Starting phenix.real_space_refine on Sun Jun 22 13:23:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy7_60558/06_2025/8zy7_60558.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy7_60558/06_2025/8zy7_60558.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy7_60558/06_2025/8zy7_60558.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy7_60558/06_2025/8zy7_60558.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy7_60558/06_2025/8zy7_60558.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy7_60558/06_2025/8zy7_60558.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 126 5.16 5 C 16436 2.51 5 N 4199 2.21 5 O 5129 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25890 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8306 Classifications: {'peptide': 1065} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 45, 'TRANS': 1019} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 8309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8309 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 45, 'TRANS': 1019} Chain breaks: 3 Chain: "C" Number of atoms: 8309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1065, 8309 Classifications: {'peptide': 1065} Link IDs: {'PTRANS': 45, 'TRANS': 1019} Chain breaks: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 14.40, per 1000 atoms: 0.56 Number of scatterers: 25890 At special positions: 0 Unit cell: (131.4, 146.183, 183.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 126 16.00 O 5129 8.00 N 4199 7.00 C 16436 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 163 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 497 " distance=2.03 Simple disulfide: pdb=" SG CYS A 510 " - pdb=" SG CYS A 562 " distance=2.03 Simple disulfide: pdb=" SG CYS A 589 " - pdb=" SG CYS A 621 " distance=2.03 Simple disulfide: pdb=" SG CYS A 634 " - pdb=" SG CYS A 643 " distance=2.03 Simple disulfide: pdb=" SG CYS A 706 " - pdb=" SG CYS A 728 " distance=2.03 Simple disulfide: pdb=" SG CYS A 711 " - pdb=" SG CYS A 717 " distance=2.03 Simple disulfide: pdb=" SG CYS A 808 " - pdb=" SG CYS A 819 " distance=2.03 Simple disulfide: pdb=" SG CYS A1000 " - pdb=" SG CYS A1011 " distance=2.03 Simple disulfide: pdb=" SG CYS A1050 " - pdb=" SG CYS A1094 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 163 " distance=2.02 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.02 Simple disulfide: pdb=" SG CYS B 327 " - pdb=" SG CYS B 352 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 497 " distance=2.03 Simple disulfide: pdb=" SG CYS B 510 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 589 " - pdb=" SG CYS B 621 " distance=2.03 Simple disulfide: pdb=" SG CYS B 634 " - pdb=" SG CYS B 643 " distance=2.03 Simple disulfide: pdb=" SG CYS B 706 " - pdb=" SG CYS B 728 " distance=2.03 Simple disulfide: pdb=" SG CYS B 711 " - pdb=" SG CYS B 717 " distance=2.03 Simple disulfide: pdb=" SG CYS B 808 " - pdb=" SG CYS B 819 " distance=2.03 Simple disulfide: pdb=" SG CYS B1000 " - pdb=" SG CYS B1011 " distance=2.03 Simple disulfide: pdb=" SG CYS B1050 " - pdb=" SG CYS B1094 " distance=2.04 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 163 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.02 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 497 " distance=2.03 Simple disulfide: pdb=" SG CYS C 510 " - pdb=" SG CYS C 562 " distance=2.03 Simple disulfide: pdb=" SG CYS C 589 " - pdb=" SG CYS C 621 " distance=2.03 Simple disulfide: pdb=" SG CYS C 634 " - pdb=" SG CYS C 643 " distance=2.03 Simple disulfide: pdb=" SG CYS C 706 " - pdb=" SG CYS C 728 " distance=2.03 Simple disulfide: pdb=" SG CYS C 711 " - pdb=" SG CYS C 717 " distance=2.03 Simple disulfide: pdb=" SG CYS C 808 " - pdb=" SG CYS C 819 " distance=2.03 Simple disulfide: pdb=" SG CYS C1000 " - pdb=" SG CYS C1011 " distance=2.03 Simple disulfide: pdb=" SG CYS C1050 " - pdb=" SG CYS C1094 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 125 " " NAG A1302 " - " ASN A 322 " " NAG A1303 " - " ASN A 588 " " NAG A1304 " - " ASN A 629 " " NAG A1305 " - " ASN A 273 " " NAG A1306 " - " ASN A 115 " " NAG A1307 " - " ASN A 65 " " NAG A1308 " - " ASN A 162 " " NAG A1309 " - " ASN A 298 " " NAG A1310 " - " ASN A 677 " " NAG A1311 " - " ASN A 769 " " NAG B1301 " - " ASN B 125 " " NAG B1302 " - " ASN B 322 " " NAG B1303 " - " ASN B 588 " " NAG B1304 " - " ASN B 629 " " NAG B1305 " - " ASN B 273 " " NAG B1306 " - " ASN B 115 " " NAG B1307 " - " ASN B 65 " " NAG B1308 " - " ASN B 162 " " NAG B1309 " - " ASN B 298 " " NAG B1310 " - " ASN B 677 " " NAG B1311 " - " ASN B 769 " " NAG C1301 " - " ASN C 125 " " NAG C1302 " - " ASN C 322 " " NAG C1303 " - " ASN C 588 " " NAG C1304 " - " ASN C 629 " " NAG C1305 " - " ASN C 273 " " NAG C1306 " - " ASN C 115 " " NAG C1307 " - " ASN C 65 " " NAG C1309 " - " ASN C 298 " " NAG C1310 " - " ASN C 677 " " NAG C1311 " - " ASN C 769 " " NAG D 1 " - " ASN A 334 " " NAG E 1 " - " ASN A 361 " " NAG F 1 " - " ASN A 231 " " NAG G 1 " - " ASN A 685 " " NAG H 1 " - " ASN A1042 " " NAG I 1 " - " ASN A1102 " " NAG J 1 " - " ASN B 334 " " NAG K 1 " - " ASN B 361 " " NAG L 1 " - " ASN B 231 " " NAG M 1 " - " ASN B 685 " " NAG N 1 " - " ASN B1042 " " NAG O 1 " - " ASN B1102 " " NAG P 1 " - " ASN C 334 " " NAG Q 1 " - " ASN C 361 " " NAG R 1 " - " ASN C 231 " " NAG S 1 " - " ASN C 685 " " NAG T 1 " - " ASN C1042 " " NAG U 1 " - " ASN C1102 " Time building additional restraints: 5.95 Conformation dependent library (CDL) restraints added in 3.2 seconds 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6024 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 49 sheets defined 23.2% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 146 through 150 removed outlier: 3.571A pdb=" N GLY A 149 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.524A pdb=" N VAL A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 333' Processing helix chain 'A' and resid 340 through 344 removed outlier: 3.540A pdb=" N TRP A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 396 through 401 removed outlier: 4.725A pdb=" N ARG A 399 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 477 Processing helix chain 'A' and resid 591 through 596 Processing helix chain 'A' and resid 605 through 609 Processing helix chain 'A' and resid 705 through 711 removed outlier: 3.540A pdb=" N TYR A 709 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 722 removed outlier: 3.945A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU A 722 " --> pdb=" O SER A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 750 removed outlier: 3.978A pdb=" N THR A 729 " --> pdb=" O GLY A 725 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN A 730 " --> pdb=" O SER A 726 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU A 731 " --> pdb=" O PHE A 727 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER A 736 " --> pdb=" O ASN A 732 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 740 " --> pdb=" O SER A 736 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU A 741 " --> pdb=" O GLY A 737 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS A 744 " --> pdb=" O VAL A 740 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N THR A 746 " --> pdb=" O GLN A 742 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 749 " --> pdb=" O ASN A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 791 Processing helix chain 'A' and resid 805 through 810 removed outlier: 3.885A pdb=" N LEU A 809 " --> pdb=" O TYR A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 824 Processing helix chain 'A' and resid 834 through 852 Processing helix chain 'A' and resid 865 through 876 Processing helix chain 'A' and resid 881 through 887 removed outlier: 3.977A pdb=" N TYR A 885 " --> pdb=" O GLN A 881 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU A 886 " --> pdb=" O ASN A 882 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 909 removed outlier: 3.530A pdb=" N LEU A 906 " --> pdb=" O ILE A 902 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR A 907 " --> pdb=" O GLN A 903 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR A 909 " --> pdb=" O SER A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 933 removed outlier: 3.610A pdb=" N ASN A 923 " --> pdb=" O VAL A 919 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 953 through 1001 removed outlier: 4.286A pdb=" N GLU A 958 " --> pdb=" O LYS A 954 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL A 959 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N GLN A 960 " --> pdb=" O GLU A 956 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG A 963 " --> pdb=" O VAL A 959 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN