc_final: 0.5191 (tt) REVERT: B 473 TYR cc_start: 0.3503 (OUTLIER) cc_final: 0.2645 (t80) REVERT: B 569 ILE cc_start: 0.5612 (OUTLIER) cc_final: 0.5221 (mm) REVERT: B 740 MET cc_start: 0.8858 (tpp) cc_final: 0.8494 (tpp) REVERT: B 780 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8354 (mm-30) REVERT: C 86 PHE cc_start: 0.6463 (OUTLIER) cc_final: 0.6036 (t80) REVERT: C 133 PHE cc_start: 0.6025 (m-80) cc_final: 0.5758 (m-80) REVERT: C 153 MET cc_start: 0.4547 (ptp) cc_final: 0.3334 (ptm) REVERT: C 158 ARG cc_start: 0.4043 (tpt-90) cc_final: 0.3509 (ttt90) REVERT: C 233 ILE cc_start: 0.6858 (tp) cc_final: 0.6398 (tt) REVERT: C 353 TRP cc_start: 0.4424 (p-90) cc_final: 0.4174 (p-90) REVERT: C 740 MET cc_start: 0.8822 (ttt) cc_final: 0.8458 (ttp) REVERT: C 902 MET cc_start: 0.9059 (tpt) cc_final: 0.8813 (mmt) REVERT: H 19 ARG cc_start: 0.5109 (tmm-80) cc_final: 0.4538 (tpt170) REVERT: H 50 VAL cc_start: 0.4231 (OUTLIER) cc_final: 0.3963 (p) REVERT: H 69 ILE cc_start: 0.1707 (pt) cc_final: 0.1329 (tt) REVERT: H 109 GLN cc_start: 0.5199 (mm-40) cc_final: 0.4979 (pp30) REVERT: H 201 ASN cc_start: 0.3476 (OUTLIER) cc_final: 0.3209 (t0) REVERT: L 36 TRP cc_start: 0.1747 (m100) cc_final: 0.1466 (m100) REVERT: L 40 LYS cc_start: 0.2802 (mmtt) cc_final: 0.2126 (tptm) REVERT: L 108 LYS cc_start: 0.2350 (OUTLIER) cc_final: 0.1930 (tptt) REVERT: G 134 SER cc_start: -0.0705 (OUTLIER) cc_final: -0.1272 (t) outliers start: 128 outliers final: 78 residues processed: 286 average time/residue: 0.1774 time to fit residues: 86.2817 Evaluate side-chains 233 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 145 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 453 TYR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL 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 692 ILE 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 859 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 108 LYS Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 104 PHE Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 176 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 338 optimal weight: 40.0000 chunk 324 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 220 optimal weight: 6.9990 chunk 178 optimal weight: 3.9990 chunk 225 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 307 optimal weight: 20.0000 chunk 80 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 487 ASN A 856 ASN A1101 HIS B 30 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN B1135 ASN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 164 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN L 38 GLN G 168 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.152130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.093115 restraints weight = 68295.311| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 3.59 r_work: 0.3006 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 31751 Z= 0.206 Angle : 0.714 11.230 43318 Z= 0.346 Chirality : 0.048 0.445 5083 Planarity : 0.005 0.051 5462 Dihedral : 5.847 59.620 4184 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.91 % Favored : 92.93 % Rotamer: Outliers : 4.19 % Allowed : 21.09 % Favored : 74.72 % 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: -1.29 (0.13), residues: 3792 helix: 1.38 (0.21), residues: 676 sheet: -0.24 (0.15), residues: 1081 loop : -2.09 (0.12), residues: 2035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1107 TYR 0.021 0.002 TYR C 380 PHE 0.030 0.002 PHE G 170 TRP 0.042 0.002 TRP H 36 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (31635) covalent geometry : angle 0.68697 / 0.34 (43016) SS BOND : bond 0.00436 / 0.29 ( 46) SS BOND : angle 1.63567 / 1.18 ( 92) hydrogen bonds : bond 0.04474 / 2.88 ( 1095) hydrogen bonds : angle 5.36000 / 3.63 ( 3189) link_BETA1-4 : bond 0.00484 / 0.24 ( 22) link_BETA1-4 : angle 2.06570 / 1.41 ( 66) link_NAG-ASN : bond 