Starting phenix.real_space_refine on Sun Jul 5 08:27:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.map" model { file = "/net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnq_33323/07_2026/7xnq_33323.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.067 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 114 5.16 5 C 16854 2.51 5 N 4305 2.21 5 O 5190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26463 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8499 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1030} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8499 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1030} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 8499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1089, 8499 Classifications: {'peptide': 1089} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1030} Chain breaks: 2 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 11 Time building chain proxies: 4.93, per 1000 atoms: 0.19 Number of scatterers: 26463 At special positions: 0 Unit cell: (161.2, 157.04, 178.88, 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 114 16.00 O 5190 8.00 N 4305 7.00 C 16854 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 164 " distance=2.04 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 299 " distance=2.03 Simple disulfide: pdb=" SG CYS A 334 " - pdb=" SG CYS A 359 " distance=2.02 Simple disulfide: pdb=" SG CYS A 377 " - pdb=" SG CYS A 430 " distance=2.03 Simple disulfide: pdb=" SG CYS A 389 " - pdb=" SG CYS A 523 " distance=2.04 Simple disulfide: pdb=" SG CYS A 478 " - pdb=" SG CYS A 486 " distance=2.03 Simple disulfide: pdb=" SG CYS A 615 " - pdb=" SG CYS A 647 " distance=2.03 Simple disulfide: pdb=" SG CYS A 660 " - pdb=" SG CYS A 669 " distance=2.03 Simple disulfide: pdb=" SG CYS A 736 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 741 " - pdb=" SG CYS A 747 " distance=2.03 Simple disulfide: pdb=" SG CYS A1030 " - pdb=" SG CYS A1041 " distance=2.03 Simple disulfide: pdb=" SG CYS A1080 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 164 " distance=2.04 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 299 " distance=2.03 Simple disulfide: pdb=" SG CYS B 334 " - pdb=" SG CYS B 359 " distance=2.02 Simple disulfide: pdb=" SG CYS B 377 " - pdb=" SG CYS B 430 " distance=2.03 Simple disulfide: pdb=" SG CYS B 389 " - pdb=" SG CYS B 523 " distance=2.04 Simple disulfide: pdb=" SG CYS B 478 " - pdb=" SG CYS B 486 " distance=2.03 Simple disulfide: pdb=" SG CYS B 615 " - pdb=" SG CYS B 647 " distance=2.03 Simple disulfide: pdb=" SG CYS B 660 " - pdb=" SG CYS B 669 " distance=2.03 Simple disulfide: pdb=" SG CYS B 736 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 741 " - pdb=" SG CYS B 747 " distance=2.03 Simple disulfide: pdb=" SG CYS B1030 " - pdb=" SG CYS B1041 " distance=2.03 Simple disulfide: pdb=" SG CYS B1080 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 164 " distance=2.04 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 299 " distance=2.03 Simple disulfide: pdb=" SG CYS C 334 " - pdb=" SG CYS C 359 " distance=2.02 Simple disulfide: pdb=" SG CYS C 377 " - pdb=" SG CYS C 430 " distance=2.03 Simple disulfide: pdb=" SG CYS C 389 " - pdb=" SG CYS C 523 " distance=2.04 Simple disulfide: pdb=" SG CYS C 478 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 615 " - pdb=" SG CYS C 647 " distance=2.03 Simple disulfide: pdb=" SG CYS C 660 " - pdb=" SG CYS C 669 " distance=2.03 Simple disulfide: pdb=" SG CYS C 736 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 741 " - pdb=" SG CYS C 747 " distance=2.03 Simple disulfide: pdb=" SG CYS C1030 " - pdb=" SG CYS C1041 " distance=2.03 Simple disulfide: pdb=" SG CYS C1080 " - pdb=" SG CYS C1124 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, 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 61 " " NAG A1302 " - " ASN A 72 " " NAG A1303 " - " ASN A 120 " " NAG A1304 " - " ASN A 147 " " NAG A1305 " - " ASN A 163 " " NAG A1306 " - " ASN A 232 " " NAG A1307 " - " ASN A 329 " " NAG A1308 " - " ASN A 601 " " NAG A1309 " - " ASN A 614 " " NAG A1310 " - " ASN A 655 " " NAG A1311 " - " ASN A1096 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 72 " " NAG B1303 " - " ASN B 120 " " NAG B1304 " - " ASN B 147 " " NAG B1305 " - " ASN B 163 " " NAG B1306 " - " ASN B 232 " " NAG B1307 " - " ASN B 329 " " NAG B1308 " - " ASN B 601 " " NAG B1309 " - " ASN B 614 " " NAG B1310 " - " ASN B 655 " " NAG B1311 " - " ASN B1096 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 72 " " NAG C1303 " - " ASN C 120 " " NAG C1304 " - " ASN C 147 " " NAG C1305 " - " ASN C 163 " " NAG C1306 " - " ASN C 232 " " NAG C1307 " - " ASN C 329 " " NAG C1308 " - " ASN C 601 " " NAG C1309 " - " ASN C 614 " " NAG C1310 " - " ASN C 655 " " NAG C1311 " - " ASN C1096 " " NAG D 1 " - " ASN A 280 " " NAG E 1 " - " ASN A 707 " " NAG F 1 " - " ASN A 715 " " NAG G 1 " - " ASN A 799 " " NAG H 1 " - " ASN A1072 " " NAG I 1 " - " ASN A1132 " " NAG J 1 " - " ASN B 280 " " NAG K 1 " - " ASN B 707 " " NAG L 1 " - " ASN B 715 " " NAG M 1 " - " ASN B 799 " " NAG N 1 " - " ASN B1072 " " NAG O 1 " - " ASN B1132 " " NAG P 1 " - " ASN C 280 " " NAG Q 1 " - " ASN C 707 " " NAG R 1 " - " ASN C 715 " " NAG S 1 " - " ASN C 799 " " NAG T 1 " - " ASN C1072 " " NAG U 1 " - " ASN C1132 " Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.0 seconds 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6108 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 56 sheets defined 24.5% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 292 through 301 Processing helix chain 'A' and resid 336 through 342 removed outlier: 4.028A pdb=" N PHE A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN A 341 " --> pdb=" O ASP A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 368 removed outlier: 3.682A pdb=" N LEU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.854A pdb=" N ILE A 408 " --> pdb=" O VAL A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 419 removed outlier: 3.607A pdb=" N TYR A 419 " --> pdb=" O ASN A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 450 removed outlier: 3.793A pdb=" N TYR A 449 " --> pdb=" O ASN A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 504 removed outlier: 3.670A pdb=" N GLN A 504 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 635 removed outlier: 3.634A pdb=" N TYR A 634 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 740 Processing helix chain 'A' and resid 744 through 753 removed outlier: 3.605A pdb=" N LEU A 750 " --> pdb=" O GLU A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 781 removed outlier: 3.650A pdb=" N GLN A 760 " --> pdb=" O SER A 756 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 761 " --> pdb=" O PHE A 757 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLN A 777 " --> pdb=" O ASP A 773 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 848 through 853 removed outlier: 3.757A pdb=" N LYS A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE A 853 " --> pdb=" O CYS A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 848 through 853' Processing helix chain 'A' and resid 864 through 883 Processing helix chain 'A' and resid 884 through 888 Processing helix chain 'A' and resid 895 through 905 Processing helix chain 'A' and resid 911 through 917 removed outlier: 3.770A pdb=" N TYR A 915 " --> pdb=" O GLN A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 939 removed outlier: 3.596A pdb=" N ILE A 932 " --> pdb=" O ALA A 928 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLN A 933 " --> pdb=" O ILE A 929 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASP A 934 " --> pdb=" O GLY A 930 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER A 937 " --> pdb=" O GLN A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 943 through 962 removed outlier: 3.503A pdb=" N VAL A 950 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 963 through 966 Processing helix chain 'A' and resid 974 through 982 removed outlier: 3.980A pdb=" N ILE A 978 " --> pdb=" O VAL A 974 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 979 " --> pdb=" O LEU A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 986 through 1030 removed outlier: 4.015A pdb=" N GLN A 990 " --> pdb=" O GLU A 986 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 997 " --> pdb=" O ARG A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1116 No H-bonds generated for 'chain 'A' and resid 1114 through 1116' Processing helix chain 'A' and resid 1139 through 1148 removed outlier: 3.896A pdb=" N PHE A1146 " --> pdb=" O GLU A1142 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS A1147 " --> pdb=" O LEU A1143 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 Processing helix chain 'B' and resid 336 through 342 removed outlier: 4.047A pdb=" N PHE B 340 " --> pdb=" O PHE B 336 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 368 removed outlier: 3.696A pdb=" N LEU B 366 " --> pdb=" O ASP B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.790A pdb=" N ILE B 408 " --> pdb=" O VAL B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 419 removed outlier: 3.508A pdb=" N TYR B 419 " --> pdb=" O ASN B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 450 removed outlier: 3.846A pdb=" N TYR B 449 " --> pdb=" O ASN B 446 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG B 450 " --> pdb=" O TYR B 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 446 through 450' Processing helix