A 970 " --> pdb=" O THR A 966 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER A 971 " --> pdb=" O GLY A 967 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 329 through 334 Processing helix chain 'B' and resid 340 through 344 removed outlier: 3.512A pdb=" N TRP B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 360 removed outlier: 3.938A pdb=" N VAL B 358 " --> pdb=" O ASP B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 401 removed outlier: 4.444A pdb=" N ARG B 399 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 474 through 477 Processing helix chain 'B' and resid 591 through 596 Processing helix chain 'B' and resid 714 through 719 Processing helix chain 'B' and resid 720 through 724 removed outlier: 3.558A pdb=" N GLN B 723 " --> pdb=" O LEU B 720 " (cutoff:3.500A) Processing helix chain 'B' and resid 725 through 750 removed outlier: 4.193A pdb=" N THR B 729 " --> pdb=" O GLY B 725 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 730 " --> pdb=" O SER B 726 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU B 731 " --> pdb=" O PHE B 727 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA B 734 " --> pdb=" O GLN B 730 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER B 736 " --> pdb=" O ASN B 732 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLY B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 739 " --> pdb=" O LEU B 735 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL B 740 " --> pdb=" O SER B 736 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 741 " --> pdb=" O GLY B 737 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N THR B 746 " --> pdb=" O GLN B 742 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 747 " --> pdb=" O ASP B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 791 Processing helix chain 'B' and resid 811 through 815 removed outlier: 3.669A pdb=" N ALA B 814 " --> pdb=" O GLY B 811 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 removed outlier: 3.598A pdb=" N ALA B 820 " --> pdb=" O ASP B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 852 Processing helix chain 'B' and resid 865 through 876 Processing helix chain 'B' and resid 881 through 887 removed outlier: 3.837A pdb=" N TYR B 885 " --> pdb=" O GLN B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 887 through 909 removed outlier: 3.510A pdb=" N LEU B 906 " --> pdb=" O ILE B 902 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N THR B 907 " --> pdb=" O GLN B 903 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 908 " --> pdb=" O GLU B 904 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR B 909 " --> pdb=" O SER B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 933 removed outlier: 3.800A pdb=" N VAL B 919 " --> pdb=" O LYS B 915 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL B 920 " --> pdb=" O LEU B 916 " (cutoff:3.500A) Processing helix chain 'B' and resid 934 through 936 No H-bonds generated for 'chain 'B' and resid 934 through 936' Processing helix chain 'B' and resid 945 through 950 Processing helix chain 'B' and resid 957 through 1001 removed outlier: 3.705A pdb=" N ASP B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ARG B 963 " --> pdb=" O VAL B 959 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN B 970 " --> pdb=" O THR B 966 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 971 " --> pdb=" O GLY B 967 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B1001 " --> pdb=" O MET B 997 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 340 through 344 removed outlier: 3.641A pdb=" N TRP C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 360 removed outlier: 3.972A pdb=" N VAL C 358 " --> pdb=" O ASP C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 380 removed outlier: 3.551A pdb=" N ASP C 380 " --> pdb=" O LYS C 377 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 396 through 401 removed outlier: 4.378A pdb=" N ARG C 399 " --> pdb=" O SER C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 474 through 477 Processing helix chain 'C' and resid 591 through 597 Processing helix chain 'C' and resid 605 through 609 Processing helix chain 'C' and resid 714 through 722 removed outlier: 3.810A pdb=" N LEU C 720 " --> pdb=" O GLU C 716 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU C 722 " --> pdb=" O SER C 718 " (cutoff:3.500A) Processing helix chain 'C' and resid 723 through 727 removed outlier: 5.318A pdb=" N SER C 726 " --> pdb=" O GLN C 723 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 750 removed outlier: 3.596A pdb=" N ALA C 734 " --> pdb=" O GLN C 730 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 736 " --> pdb=" O ASN C 732 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU C 741 " --> pdb=" O GLY C 737 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP C 743 " --> pdb=" O ALA C 739 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS C 744 " --> pdb=" O VAL C 740 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR C 746 " --> pdb=" O GLN C 742 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN C 747 " --> pdb=" O ASP C 743 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL C 749 " --> pdb=" O ASN C 745 " (cutoff:3.500A) Processing helix chain 'C' and resid 784 through 791 Processing helix chain 'C' and resid 805 through 811 removed outlier: 4.284A pdb=" N GLY C 811 " --> pdb=" O ASP C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 818 through 824 Processing helix chain 'C' and resid 834 through 852 Processing helix chain 'C' and resid 865 through 875 Processing helix chain 'C' and resid 881 through 886 removed outlier: 4.047A pdb=" N TYR C 885 " --> pdb=" O GLN C 881 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 886 " --> pdb=" O ASN C 882 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 881 through 886' Processing helix chain 'C' and resid 887 through 909 removed outlier: 4.201A pdb=" N THR C 907 " --> pdb=" O GLN C 903 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 908 " --> pdb=" O GLU C 904 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR C 909 " --> pdb=" O SER C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 933 removed outlier: 3.833A pdb=" N VAL C 919 " --> pdb=" O LYS C 915 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL C 920 " --> pdb=" O LEU C 916 " (cutoff:3.500A) Processing helix chain 'C' and resid 934 through 936 No H-bonds generated for 'chain 'C' and resid 934 through 936' Processing helix chain 'C' and resid 945 through 950 removed outlier: 3.531A pdb=" N LEU C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 1001 removed outlier: 3.513A pdb=" N ASP C 962 " --> pdb=" O GLU C 958 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG C 963 " --> pdb=" O VAL C 959 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN C 970 " --> pdb=" O THR C 966 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER C 971 " --> pdb=" O GLY C 967 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL C1001 " --> pdb=" O MET C 997 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 removed outlier: 3.701A pdb=" N SER A 64 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 8.535A pdb=" N ASN A 65 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 260 " --> pdb=" O ASN A 65 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR A 67 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL A 258 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 255 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 93 " --> pdb=" O PHE A 191 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 224 " --> pdb=" O VAL A 200 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLN A 202 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 59 removed outlier: 3.517A pdb=" N ASP A 57 " --> pdb=" O SER A 264 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP A 278 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 104 through 108 removed outlier: 3.940A pdb=" N GLY A 106 " --> pdb=" O VAL A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 removed outlier: 3.652A pdb=" N TYR A 165 " --> pdb=" O VAL A 133 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N TYR A 135 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS A 163 " --> pdb=" O TYR A 135 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.819A pdb=" N TYR A 584 " --> pdb=" O CYS A 621 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N CYS A 621 " --> pdb=" O TYR A 584 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 316 through 319 removed outlier: 5.174A pdb=" N ASP A 546 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER A 547 " --> pdb=" O GLY A 538 