0.00486 / 0.31 ( 48) link_NAG-ASN : angle 2.96802 / 1.92 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 157 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1331 (mpp) cc_final: -0.1539 (mmt) REVERT: A 227 VAL cc_start: 0.8444 (OUTLIER) cc_final: 0.8164 (p) REVERT: A 269 TYR cc_start: 0.7345 (m-10) cc_final: 0.6714 (m-10) REVERT: A 357 ARG cc_start: 0.7325 (ttp80) cc_final: 0.7021 (ttp-170) REVERT: A 517 LEU cc_start: 0.6769 (mm) cc_final: 0.6397 (tt) REVERT: A 532 ASN cc_start: 0.7566 (OUTLIER) cc_final: 0.6881 (m-40) REVERT: A 1005 GLN cc_start: 0.8776 (tt0) cc_final: 0.8450 (tt0) REVERT: A 1142 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8767 (tm-30) REVERT: B 52 GLN cc_start: 0.8534 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 87 ASN cc_start: 0.6955 (m-40) cc_final: 0.5946 (t0) REVERT: B 335 LEU cc_start: 0.5467 (OUTLIER) cc_final: 0.5156 (tt) REVERT: B 473 TYR cc_start: 0.3266 (OUTLIER) cc_final: 0.2612 (t80) REVERT: B 569 ILE cc_start: 0.5702 (OUTLIER) cc_final: 0.5315 (mm) REVERT: B 740 MET cc_start: 0.8951 (tpp) cc_final: 0.8696 (tpp) REVERT: B 780 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8332 (mm-30) REVERT: B 884 SER cc_start: 0.9644 (OUTLIER) cc_final: 0.9384 (p) REVERT: C 86 PHE cc_start: 0.6551 (OUTLIER) cc_final: 0.6027 (t80) REVERT: C 133 PHE cc_start: 0.6433 (m-80) cc_final: 0.5980 (m-80) REVERT: C 153 MET cc_start: 0.4510 (ptp) cc_final: 0.3316 (ptm) REVERT: C 158 ARG cc_start: 0.3987 (tpt-90) cc_final: 0.3522 (ttt90) REVERT: C 233 ILE cc_start: 0.6550 (tp) cc_final: 0.5977 (tt) REVERT: C 353 TRP cc_start: 0.4504 (p-90) cc_final: 0.4182 (p-90) REVERT: C 786 LYS cc_start: 0.8914 (mtmm) cc_final: 0.8693 (mttp) REVERT: C 985 ASP cc_start: 0.8529 (p0) cc_final: 0.8323 (p0) REVERT: H 19 ARG cc_start: 0.5169 (tmm-80) cc_final: 0.4422 (tpt170) REVERT: H 50 VAL cc_start: 0.4002 (OUTLIER) cc_final: 0.3721 (p) REVERT: H 69 ILE cc_start: 0.1894 (pt) cc_final: 0.1564 (tt) REVERT: H 201 ASN cc_start: 0.3349 (OUTLIER) cc_final: 0.3086 (t0) REVERT: L 36 TRP cc_start: 0.1898 (m100) cc_final: 0.1667 (m100) REVERT: L 40 LYS cc_start: 0.2295 (mmtt) cc_final: 0.2035 (tptp) outliers start: 141 outliers final: 92 residues processed: 289 average time/residue: 0.1762 time to fit residues: 87.5514 Evaluate side-chains 244 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 143 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL 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 642 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 878 LEU Chi-restraints excluded: chain B residue 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 86 PHE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 213 VAL Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 990 GLU 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain H residue 201 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 70 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 166 optimal weight: 2.9990 chunk 308 optimal weight: 6.9990 chunk 253 optimal weight: 5.9990 chunk 118 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 chunk 231 optimal weight: 6.9990 chunk 362 optimal weight: 0.0980 chunk 217 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN G 32 ASN ** F 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.151095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.092669 restraints weight = 67398.698| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 3.60 r_work: 0.2987 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31751 Z= 0.192 Angle : 0.696 11.476 43318 Z= 0.337 Chirality : 0.048 0.423 5083 Planarity : 0.004 0.056 5462 Dihedral : 5.623 56.959 4176 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.38 % Favored : 93.49 % Rotamer: Outliers : 3.90 % Allowed : 21.65 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 3792 helix: 1.35 (0.21), residues: 679 sheet: -0.22 (0.15), residues: 1100 loop : -2.01 (0.12), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 765 TYR 0.023 0.001 TYR C 380 PHE 0.022 0.002 PHE A 86 TRP 0.033 0.001 TRP H 36 HIS 0.007 0.001 HIS C 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (31635) covalent geometry : angle 0.66917 / 0.33 (43016) SS BOND : bond 0.00746 / 0.59 ( 46) SS BOND : angle 1.88632 / 1.52 ( 92) hydrogen bonds : bond 0.04343 / 2.80 ( 1095) hydrogen bonds : angle 5.30160 / 3.59 ( 3189) link_BETA1-4 : bond 0.00480 / 0.24 ( 22) link_BETA1-4 : angle 1.95364 / 1.34 ( 66) link_NAG-ASN : bond 0.00437 / 0.27 ( 48) link_NAG-ASN : angle 2.79817 / 1.82 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 150 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1583 (mpp) cc_final: -0.1376 (mmt) REVERT: A 227 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8258 (p) REVERT: A 357 ARG cc_start: 0.7405 (ttp80) cc_final: 0.7132 (ttp-170) REVERT: A 532 ASN cc_start: 0.7608 (OUTLIER) cc_final: 0.6898 (m-40) REVERT: A 1005 GLN cc_start: 0.8838 (tt0) cc_final: 0.8495 (tt0) REVERT: A 1142 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8726 (tm-30) REVERT: B 52 GLN cc_start: 0.8637 (tm-30) cc_final: 0.8340 (tm-30) REVERT: B 87 ASN cc_start: 0.7068 (m-40) cc_final: 0.6168 (t0) REVERT: B 335 LEU cc_start: 0.5274 (OUTLIER) cc_final: 0.4994 (tt) REVERT: B 473 TYR cc_start: 0.3502 (OUTLIER) cc_final: 0.2941 (t80) REVERT: B 569 ILE cc_start: 0.5685 (OUTLIER) cc_final: 0.5317 (mm) REVERT: B 884 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.9400 (p) REVERT: C 153 MET cc_start: 0.4611 (ptp) cc_final: 0.3462 (ptm) REVERT: C 158 ARG cc_start: 0.4299 (tpt-90) cc_final: 0.3465 (ttt90) REVERT: C 982 SER cc_start: 0.8805 (OUTLIER) cc_final: 0.8507 (m) REVERT: H 19 ARG cc_start: 0.4920 (tmm-80) cc_final: 0.4255 (tpt170) REVERT: H 50 VAL cc_start: 0.4356 (OUTLIER) cc_final: 0.3992 (p) REVERT: H 69 ILE cc_start: 0.2273 (pt) cc_final: 0.1907 (tp) outliers start: 131 outliers final: 90 residues processed: 271 average time/residue: 0.1762 time to fit residues: 82.8212 Evaluate side-chains 238 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 140 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 738 CYS 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 884 SER Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 1081 ILE 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 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 50 VAL Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 378 optimal weight: 30.0000 chunk 62 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 370 optimal weight: 0.9980 chunk 282 optimal weight: 3.9990 chunk 178 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 196 optimal weight: 0.0670 chunk 304 optimal weight: 3.9990 chunk 249 optimal weight: 7.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 239 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN L 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.151295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.091766 restraints weight = 67542.637| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.23 r_work: 0.3017 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 31751 Z= 0.156 Angle : 0.684 19.162 43318 Z= 0.330 Chirality : 0.047 0.403 5083 Planarity : 0.004 0.052 5462 Dihedral : 5.346 55.731 4168 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.20 % Favored : 93.64 % Rotamer: Outliers : 3.51 % Allowed : 22.07 % Favored : 74.42 % 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: -1.13 (0.13), residues: 3792 helix: 1.43 (0.21), residues: 678 sheet: -0.12 (0.15), residues: 1123 loop : -1.99 (0.12), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 143 TYR 0.020 0.001 TYR B1067 PHE 0.019 0.001 PHE A 86 TRP 0.037 0.001 TRP H 36 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (31635) covalent geometry : angle 0.65513 / 