chain 'B' and resid 500 through 504 removed outlier: 3.575A pdb=" N GLN B 504 " --> pdb=" O VAL B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 removed outlier: 3.634A pdb=" N TYR B 634 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 735 through 740 Processing helix chain 'B' and resid 744 through 753 removed outlier: 3.691A pdb=" N LEU B 750 " --> pdb=" O GLU B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 781 removed outlier: 3.541A pdb=" N ASP B 773 " --> pdb=" O ALA B 769 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 777 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU B 778 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL B 779 " --> pdb=" O ASN B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 823 Processing helix chain 'B' and resid 848 through 853 removed outlier: 3.700A pdb=" N LYS B 852 " --> pdb=" O ILE B 848 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE B 853 " --> pdb=" O CYS B 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 848 through 853' Processing helix chain 'B' and resid 864 through 883 Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 895 through 905 removed outlier: 3.540A pdb=" N ALA B 901 " --> pdb=" O PRO B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 917 removed outlier: 3.937A pdb=" N TYR B 915 " --> pdb=" O GLN B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 917 through 939 removed outlier: 3.603A pdb=" N ILE B 932 " --> pdb=" O ALA B 928 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLN B 933 " --> pdb=" O ILE B 929 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP B 934 " --> pdb=" O GLY B 930 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER B 937 " --> pdb=" O GLN B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 943 through 963 Processing helix chain 'B' and resid 964 through 966 No H-bonds generated for 'chain 'B' and resid 964 through 966' Processing helix chain 'B' and resid 974 through 982 removed outlier: 3.907A pdb=" N ILE B 978 " --> pdb=" O VAL B 974 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU B 979 " --> pdb=" O LEU B 975 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1030 removed outlier: 4.218A pdb=" N GLU B 988 " --> pdb=" O PRO B 984 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N VAL B 989 " --> pdb=" O PRO B 985 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLN B 990 " --> pdb=" O GLU B 986 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG B 993 " --> pdb=" O VAL B 989 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 997 " --> pdb=" O ARG B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1116 No H-bonds generated for 'chain 'B' and resid 1114 through 1116' Processing helix chain 'B' and resid 1139 through 1148 removed outlier: 3.876A pdb=" N PHE B1146 " --> pdb=" O GLU B1142 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B1147 " --> pdb=" O LEU B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 336 through 342 removed outlier: 4.055A pdb=" N PHE C 340 " --> pdb=" O PHE C 336 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 362 through 368 removed outlier: 3.725A pdb=" N LEU C 366 " --> pdb=" O ASP C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 3.905A pdb=" N ILE C 408 " --> pdb=" O VAL C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 419 removed outlier: 3.533A pdb=" N TYR C 419 " --> pdb=" O ASN C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 446 through 450 removed outlier: 3.940A pdb=" N TYR C 449 " --> pdb=" O ASN C 446 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG C 450 " --> pdb=" O TYR C 447 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 446 through 450' Processing helix chain 'C' and resid 500 through 504 removed outlier: 3.615A pdb=" N GLN C 504 " --> pdb=" O VAL C 501 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 635 removed outlier: 3.610A pdb=" N TYR C 634 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 735 through 740 Processing helix chain 'C' and resid 744 through 753 removed outlier: 3.675A pdb=" N LEU C 750 " --> pdb=" O GLU C 746 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 781 removed outlier: 3.765A pdb=" N LEU C 761 " --> pdb=" O PHE C 757 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN C 777 " --> pdb=" O ASP C 773 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU C 778 " --> pdb=" O LYS C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 823 Processing helix chain 'C' and resid 848 through 853 removed outlier: 3.710A pdb=" N LYS C 852 " --> pdb=" O ILE C 848 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE C 853 " --> pdb=" O CYS C 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 848 through 853' Processing helix chain 'C' and resid 864 