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 348 through 349 removed outlier: 3.939A pdb=" N VAL A 386 " --> pdb=" O ILE A 349 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 387 " --> pdb=" O SER A 486 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER A 486 " --> pdb=" O TYR A 387 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.569A pdb=" N CYS A 352 " --> pdb=" O CYS A 497 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 435 through 440 Processing sheet with id=AB1, first strand: chain 'A' and resid 626 through 627 removed outlier: 6.366A pdb=" N GLU A 626 " --> pdb=" O ALA A 662 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N THR A 664 " --> pdb=" O GLU A 626 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 669 through 671 removed outlier: 6.996A pdb=" N ALA A 669 " --> pdb=" O MET C 756 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 680 through 681 removed outlier: 3.857A pdb=" N THR A1044 " --> pdb=" O SER A1065 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA A1046 " --> pdb=" O PHE A1063 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE A1063 " --> pdb=" O ALA A1046 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 696 removed outlier: 6.238A pdb=" N TYR A1035 " --> pdb=" O HIS A1016 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N HIS A1016 " --> pdb=" O TYR A1035 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 755 through 757 removed outlier: 5.574A pdb=" N MET A 756 " --> pdb=" O ASN B 671 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 764 through 765 removed outlier: 3.653A pdb=" N PHE A 768 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1088 through 1091 removed outlier: 3.547A pdb=" N CYS A1050 " --> pdb=" O ILE A1101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 32 through 34 removed outlier: 3.562A pdb=" N THR B 67 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL B 258 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 93 " --> pdb=" O PHE B 191 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 191 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU B 99 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASP B 185 " --> pdb=" O GLU B 99 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 224 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLN B 202 " --> pdb=" O PRO B 222 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 54 through 59 removed outlier: 3.950A pdb=" N ASP B 278 " --> pdb=" O SER B 269 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 107 through 108 removed outlier: 3.562A pdb=" N VAL B 108 " --> pdb=" O ARG B 236 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 122 through 124 removed outlier: 3.709A pdb=" N TYR B 165 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N TYR B 135 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N CYS B 163 " --> pdb=" O TYR B 135 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 150 through 152 removed outlier: 3.613A pdb=" N VAL B 152 " --> pdb=" O THR B 145 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 145 " --> pdb=" O VAL B 152 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N TYR B 144 " --> pdb=" O MET B 241 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 302 through 306 removed outlier: 4.885A pdb=" N VAL B 567 " --> pdb=" O THR B 306 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N TYR B 584 " --> pdb=" O CYS B 621 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N CYS B 621 " --> pdb=" O TYR B 584 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY B 620 " --> pdb=" O THR B 617 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 348 through 349 removed outlier: 3.794A pdb=" N VAL B 386 " --> pdb=" O ILE B 349 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 387 " --> pdb=" O SER B 486 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N SER B 486 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N CYS B 423 " --> pdb=" O LEU B 485 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 352 through 353 removed outlier: 6.506A pdb=" N CYS B 352 " --> pdb=" O CYS B 497 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 435 through 439 removed outlier: 3.562A pdb=" N TYR B 437 " --> pdb=" O TYR B 467 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 510 through 515 removed outlier: 3.531A pdb=" N GLY B 520 " --> pdb=" O PHE B 513 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG B 555 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASP B 550 " --> pdb=" O ARG B 555 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ASP B 546 " --> pdb=" O ILE B 559 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 547 " --> pdb=" O GLY B 538 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 626 through 627 removed outlier: 6.487A pdb=" N GLU B 626 " --> pdb=" O ALA B 662 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N THR B 664 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE B 642 " --> pdb=" O ILE B 638 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 680 through 681 removed outlier: 3.932A pdb=" N THR B1044 " --> pdb=" O SER B1065 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN B1074 " --> pdb=" O SER B1079 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N SER B1079 " --> pdb=" O GLN B1074 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 686 through 696 removed outlier: 3.677A pdb=" N MET B1018 " --> pdb=" O VAL B1033 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYR B1035 " --> pdb=" O HIS B1016 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N HIS B1016 " --> pdb=" O TYR B1035 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD5, first strand: chain 'B' and resid 755 through 757 Processing sheet with id=AD6, first strand: chain 'B' and resid 764 through 765 removed outlier: 3.593A pdb=" N PHE B 768 " --> pdb=" O PHE B 765 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1088 through 1091 Processing sheet with id=AD8, first strand: chain 'C' and resid 32 through 34 removed outlier: 8.473A pdb=" N ASN C 65 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN C 260 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 67 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 258 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 93 " --> pdb=" O PHE C 191 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU C 99 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP C 185 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N THR C 184 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU C 224 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLN C 202 " --> pdb=" O PRO C 222 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 54 through 59 removed outlier: 7.636A pdb=" N THR C 265 " --> pdb=" O ASP C 281 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N ASP C 281 " --> pdb=" O THR C 265 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N MET C 267 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA C 279 " --> pdb=" O MET C 267 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER C 269 " --> pdb=" O VAL C 277 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 143 through 145 removed outlier: 3.759A pdb=" N MET C 241 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLY C 106 " --> pdb=" O VAL C 238 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG C 132 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE C 131 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASP C 166 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL C 133 " --> pdb=" O THR C 164 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 135 " --> pdb=" O ASN C 162 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ASN C 162 " --> pdb=" O TYR C 135 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 302 through 305 removed outlier: 3.610A pdb=" N CYS C 621 " --> pdb=" O TYR C 584 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 316 through 319 Processing sheet with id=AE4, first strand: chain 'C' and resid 316 through 319 removed outlier: 4.188A pdb=" N SER C 547 " --> pdb=" O GLY C 538 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 348 through 349 removed outlier: 3.965A pdb=" N VAL C 386 " --> pdb=" O ILE C 349 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER C 486 " --> pdb=" O TYR C 387 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 352 through 353 removed outlier: 6.236A pdb=" N CYS C 352 " --> pdb=" O CYS C 497 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 435 through 440 Processing sheet with id=AE8, first strand: chain 'C' and resid 626 through 627 removed outlier: 6.408A pdb=" N GLU C 626 " --> pdb=" O