0.32 (43016) SS BOND : bond 0.00602 / 0.43 ( 46) SS BOND : angle 2.40845 / 1.94 ( 92) hydrogen bonds : bond 0.04086 / 2.65 ( 1095) hydrogen bonds : angle 5.21474 / 3.54 ( 3189) link_BETA1-4 : bond 0.00509 / 0.26 ( 22) link_BETA1-4 : angle 1.88006 / 1.29 ( 66) link_NAG-ASN : bond 0.00429 / 0.28 ( 48) link_NAG-ASN : angle 2.67391 / 1.74 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 154 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.1448 (mpp) cc_final: 0.1063 (pmm) REVERT: A 190 ARG cc_start: 0.7649 (mtt90) cc_final: 0.7320 (mtt90) REVERT: A 517 LEU cc_start: 0.7280 (mm) cc_final: 0.6817 (tt) REVERT: A 532 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.6914 (m-40) REVERT: A 1005 GLN cc_start: 0.8756 (tt0) cc_final: 0.8366 (mt0) REVERT: A 1142 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8713 (tm-30) REVERT: B 52 GLN cc_start: 0.8728 (tm-30) cc_final: 0.8392 (tm-30) REVERT: B 87 ASN cc_start: 0.7097 (m-40) cc_final: 0.6287 (t0) REVERT: B 335 LEU cc_start: 0.5075 (OUTLIER) cc_final: 0.4773 (tt) REVERT: B 464 PHE cc_start: 0.7190 (m-80) cc_final: 0.6802 (t80) REVERT: B 473 TYR cc_start: 0.3638 (OUTLIER) cc_final: 0.3195 (t80) REVERT: B 569 ILE cc_start: 0.5631 (OUTLIER) cc_final: 0.5281 (mm) REVERT: B 780 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8313 (mm-30) REVERT: B 884 SER cc_start: 0.9603 (OUTLIER) cc_final: 0.9379 (p) REVERT: C 153 MET cc_start: 0.4642 (ptp) cc_final: 0.3451 (ptm) REVERT: C 158 ARG cc_start: 0.4353 (tpt-90) cc_final: 0.3404 (ttt90) REVERT: C 233 ILE cc_start: 0.6502 (tp) cc_final: 0.6043 (tt) REVERT: C 982 SER cc_start: 0.8783 (OUTLIER) cc_final: 0.8505 (m) REVERT: H 19 ARG cc_start: 0.4818 (tmm-80) cc_final: 0.4172 (tpt170) REVERT: H 69 ILE cc_start: 0.2295 (pt) cc_final: 0.1854 (tp) outliers start: 118 outliers final: 85 residues processed: 262 average time/residue: 0.1758 time to fit residues: 79.8878 Evaluate side-chains 230 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 139 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 746 SER Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR 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 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS 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 884 SER Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 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 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 990 GLU 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 234 optimal weight: 8.9990 chunk 206 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 377 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 322 optimal weight: 3.9990 chunk 360 optimal weight: 6.9990 chunk 125 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN A1135 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.149514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.095609 restraints weight = 68470.539| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 3.76 r_work: 0.2995 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31751 Z= 0.206 Angle : 0.721 14.980 43318 Z= 0.349 Chirality : 0.048 0.414 5083 Planarity : 0.005 0.056 5462 Dihedral : 5.475 54.540 4165 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.07 % Favored : 92.80 % Rotamer: Outliers : 3.54 % Allowed : 22.01 % Favored : 74.45 % 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: -1.20 (0.13), residues: 3792 helix: 1.26 (0.21), residues: 689 sheet: -0.19 (0.15), residues: 1136 loop : -2.01 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 466 TYR 0.022 0.002 TYR H 180 PHE 0.022 0.002 PHE A 86 TRP 0.033 0.002 TRP H 36 HIS 0.005 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00495 / 0.21 (31635) covalent geometry : angle 0.69326 / 0.34 (43016) SS BOND : bond 0.00437 / 0.29 ( 46) SS BOND : angle 2.34504 / 1.79 ( 92) hydrogen bonds : bond 0.04597 / 2.97 ( 1095) hydrogen