ALA C 662 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N THR C 664 " --> pdb=" O GLU C 626 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 680 through 681 removed outlier: 3.869A pdb=" N THR C1044 " --> pdb=" O SER C1065 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA C1046 " --> pdb=" O PHE C1063 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE C1063 " --> pdb=" O ALA C1046 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 686 through 696 removed outlier: 6.933A pdb=" N GLY C1027 " --> pdb=" O SER C1023 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER C1023 " --> pdb=" O GLY C1027 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C1029 " --> pdb=" O PRO C1021 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LEU C1031 " --> pdb=" O SER C1019 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER C1019 " --> pdb=" O LEU C1031 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL C1033 " --> pdb=" O LEU C1017 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TYR C1015 " --> pdb=" O TYR C1035 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 701 through 704 removed outlier: 4.497A pdb=" N LYS C 701 " --> pdb=" O LEU C 829 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 764 through 765 removed outlier: 3.577A pdb=" N PHE C 768 " --> pdb=" O PHE C 765 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1049 through 1050 824 hydrogen bonds defined for protein. 2226 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: 11.43 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7716 1.34 - 1.46: 5714 1.46 - 1.58: 12847 1.58 - 1.70: 0 1.70 - 1.82: 171 Bond restraints: 26448 Sorted by residual: bond pdb=" N VAL C 473 " pdb=" CA VAL C 473 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.23e-02 6.61e+03 7.06e+00 bond pdb=" N LEU C 475 " pdb=" CA LEU C 475 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.20e-02 6.94e+03 5.24e+00 bond pdb=" C4 NAG T 1 " pdb=" O4 NAG T 1 " ideal model delta sigma weight residual 1.409 1.444 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" C VAL C 473 " pdb=" N PRO C 474 " ideal model delta sigma weight residual 1.331 1.353 -0.022 1.27e-02 6.20e+03 3.09e+00 bond pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 1.409 1.444 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 26443 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 35634 2.45 - 4.90: 304 4.90 - 7.35: 38 7.35 - 9.80: 9 9.80 - 12.25: 5 Bond angle restraints: 35990 Sorted by residual: angle pdb=" C LYS C 170 " pdb=" CA LYS C 170 " pdb=" CB LYS C 170 " ideal model delta sigma weight residual 116.54 111.20 5.34 1.15e+00 7.56e-01 2.16e+01 angle pdb=" N LYS B 793 " pdb=" CA LYS B 793 " pdb=" C LYS B 793 " ideal model delta sigma weight residual 114.56 108.98 5.58 1.27e+00 6.20e-01 1.93e+01 angle pdb=" C3 NAG N 1 " pdb=" C4 NAG N 1 " pdb=" O4 NAG N 1 " ideal model delta sigma weight residual 107.29 119.54 -12.25 3.00e+00 1.11e-01 1.67e+01 angle pdb=" C3 NAG H 1 " pdb=" C4 NAG H 1 " pdb=" O4 NAG H 1 " ideal model delta sigma weight residual 107.29 119.36 -12.07 3.00e+00 1.11e-01 1.62e+01 angle pdb=" C3 NAG T 1 " pdb=" C4 NAG T 1 " pdb=" O4 NAG T 1 " ideal model delta sigma weight residual 107.29 118.70 -11.41 3.00e+00 1.11e-01 1.45e+01 ... (remaining 35985 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.91: 14778 18.91 - 37.83: 1465 37.83 - 56.74: 326 56.74 - 75.66: 62 75.66 - 94.57: 14 Dihedral angle restraints: 16645 sinusoidal: 7294 harmonic: 9351 Sorted by residual: dihedral pdb=" CB CYS A 808 " pdb=" SG CYS A 808 " pdb=" SG CYS A 819 " pdb=" CB CYS A 819 " ideal model delta sinusoidal sigma weight residual -86.00 -175.34 89.34 1 1.00e+01 1.00e-02 9.49e+01 dihedral pdb=" CB CYS B 808 " pdb=" SG CYS B 808 " pdb=" SG CYS B 819 " pdb=" CB CYS B 819 " ideal model delta sinusoidal sigma weight residual 93.00 -177.80 -89.20 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A 589 " pdb=" SG CYS A 589 " pdb=" SG CYS A 621 " pdb=" CB CYS A 621 " ideal model delta sinusoidal sigma weight residual 93.00 155.85 -62.85 1 1.00e+01 1.00e-02 5.22e+01 ... (remaining 16642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 4020 0.095 - 0.190: 279 0.190 - 0.286: 10 0.286 - 0.381: 3 0.381 - 0.476: 7 Chirality restraints: 4319 Sorted by residual: chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 125 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.92 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 125 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.94 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 125 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.13e+00 ... (remaining 4316 not shown) Planarity restraints: 4597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C1110 " -0.010 2.00e-02 2.50e+03 2.04e-02 4.16e+00 pdb=" C GLN C1110 " 0.035 2.00e-02 2.50e+03 pdb=" O GLN C1110 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C1111 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B1110 " 0.033 5.00e-02 4.00e+02 5.05e-02 4.07e+00 pdb=" N PRO B1111 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B1111 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B1111 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 448 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO A 449 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " -0.026 5.00e-02 4.00e+02 ... (remaining 4594 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 6477 2.79 - 3.32: 20593 3.32 - 3.85: 40074 3.85 - 4.37: 44727 4.37 - 4.90: 81586 Nonbonded interactions: 193457 Sorted by model distance: nonbonded pdb=" OH TYR B 41 " pdb=" O TYR B 58 " model vdw 2.267 3.040 nonbonded pdb=" OH TYR A 41 " pdb=" O TYR A 58 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR B 617 " pdb=" O GLY B 620 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 791 " pdb=" OD1 ASP A 835 " model vdw 2.303 3.040 nonbonded pdb=" OG1 THR B 112 " pdb=" OD1 ASP B 114 " model vdw 2.304 3.040 ... (remaining 193452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 30 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 1114 or resid 1301 through 1311 \ )) selection = (chain 'C' and (resid 30 through 458 or (resid 459 and (name N or name CA or nam \ e C or name O or name CB )) or resid 460 through 1114 or resid 1301 through 1311 \ )) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.170 Set scattering table: 0.240 Process input model: 57.660 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.160 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 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 : 0.003 0.050 26555 Z= 0.139 Angle : 0.692 20.217 36272 Z= 0.329 Chirality : 0.051 0.476 4319 Planarity : 0.004 0.050 4547 Dihedral : 15.428 94.573 10504 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.66 % Allowed : 19.79 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.14), residues: 3171 helix: -0.73 (0.19), residues: 597 sheet: -0.37 (0.19), residues: 750 loop : -1.90 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 605 HIS 0.006 0.001 HIS A 128 PHE 0.024 0.001 PHE A 895 TYR 0.019 0.001 TYR A1035 ARG 0.002 0.000 ARG C 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00725 ( 50) link_NAG-ASN : angle 3.61905 ( 150) link_BETA1-4 : bond 0.01959 ( 18) link_BETA1-4 : angle 5.21569 ( 54) hydrogen bonds : bond 0.20899 ( 821) hydrogen bonds : angle 7.50961 ( 2226) SS BOND : bond 0.00348 ( 39) SS BOND : angle 1.31966 ( 78) covalent geometry : bond 0.00277 (26448) covalent geometry : angle 0.61958 (35990) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 116 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.6960 (OUTLIER) cc_final: 0.6609 (mt) REVERT: A 134 CYS cc_start: 0.6386 (OUTLIER) cc_final: 0.5868 (m) REVERT: A 596 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8990 (mm) REVERT: A 818 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8268 (tt) REVERT: A 1104 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 167 ARG cc_start: 0.8807 (ptm160) cc_final: 0.8395 (ptp-170) REVERT: B 172 PHE cc_start: 0.0210 (OUTLIER) cc_final: -0.1519 (t80) REVERT: B 453 ASP cc_start: 0.7969 (p0) cc_final: 0.7583 (p0) REVERT: B 512 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8254 (p0) REVERT: B 756 MET cc_start: 0.8779 (mmm) cc_final: 0.8515 (mmm) REVERT: B 802 MET cc_start: 0.7548 (tpp) cc_final: 0.6935 (mmm) REVERT: C 65 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7784 (p0) REVERT: C 239 MET cc_start: 0.8215 (mtp) cc_final: 0.7418 (mmm) REVERT: C 369 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7929 (p0) REVERT: C 399 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.7582 (ptt90) REVERT: C 695 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7860 (mtp) REVERT: C 699 MET cc_start: 0.8659 (ptt) cc_final: 0.8344 (ptt) outliers start: 102 outliers final: 88 residues processed: 205 average time/residue: 0.3277 time to fit residues: 115.3007 Evaluate side-chains 212 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 113 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 134 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 311 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 621 CYS Chi-restraints excluded: chain A residue 665 MET Chi-restraints excluded: chain A residue 818 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1073 THR Chi-restraints excluded: chain A residue 1087 ASN Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 139 CYS Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 179 LYS Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 340 SER Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 512 ASN Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 139 CYS Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 174 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 340 SER Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 367 THR Chi-restraints excluded: chain C residue 369 ASN Chi-restraints excluded: chain C residue 399 ARG Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 834 THR Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 268 optimal weight: 0.9980 chunk 241 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 249 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 0.0010 chunk 185 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN C 151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.111756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.086509 restraints weight = 41553.701| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.54 r_work: 0.2900 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.0619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26555 Z= 0.115 Angle : 0.580 17.761 36272 Z= 0.279 Chirality : 0.047 0.428 4319 Planarity : 0.003 0.040 4547 Dihedral : 8.729 91.603 5040 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.44 % Allowed : 19.11 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.14), residues: 3171 helix: 0.17 (0.21), residues: 648 sheet: -0.26 (0.19), residues: 756 loop : -1.74 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.004 0.001 HIS A 128 PHE 0.016 0.001 PHE C 391 TYR 0.017 0.001 TYR A1035 ARG 0.002 0.000 ARG C 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 50) link_NAG-ASN : angle 3.03187 ( 150) link_BETA1-4 : bond 0.01560 ( 18) link_BETA1-4 : angle 4.48347 ( 54) hydrogen bonds : bond 0.04759 ( 821) hydrogen bonds : angle 5.41547 ( 2226) SS BOND : bond 0.00286 ( 39) SS BOND : angle 1.17712 ( 78) covalent geometry : bond 0.00250 (26448) covalent geometry : angle 0.51708 (35990) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 119 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1044 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.8935 (m) REVERT: B 143 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7406 (ptp) REVERT: B 172 PHE cc_start: 0.0075 (OUTLIER) cc_final: -0.1709 (t80) REVERT: B 756 MET cc_start: 0.8889 (mmm) cc_final: 0.8401 (mmm) REVERT: B 802 MET cc_start: 0.7728 (tpp) cc_final: 0.7118 (mmm) REVERT: B 1069 PHE cc_start: 0.8550 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: C 467 TYR cc_start: 0.9049 (OUTLIER) cc_final: 0.8321 (p90) REVERT: C 487 PHE cc_start: 0.9212 (m-80) cc_final: 0.8963 (m-80) REVERT: C 699 MET cc_start: 0.9068 (ptt) cc_final: 0.8756 (ptt) outliers start: 96 outliers final: 70 residues processed: 205 average time/residue: 0.3111 time to fit residues: 109.5266 Evaluate side-chains 183 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 108 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 870 MET Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1028 VAL Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 813 ASN Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 63 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 284 optimal weight: 0.0870 chunk 17 optimal weight: 0.0070 chunk 84 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 chunk 280 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 303 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.112992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.087601 restraints weight = 41398.686| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.56 r_work: 0.2905 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.0802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 26555 Z= 0.096 Angle : 0.545 17.203 36272 Z= 0.258 Chirality : 0.046 0.430 4319 Planarity : 0.003 0.039 4547 Dihedral : 8.100 89.454 4947 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.09 % Allowed : 18.68 % Favored : 77.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3171 helix: 0.51 (0.21), residues: 666 sheet: -0.14 (0.19), residues: 750 loop : -1.58 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.005 0.000 HIS A 128 PHE 0.012 0.001 PHE A1089 TYR 0.017 0.001 TYR A1035 ARG 0.001 0.000 ARG C 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00515 ( 50) link_NAG-ASN : angle 2.94369 ( 150) link_BETA1-4 : bond 0.01608 ( 18) link_BETA1-4 : angle 4.38839 ( 54) hydrogen bonds : bond 0.04139 ( 821) hydrogen bonds : angle 4.97417 ( 2226) SS BOND : bond 0.00261 ( 39) SS BOND : angle 0.96294 ( 78) covalent geometry : bond 0.00205 (26448) covalent geometry : angle 0.48210 (35990) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 121 time to evaluate : 3.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 THR cc_start: 0.9442 (OUTLIER) cc_final: 0.9241 (t) REVERT: A 458 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5342 (tm-30) REVERT: A 1044 THR cc_start: 0.9276 (OUTLIER) cc_final: 0.8904 (m) REVERT: B 143 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7368 (ptp) REVERT: B 172 PHE cc_start: -0.0055 (OUTLIER) cc_final: -0.1895 (t80) REVERT: B 199 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8094 (m) REVERT: B 519 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8437 (ttpp) REVERT: B 802 MET cc_start: 0.7688 (tpp) cc_final: 0.7123 (mmm) REVERT: B 1069 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: C 179 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7192 (mtmm) REVERT: C 239 MET cc_start: 0.8301 (mtp) cc_final: 0.7544 (mmm) REVERT: C 699 MET cc_start: 0.9053 (ptt) cc_final: 0.8637 (ptt) outliers start: 114 outliers final: 86 residues processed: 221 average time/residue: 0.3565 time to fit residues: 135.3405 Evaluate side-chains 204 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 109 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 144 TYR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 203 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 121 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 199 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 707 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 813 ASN Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 289 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 67 optimal weight: 4.9990 chunk 286 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 HIS A 792 ASN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 597 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.102732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.077490 restraints weight = 42444.615| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.61 r_work: 0.2736 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.072 26555 Z= 0.354 Angle : 0.764 17.908 36272 Z= 0.376 Chirality : 0.054 0.397 4319 Planarity : 0.004 0.055 4547 Dihedral : 8.697 81.925 4944 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 5.74 % Allowed : 18.04 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3171 helix: -0.06 (0.20), residues: 675 sheet: -0.75 (0.19), residues: 717 loop : -1.85 (0.13), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 427 HIS 0.005 0.001 HIS A 53 PHE 0.021 0.002 PHE C 333 TYR 0.032 0.003 TYR C 204 ARG 0.006 0.001 ARG C 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00462 ( 50) link_NAG-ASN : angle 3.32771 ( 150) link_BETA1-4 : bond 0.01686 ( 18) link_BETA1-4 : angle 4.52728 ( 54) hydrogen bonds : bond 0.06165 ( 821) hydrogen bonds : angle 5.41573 ( 2226) SS BOND : bond 0.00656 ( 39) SS BOND : angle 1.65390 ( 78) covalent geometry : bond 0.00865 (26448) covalent geometry : angle 0.71097 (35990) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 107 time to evaluate : 2.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.7805 (p90) REVERT: A 458 GLU cc_start: 0.6237 (OUTLIER) cc_final: 0.5128 (tm-30) REVERT: B 172 PHE cc_start: 0.0508 (OUTLIER) cc_final: -0.1213 (t80) REVERT: B 360 TYR cc_start: 0.9240 (OUTLIER) cc_final: 0.8893 (m-80) REVERT: B 969 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9180 (mm) REVERT: B 1069 PHE cc_start: 0.8651 (OUTLIER) cc_final: 0.7493 (m-80) REVERT: C 323 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8425 (mt) REVERT: C 537 PHE cc_start: 0.8401 (OUTLIER) cc_final: 0.7436 (p90) REVERT: C 699 MET cc_start: 0.9088 (ptt) cc_final: 0.8812 (ptt) outliers start: 160 outliers final: 119 residues processed: 254 average time/residue: 0.3734 time to fit residues: 166.0416 Evaluate side-chains 228 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 101 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 258 VAL Chi-restraints excluded: chain A residue 267 MET Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 353 VAL Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 502 SER Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 907 THR Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1101 ILE Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 128 HIS Chi-restraints excluded: chain B residue 143 MET Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 204 TYR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 360 TYR Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 969 LEU Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1101 ILE Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 323 ILE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 416 LEU Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 463 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 759 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 907 THR Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 279 optimal weight: 0.8980 chunk 249 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 276 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.0010 chunk 20 optimal weight: 3.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.106754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.081404 restraints weight = 41654.998| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.58 r_work: 0.2835 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2693 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26555 Z= 0.111 Angle : 0.576 17.143 36272 Z= 0.275 Chirality : 0.047 0.429 4319 Planarity : 0.003 0.037 4547 Dihedral : 8.250 81.224 4937 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.91 % Allowed : 19.83 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.15), residues: 3171 helix: 0.56 (0.21), residues: 660 sheet: -0.37 (0.19), residues: 744 loop : -1.72 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.004 0.001 HIS A 128 PHE 0.012 0.001 PHE B1089 TYR 0.018 0.001 TYR B 467 ARG 0.001 0.000 ARG B 394 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 50) link_NAG-ASN : angle 2.99380 ( 150) link_BETA1-4 : bond 0.01562 ( 18) link_BETA1-4 : angle 4.37636 ( 54) hydrogen bonds : bond 0.04252 ( 821) hydrogen bonds : angle 4.95518 ( 2226) SS BOND : bond 0.00297 ( 39) SS BOND : angle 1.41842 ( 78) covalent geometry : bond 0.00246 (26448) covalent geometry : angle 0.51390 (35990) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 112 time to evaluate : 2.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5028 (tm-30) REVERT: A 1044 THR cc_start: 0.9235 (OUTLIER) cc_final: 0.8864 (m) REVERT: A 1104 THR cc_start: 0.9140 (OUTLIER) cc_final: 0.8807 (p) REVERT: B 143 MET cc_start: 0.8096 (ptp) cc_final: 0.7229 (ptt) REVERT: B 172 PHE cc_start: 0.0135 (OUTLIER) cc_final: -0.1629 (t80) REVERT: B 489 LEU cc_start: 0.7959 (mp) cc_final: 0.7350 (mp) REVERT: B 519 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8425 (ttpp) REVERT: B 906 LEU cc_start: 0.9465 (OUTLIER) cc_final: 0.9145 (mt) REVERT: B 1044 THR cc_start: 0.9293 (OUTLIER) cc_final: 0.8867 (m) REVERT: B 1069 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.7368 (m-80) REVERT: B 1072 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8593 (tt) REVERT: C 179 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7322 (mtmm) REVERT: C 239 MET cc_start: 0.8296 (mtp) cc_final: 0.7676 (mmm) REVERT: C 537 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7528 (p90) REVERT: C 699 MET cc_start: 0.9022 (ptt) cc_final: 0.8706 (ptt) REVERT: C 1016 HIS cc_start: 0.9211 (OUTLIER) cc_final: 0.8873 (t-90) outliers start: 109 outliers final: 76 residues processed: 212 average time/residue: 0.3253 time to fit residues: 117.4904 Evaluate side-chains 196 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 108 time to evaluate : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 519 LYS Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1016 HIS Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 133 optimal weight: 4.9990 chunk 316 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 306 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 153 optimal weight: 0.6980 chunk 195 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN ** C 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.105477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.079993 restraints weight = 41613.082| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.54 r_work: 0.2801 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2659 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26555 Z= 0.182 Angle : 0.616 17.217 36272 Z= 0.295 Chirality : 0.048 0.410 4319 Planarity : 0.003 0.035 4547 Dihedral : 8.195 76.070 4935 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.55 % Allowed : 19.43 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.15), residues: 3171 helix: 0.57 (0.21), residues: 660 sheet: -0.43 (0.19), residues: 750 loop : -1.75 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 427 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A1089 TYR 0.021 0.001 TYR A1035 ARG 0.003 0.000 ARG C 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00456 ( 50) link_NAG-ASN : angle 3.05354 ( 150) link_BETA1-4 : bond 0.01587 ( 18) link_BETA1-4 : angle 4.40375 ( 54) hydrogen bonds : bond 0.04703 ( 821) hydrogen bonds : angle 4.96806 ( 2226) SS BOND : bond 0.00409 ( 39) SS BOND : angle 1.31220 ( 78) covalent geometry : bond 0.00437 (26448) covalent geometry : angle 0.55782 (35990) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 109 time to evaluate : 2.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7327 (OUTLIER) cc_final: 0.6818 (mt) REVERT: A 458 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.5383 (tm-30) REVERT: A 1104 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8797 (p) REVERT: B 172 PHE cc_start: 0.0162 (OUTLIER) cc_final: -0.1595 (t80) REVERT: B 489 LEU cc_start: 0.7685 (mp) cc_final: 0.6968 (mp) REVERT: B 906 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9142 (mt) REVERT: B 1069 PHE cc_start: 0.8559 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: B 1072 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8615 (tt) REVERT: C 239 MET cc_start: 0.8250 (mtp) cc_final: 0.7421 (mmm) REVERT: C 537 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7530 (p90) REVERT: C 699 MET cc_start: 0.9042 (ptt) cc_final: 0.8730 (ptt) REVERT: C 899 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8726 (mm) REVERT: C 1016 HIS cc_start: 0.9164 (OUTLIER) cc_final: 0.8895 (t-90) outliers start: 127 outliers final: 107 residues processed: 224 average time/residue: 0.3203 time to fit residues: 122.6230 Evaluate side-chains 224 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 107 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 919 VAL Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 295 LYS Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 899 ILE Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1016 HIS Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 235 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 20 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 234 optimal weight: 3.9990 chunk 165 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 249 optimal weight: 0.2980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.106530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.080836 restraints weight = 41733.027| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.63 r_work: 0.2784 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26555 Z= 0.123 Angle : 0.576 17.012 36272 Z= 0.273 Chirality : 0.047 0.422 4319 Planarity : 0.003 0.036 4547 Dihedral : 8.021 70.764 4935 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.80 % Allowed : 19.47 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.15), residues: 3171 helix: 0.73 (0.21), residues: 660 sheet: -0.34 (0.19), residues: 744 loop : -1.66 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.004 0.001 HIS A 128 PHE 0.015 0.001 PHE A1089 TYR 0.018 0.001 TYR A1035 ARG 0.001 0.000 ARG A 399 Details of bonding type rmsd link_NAG-ASN : bond 0.00488 ( 50) link_NAG-ASN : angle 2.95243 ( 150) link_BETA1-4 : bond 0.01572 ( 18) link_BETA1-4 : angle 4.35814 ( 54) hydrogen bonds : bond 0.04169 ( 821) hydrogen bonds : angle 4.80398 ( 2226) SS BOND : bond 0.00320 ( 39) SS BOND : angle 1.38479 ( 78) covalent geometry : bond 0.00284 (26448) covalent geometry : angle 0.51499 (35990) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 111 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7160 (OUTLIER) cc_final: 0.6834 (mt) REVERT: A 458 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5061 (tm-30) REVERT: A 596 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8964 (mm) REVERT: A 1044 THR cc_start: 0.9190 (OUTLIER) cc_final: 0.8806 (p) REVERT: A 1104 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8794 (p) REVERT: B 172 PHE cc_start: 0.0380 (OUTLIER) cc_final: -0.1171 (t80) REVERT: B 489 LEU cc_start: 0.7783 (mp) cc_final: 0.7172 (mp) REVERT: B 537 PHE cc_start: 0.8311 (OUTLIER) cc_final: 0.7996 (p90) REVERT: B 1069 PHE cc_start: 0.8431 (OUTLIER) cc_final: 0.7286 (m-80) REVERT: B 1072 ILE cc_start: 0.8973 (OUTLIER) cc_final: 0.8532 (tt) REVERT: C 239 MET cc_start: 0.8264 (mtp) cc_final: 0.7555 (mmm) REVERT: C 537 PHE cc_start: 0.8388 (OUTLIER) cc_final: 0.7532 (p90) REVERT: C 699 MET cc_start: 0.8925 (ptt) cc_final: 0.8608 (ptt) REVERT: C 1016 HIS cc_start: 0.9170 (OUTLIER) cc_final: 0.8933 (t-90) outliers start: 134 outliers final: 107 residues processed: 234 average time/residue: 0.3203 time to fit residues: 128.1308 Evaluate side-chains 224 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 106 time to evaluate : 2.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 626 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 884 LEU Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 1011 CYS Chi-restraints excluded: chain C residue 1016 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1038 SER Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 60 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 249 optimal weight: 0.8980 chunk 212 optimal weight: 10.0000 chunk 167 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 310 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 202 optimal weight: 0.0040 chunk 81 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.080842 restraints weight = 41805.346| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.53 r_work: 0.2815 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26555 Z= 0.152 Angle : 0.594 17.099 36272 Z= 0.282 Chirality : 0.047 0.411 4319 Planarity : 0.003 0.035 4547 Dihedral : 7.988 64.933 4935 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.95 % Allowed : 19.36 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.15), residues: 3171 helix: 0.69 (0.21), residues: 666 sheet: -0.43 (0.19), residues: 759 loop : -1.66 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 427 HIS 0.004 0.001 HIS A 128 PHE 0.013 0.001 PHE A1089 TYR 0.020 0.001 TYR A1035 ARG 0.002 0.000 ARG C 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00468 ( 50) link_NAG-ASN : angle 2.98088 ( 150) link_BETA1-4 : bond 0.01587 ( 18) link_BETA1-4 : angle 4.36525 ( 54) hydrogen bonds : bond 0.04395 ( 821) hydrogen bonds : angle 4.82345 ( 2226) SS BOND : bond 0.00360 ( 39) SS BOND : angle 1.32155 ( 78) covalent geometry : bond 0.00362 (26448) covalent geometry : angle 0.53474 (35990) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 111 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.6959 (mt) REVERT: A 458 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5017 (tm-30) REVERT: A 1044 THR cc_start: 0.9239 (OUTLIER) cc_final: 0.8872 (p) REVERT: A 1104 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8800 (p) REVERT: B 172 PHE cc_start: 0.0372 (OUTLIER) cc_final: -0.1308 (t80) REVERT: B 378 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8599 (pt) REVERT: B 489 LEU cc_start: 0.7852 (mp) cc_final: 0.7225 (mp) REVERT: B 537 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7992 (p90) REVERT: B 906 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8978 (mt) REVERT: B 1069 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.7399 (m-80) REVERT: B 1072 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8606 (tt) REVERT: C 239 MET cc_start: 0.8281 (mtp) cc_final: 0.7572 (mmm) REVERT: C 537 PHE cc_start: 0.8416 (OUTLIER) cc_final: 0.7547 (p90) REVERT: C 699 MET cc_start: 0.9034 (ptt) cc_final: 0.8719 (ptt) REVERT: C 1016 HIS cc_start: 0.9188 (OUTLIER) cc_final: 0.8932 (t-90) outliers start: 138 outliers final: 117 residues processed: 239 average time/residue: 0.3128 time to fit residues: 128.5841 Evaluate side-chains 236 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 107 time to evaluate : 2.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 199 THR Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 458 GLU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 472 TYR Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 590 THR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 786 ILE Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1011 CYS Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1050 CYS Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 273 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 502 SER Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 574 THR Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 906 LEU Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 925 GLN Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1104 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 111 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 278 ASP Chi-restraints excluded: chain C residue 303 ILE Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 472 TYR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 537 PHE Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 614 VAL Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 691 THR Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 884 LEU Chi-restraints excluded: chain C residue 1016 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 212 optimal weight: 10.0000 chunk 83 optimal weight: 0.2980 chunk 19 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 chunk 285 optimal weight: 0.2980 chunk 270 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 143 optimal weight: 0.9980 chunk 113 optimal weight: 4.9990 chunk 36 optimal weight: 0.0270 chunk 263 optimal weight: 2.9990 overall best weight: 0.4038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 ASN ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 869 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.108727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.083554 restraints weight = 41571.249| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.57 r_work: 0.2860 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 26555 Z= 0.091 Angle : 0.547 16.769 36272 Z= 0.257 Chirality : 0.045 0.431 4319 Planarity : 0.003 0.036 4547 Dihedral : 7.671 61.032 4934 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.80 % Allowed : 20.58 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 3171 helix: 0.84 (0.21), residues: 669 sheet: -0.25 (0.19), residues: 753 loop : -1.50 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 427 HIS 0.003 0.000 HIS A 128 PHE 0.011 0.001 PHE A1089 TYR 0.015 0.001 TYR A1035 ARG 0.001 0.000 ARG B 481 Details of bonding type rmsd link_NAG-ASN : bond 0.00539 ( 50) link_NAG-ASN : angle 2.85448 ( 150) link_BETA1-4 : bond 0.01570 ( 18) link_BETA1-4 : angle 4.30342 ( 54) hydrogen bonds : bond 0.03530 ( 821) hydrogen bonds : angle 4.58704 ( 2226) SS BOND : bond 0.00237 ( 39) SS BOND : angle 1.07645 ( 78) covalent geometry : bond 0.00194 (26448) covalent geometry : angle 0.48726 (35990) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 125 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6992 (mt) REVERT: A 596 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 1044 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8776 (m) REVERT: A 1104 THR cc_start: 0.9139 (OUTLIER) cc_final: 0.8808 (p) REVERT: B 172 PHE cc_start: 0.0141 (OUTLIER) cc_final: -0.1446 (t80) REVERT: B 378 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8430 (pt) REVERT: B 489 LEU cc_start: 0.7863 (mp) cc_final: 0.7338 (mp) REVERT: B 537 PHE cc_start: 0.8101 (OUTLIER) cc_final: 0.7854 (p90) REVERT: B 802 MET cc_start: 0.7715 (tpp) cc_final: 0.7179 (mmm) REVERT: B 1069 PHE cc_start: 0.8532 (OUTLIER) cc_final: 0.7342 (m-80) REVERT: B 1072 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8582 (tt) REVERT: C 239 MET cc_start: 0.8277 (mtp) cc_final: 0.7602 (mmm) REVERT: C 699 MET cc_start: 0.9117 (ptt) cc_final: 0.8539 (ptt) REVERT: C 1016 HIS cc_start: 0.9143 (OUTLIER) cc_final: 0.8920 (t-90) outliers start: 106 outliers final: 79 residues processed: 221 average time/residue: 0.3156 time to fit residues: 121.2071 Evaluate side-chains 205 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 116 time to evaluate : 2.