bonds : angle 5.29598 / 3.60 ( 3189) link_BETA1-4 : bond 0.00465 / 0.23 ( 22) link_BETA1-4 : angle 1.97572 / 1.35 ( 66) link_NAG-ASN : bond 0.00443 / 0.29 ( 48) link_NAG-ASN : angle 2.74892 / 1.81 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 152 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2057 (mpp) cc_final: 0.1622 (pmm) REVERT: A 357 ARG cc_start: 0.7483 (ttp80) cc_final: 0.7192 (ttm170) REVERT: A 517 LEU cc_start: 0.7256 (mm) cc_final: 0.6938 (tt) REVERT: A 532 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7053 (m-40) REVERT: A 558 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8389 (pttm) REVERT: B 52 GLN cc_start: 0.8731 (tm-30) cc_final: 0.8378 (tm-30) REVERT: B 87 ASN cc_start: 0.7021 (m-40) cc_final: 0.6286 (t0) REVERT: B 335 LEU cc_start: 0.5097 (OUTLIER) cc_final: 0.4871 (tt) REVERT: B 464 PHE cc_start: 0.7354 (OUTLIER) cc_final: 0.7027 (t80) REVERT: B 473 TYR cc_start: 0.3385 (OUTLIER) cc_final: 0.3135 (t80) REVERT: B 569 ILE cc_start: 0.5739 (OUTLIER) cc_final: 0.5334 (mm) REVERT: B 780 GLU cc_start: 0.8503 (mt-10) cc_final: 0.8298 (mm-30) REVERT: C 153 MET cc_start: 0.5109 (ptp) cc_final: 0.3744 (ptm) REVERT: C 158 ARG cc_start: 0.4753 (tpt-90) cc_final: 0.3651 (ttt90) REVERT: C 982 SER cc_start: 0.8790 (OUTLIER) cc_final: 0.8521 (m) REVERT: L 146 LYS cc_start: 0.3551 (mttt) cc_final: 0.2874 (tppt) outliers start: 119 outliers final: 90 residues processed: 263 average time/residue: 0.1805 time to fit residues: 81.2593 Evaluate side-chains 234 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 137 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 464 PHE Chi-restraints excluded: chain B residue 473 TYR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS 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 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 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 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 50 TYR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 202 optimal weight: 9.9990 chunk 46 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 207 optimal weight: 7.9990 chunk 88 optimal weight: 0.7980 chunk 310 optimal weight: 10.0000 chunk 343 optimal weight: 30.0000 chunk 378 optimal weight: 30.0000 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 188 ASN A1005 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1002 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.148642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.093598 restraints weight = 68540.161| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.45 r_work: 0.2966 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 31751 Z= 0.238 Angle : 0.740 12.684 43318 Z= 0.359 Chirality : 0.049 0.416 5083 Planarity : 0.005 0.057 5462 Dihedral : 5.566 53.840 4165 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.09 % Favored : 92.77 % Rotamer: Outliers : 3.12 % Allowed : 22.67 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.13), residues: 3792 helix: 1.15 (0.20), residues: 691 sheet: -0.22 (0.15), residues: 1128 loop : -2.01 (0.13), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1039 TYR 0.036 0.002 TYR H 180 PHE 0.022 0.002 PHE A 86 TRP 0.045 0.002 TRP H 36 HIS 0.006 0.001 HIS B1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.24 (31635) covalent geometry : angle 0.71158 / 0.35 (43016) SS BOND : bond 0.00408 / 0.26 ( 46) SS BOND : angle 2.48367 / 1.93 ( 92) hydrogen bonds : bond 0.04743 / 3.05 ( 1095) hydrogen bonds : angle 5.33761 / 3.62 ( 3189) link_BETA1-4 : bond 0.00435 / 0.23 ( 22) link_BETA1-4 : angle 1.98494 / 1.36 ( 66) link_NAG-ASN : bond 0.00442 / 0.29 ( 48) link_NAG-ASN : angle 2.79281 / 1.84 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 142 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2541 (OUTLIER) cc_final: -0.0652 (mmt) REVERT: A 216 LEU cc_start: 0.7332 (OUTLIER) cc_final: 