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 692 THR Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1011 CYS Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 241 MET Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1016 HIS Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 305 optimal weight: 2.9990 chunk 277 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 215 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 293 optimal weight: 0.7980 chunk 53 optimal weight: 0.2980 chunk 179 optimal weight: 0.9980 chunk 256 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.107244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.082243 restraints weight = 41677.168| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.49 r_work: 0.2841 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 26555 Z= 0.125 Angle : 0.575 16.926 36272 Z= 0.272 Chirality : 0.046 0.411 4319 Planarity : 0.003 0.034 4547 Dihedral : 7.667 58.301 4932 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.51 % Allowed : 21.01 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.15), residues: 3171 helix: 0.87 (0.21), residues: 669 sheet: -0.25 (0.19), residues: 747 loop : -1.51 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 427 HIS 0.003 0.001 HIS A 53 PHE 0.015 0.001 PHE A1089 TYR 0.018 0.001 TYR A1035 ARG 0.002 0.000 ARG C 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00476 ( 50) link_NAG-ASN : angle 2.89850 ( 150) link_BETA1-4 : bond 0.01588 ( 18) link_BETA1-4 : angle 4.31196 ( 54) hydrogen bonds : bond 0.03954 ( 821) hydrogen bonds : angle 4.63008 ( 2226) SS BOND : bond 0.00337 ( 39) SS BOND : angle 1.61435 ( 78) covalent geometry : bond 0.00293 (26448) covalent geometry : angle 0.51435 (35990) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6342 Ramachandran restraints generated. 3171 Oldfield, 0 Emsley, 3171 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 117 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LEU cc_start: 0.7302 (OUTLIER) cc_final: 0.6978 (mt) REVERT: A 802 MET cc_start: 0.7047 (ppp) cc_final: 0.6821 (ppp) REVERT: A 1044 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8825 (p) REVERT: A 1104 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8807 (p) REVERT: B 172 PHE cc_start: 0.0173 (OUTLIER) cc_final: -0.1586 (t80) REVERT: B 378 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8424 (pt) REVERT: B 489 LEU cc_start: 0.7886 (mp) cc_final: 0.7358 (mp) REVERT: B 537 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7720 (p90) REVERT: B 1069 PHE cc_start: 0.8557 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: B 1072 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8622 (tt) REVERT: B 1083 ILE cc_start: 0.9181 (mt) cc_final: 0.8940 (mt) REVERT: C 239 MET cc_start: 0.8313 (mtp) cc_final: 0.7618 (mmm) REVERT: C 699 MET cc_start: 0.9020 (ptt) cc_final: 0.8573 (ptt) REVERT: C 1016 HIS cc_start: 0.9181 (OUTLIER) cc_final: 0.8927 (t-90) outliers start: 98 outliers final: 83 residues processed: 204 average time/residue: 0.3143 time to fit residues: 109.3237 Evaluate side-chains 209 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 117 time to evaluate : 2.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 139 CYS Chi-restraints excluded: chain A residue 145 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 352 CYS Chi-restraints excluded: chain A residue 399 ARG Chi-restraints excluded: chain A residue 421 THR Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 471 GLN Chi-restraints excluded: chain A residue 473 VAL Chi-restraints excluded: chain A residue 487 PHE Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 706 CYS Chi-restraints excluded: chain A residue 773 ILE Chi-restraints excluded: chain A residue 842 THR Chi-restraints excluded: chain A residue 863 GLN Chi-restraints excluded: chain A residue 1034 THR Chi-restraints excluded: chain A residue 1044 THR Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1104 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 172 PHE Chi-restraints excluded: chain B residue 231 ASN Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 292 CYS Chi-restraints excluded: chain B residue 297 PHE Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 352 CYS Chi-restraints excluded: chain B residue 353 VAL Chi-restraints excluded: chain B residue 367 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 408 VAL Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 473 VAL Chi-restraints excluded: chain B residue 537 PHE Chi-restraints excluded: chain B residue 596 LEU Chi-restraints excluded: chain B residue 605 TRP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 772 GLN Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 903 GLN Chi-restraints excluded: chain B residue 920 VAL Chi-restraints excluded: chain B residue 1034 THR Chi-restraints excluded: chain B residue 1044 THR Chi-restraints excluded: chain B residue 1050 CYS Chi-restraints excluded: chain B residue 1064 VAL Chi-restraints excluded: chain B residue 1069 PHE Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 179 LYS Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 231 ASN Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 352 CYS Chi-restraints excluded: chain C residue 421 THR Chi-restraints excluded: chain C residue 429 THR Chi-restraints excluded: chain C residue 466 THR Chi-restraints excluded: chain C residue 467 TYR Chi-restraints excluded: chain C residue 471 GLN Chi-restraints excluded: chain C residue 473 VAL Chi-restraints excluded: chain C residue 487 PHE Chi-restraints excluded: chain C residue 502 SER Chi-restraints excluded: chain C residue 525 THR Chi-restraints excluded: chain C residue 574 THR Chi-restraints excluded: chain C residue 596 LEU Chi-restraints excluded: chain C residue 626 GLU Chi-restraints excluded: chain C residue 673 VAL Chi-restraints excluded: chain C residue 702 THR Chi-restraints excluded: chain C residue 772 GLN Chi-restraints excluded: chain C residue 880 THR Chi-restraints excluded: chain C residue 1016 HIS Chi-restraints excluded: chain C residue 1028 VAL Chi-restraints excluded: chain C residue 1072 ILE Chi-restraints excluded: chain C residue 1090 VAL Chi-restraints excluded: chain C residue 1096 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 272 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 278 optimal weight: 0.0370 chunk 240 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 315 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 254 optimal weight: 0.7980 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 881 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.108150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.082850 restraints weight = 41745.375| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 2.57 r_work: 0.2856 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 26555 Z= 0.102 Angle : 0.556 16.866 36272 Z= 0.263 Chirality : 0.046 0.418 4319 Planarity : 0.003 0.035 4547 Dihedral : 7.553 57.616 4928 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.59 % Allowed : 20.90 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 3171 helix: 0.93 (0.21), residues: 669 sheet: -0.15 (0.19), residues: 741 loop : -1.48 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 427 HIS 0.003 0.001 HIS B1016 PHE 0.012 0.001 PHE A1089 TYR 0.016 0.001 TYR A1035 ARG 0.001 0.000 ARG C 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00498 ( 50) link_NAG-ASN : angle 2.84297 ( 150) link_BETA1-4 : bond 0.01570 ( 18) link_BETA1-4 : angle 4.29120 ( 54) hydrogen bonds : bond 0.03709 ( 821) hydrogen bonds : angle 4.56270 ( 2226) SS BOND : bond 0.00352 ( 39) SS BOND : angle 1.40274 ( 78) covalent geometry : bond 0.00228 (26448) covalent geometry : angle 0.49571 (35990) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11589.59 seconds wall clock time: 201 minutes 42.57 seconds (12102.57 seconds total)