0.7043 (tt) REVERT: A 517 LEU cc_start: 0.7446 (mm) cc_final: 0.7059 (tt) REVERT: A 532 ASN cc_start: 0.7490 (OUTLIER) cc_final: 0.7038 (m-40) REVERT: A 558 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8432 (pttm) REVERT: B 87 ASN cc_start: 0.7174 (m-40) cc_final: 0.6510 (t0) REVERT: B 569 ILE cc_start: 0.5857 (OUTLIER) cc_final: 0.5492 (mm) REVERT: C 153 MET cc_start: 0.4950 (ptp) cc_final: 0.4582 (ptp) REVERT: C 982 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8574 (m) REVERT: H 19 ARG cc_start: 0.5189 (tmm-80) cc_final: 0.4486 (tpt170) REVERT: L 146 LYS cc_start: 0.3547 (mttt) cc_final: 0.2875 (tppt) REVERT: G 134 SER cc_start: -0.1650 (OUTLIER) cc_final: -0.2144 (t) outliers start: 105 outliers final: 90 residues processed: 238 average time/residue: 0.1728 time to fit residues: 71.5032 Evaluate side-chains 228 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 131 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1077 THR Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 291 CYS Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS 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 912 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1133 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 98 SER Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 576 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 791 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 146 optimal weight: 9.9990 chunk 338 optimal weight: 30.0000 chunk 113 optimal weight: 7.9990 chunk 296 optimal weight: 0.1980 chunk 56 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 137 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 236 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 388 ASN C 751 ASN C1002 GLN ** H 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.150575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.096799 restraints weight = 67789.773| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 3.47 r_work: 0.3047 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 31751 Z= 0.126 Angle : 0.662 11.860 43318 Z= 0.319 Chirality : 0.046 0.377 5083 Planarity : 0.004 0.061 5462 Dihedral : 5.220 52.743 4165 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.96 % Favored : 93.93 % Rotamer: Outliers : 2.41 % Allowed : 23.29 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.13), residues: 3792 helix: 1.53 (0.21), residues: 681 sheet: -0.04 (0.15), residues: 1116 loop : -1.87 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 355 TYR 0.032 0.001 TYR H 180 PHE 0.022 0.001 PHE B 168 TRP 0.036 0.001 TRP H 36 HIS 0.003 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (31635) covalent geometry : angle 0.63758 / 0.31 (43016) SS BOND : bond 0.00319 / 0.19 ( 46) SS BOND : angle 2.11158 / 1.73 ( 92) hydrogen bonds : bond 0.03791 / 2.44 ( 1095) hydrogen bonds : angle 5.11164 / 3.46 ( 3189) link_BETA1-4 : bond 0.00497 / 0.26 ( 22) link_BETA1-4 : angle 1.70763 / 1.18 ( 66) link_NAG-ASN : bond 0.00409 / 0.26 ( 48) link_NAG-ASN : angle 2.50126 / 1.64 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 148 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 MET cc_start: 0.2687 (OUTLIER) cc_final: 0.2255 (pmm) REVERT: A 216 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.6921 (tt) REVERT: A 517 LEU cc_start: 0.7505 (mm) cc_final: 0.7111 (tt) REVERT: A 532 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7050 (m-40) REVERT: A 722 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9208 (t) REVERT: A 1142 GLN cc_start: 0.8947 (tm-30) cc_final: 0.8677 (tm-30) REVERT: B 66 HIS cc_start: 0.6184 (OUTLIER) cc_final: 0.5858 (t-90) REVERT: C 153 MET cc_start: 0.5094 (ptp) cc_final: 0.3417 (ptm) REVERT: C 158 ARG cc_start: 0.4299 (tpt-90) cc_final: 0.3683 (ttt90) REVERT: C 380 TYR cc_start: 0.3556 (OUTLIER) cc_final: 0.2873 (m-80) REVERT: C 423 TYR cc_start: 0.6198 (t80) cc_final: 0.5748 (t80) REVERT: C 982 SER cc_start: 0.8786 (OUTLIER) cc_final: 0.8562 (m) REVERT: H 19 ARG cc_start: 0.5210 (tmm-80) cc_final: 0.4390 (mmt180) REVERT: H 109 GLN cc_start: 0.5132 (mm-40) cc_final: 0.4751 (tm-30) REVERT: L 146 LYS cc_start: 0.3654 (mttt) cc_final: 0.2808 (tppt) REVERT: G 134 SER cc_start: -0.2233 (OUTLIER) cc_final: -0.2663 (t) outliers start: 81 outliers final: 69 residues processed: 222 average time/residue: 0.1803 time to fit residues: 68.7795 Evaluate side-chains 216 residues out of total 3362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 139 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 LEU Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 532 ASN Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 590 CYS Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 649 CYS Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 722 VAL Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 66 HIS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 135 PHE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 236 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 597 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 692 ILE Chi-restraints excluded: chain B residue 738 CYS 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 1081 ILE Chi-restraints excluded: chain B residue 1133 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 98 SER Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 573 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 982 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 C residue 1136 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 164 THR Chi-restraints excluded: chain H residue 199 ILE Chi-restraints excluded: chain L residue 115 SER Chi-restraints excluded: chain L residue 177 SER Chi-restraints excluded: chain L residue 198 THR Chi-restraints excluded: chain G residue 134 SER Chi-restraints excluded: chain G residue 146 VAL Chi-restraints excluded: chain G residue 164 THR Chi-restraints excluded: chain F residue 68 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 159 optimal weight: 0.9990 chunk 310 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 262 optimal weight: 0.6980 chunk 301 optimal weight: 30.0000 chunk 139 optimal weight: 0.0040 chunk 214 optimal weight: 6.9990 overall best weight: 2.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 955 ASN A 957 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 175 GLN ** L 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.149903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.094016 restraints weight = 67950.904| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.58 r_work: 0.2991 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 31751 Z= 0.153 Angle : 0.672 11.462 43318 Z= 0.324 Chirality : 0.047 0.372 5083 Planarity : 0.004 0.056 5462 Dihedral : 5.171 51.809 4160 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.33 % Favored : 93.57 % Rotamer: Outliers : 2.77 % Allowed : 22.87 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.13), residues: 3792 helix: 1.61 (0.21), residues: 679 sheet: -0.04 (0.15), residues: 1117 loop : -1.83 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 765 TYR 0.035 0.001 TYR H 180 PHE 0.020 0.001 PHE A 86 TRP 0.036 0.001 TRP H 36 HIS 0.004 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.15 (31635) covalent geometry : angle 0.64713 / 0.32 (43016) SS BOND : bond 0.00333 / 0.20 ( 46) SS BOND : angle 2.11250 / 1.70 ( 92) hydrogen bonds : bond 0.04017 / 2.59 ( 1095) hydrogen bonds : angle 5.09091 / 3.45 ( 3189) link_BETA1-4 : bond 0.00457 / 0.23 ( 22) link_BETA1-4 : angle 1.72820 / 1.19 ( 66) link_NAG-ASN : bond 0.00381 / 0.24 ( 48) link_NAG-ASN : angle 2.55859 / 1.69 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9289.46 seconds wall clock time: 159 minutes 30.88 seconds (9570.88 seconds total)