through 882 removed outlier: 3.508A pdb=" N GLN C 870 " --> pdb=" O GLU C 866 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 888 Processing helix chain 'C' and resid 895 through 905 removed outlier: 3.517A pdb=" N ALA C 901 " --> pdb=" O PRO C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 911 through 917 removed outlier: 3.867A pdb=" N TYR C 915 " --> pdb=" O GLN C 911 " (cutoff:3.500A) Processing helix chain 'C' and resid 917 through 939 removed outlier: 3.579A pdb=" N ILE C 932 " --> pdb=" O ALA C 928 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLN C 933 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ASP C 934 " --> pdb=" O GLY C 930 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER C 937 " --> pdb=" O GLN C 933 " (cutoff:3.500A) Processing helix chain 'C' and resid 943 through 963 removed outlier: 3.514A pdb=" N VAL C 950 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 964 through 966 No H-bonds generated for 'chain 'C' and resid 964 through 966' Processing helix chain 'C' and resid 974 through 982 removed outlier: 3.967A pdb=" N ILE C 978 " --> pdb=" O VAL C 974 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU C 979 " --> pdb=" O LEU C 975 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1030 removed outlier: 4.291A pdb=" N GLU C 988 " --> pdb=" O PRO C 984 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL C 989 " --> pdb=" O PRO C 985 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN C 990 " --> pdb=" O GLU C 986 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 993 " --> pdb=" O VAL C 989 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 997 " --> pdb=" O ARG C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1114 through 1116 No H-bonds generated for 'chain 'C' and resid 1114 through 1116' Processing helix chain 'C' and resid 1139 through 1148 removed outlier: 3.895A pdb=" N PHE C1146 " --> pdb=" O GLU C1142 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS C1147 " --> pdb=" O LEU C1143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 31 Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.278A pdb=" N VAL A 36 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 9.485A pdb=" N LEU A 221 " --> pdb=" O HIS A 205 " (cutoff:3.500A) removed outlier: 9.522A pdb=" N HIS A 205 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N SER A 203 " --> pdb=" O PRO A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 127 removed outlier: 6.131A pdb=" N ARG A 100 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 274 through 276 Processing sheet with id=AA7, first strand: chain 'A' and resid 309 through 317 removed outlier: 5.235A pdb=" N ILE A 310 " --> pdb=" O THR A 597 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 597 " --> pdb=" O ILE A 310 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLN A 312 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N VAL A 595 " --> pdb=" O GLN A 312 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 314 " --> pdb=" O VAL A 593 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 322 through 324 removed outlier: 7.714A pdb=" N GLU A 322 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 322 through 324 removed outlier: 7.714A pdb=" N GLU A 322 " --> pdb=" O ASN A 538 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N ASN A 540 " --> pdb=" O GLU A 322 " (cutoff:3.500A) removed outlier: 7.985A pdb=" N ILE A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 396 through 400 removed outlier: 3.624A pdb=" N ASP A 396 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL A 510 " --> pdb=" O ASP A 396 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 507 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TRP A 434 " --> pdb=" O ARG A 507 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 471 through 472 Processing sheet with id=AB3, first strand: chain 'A' and resid 563 through 564 removed outlier: 6.542A pdb=" N PHE A 563 " --> pdb=" O PHE B 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 574 through 575 Processing sheet with id=AB5, first strand: chain 'A' and resid 662 through 665 removed outlier: 6.784A pdb=" N ILE A 668 " --> pdb=" O ILE A 664 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 699 through 700 removed outlier: 6.652A pdb=" N ALA A 699 " --> pdb=" O ILE B 786 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 709 through 720 removed outlier: 6.419A pdb=" N GLN A1069 " --> pdb=" O THR A 714 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N PHE A 716 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE A 718 " --> pdb=" O TYR A1065 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N TYR A1065 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL A 720 " --> pdb=" O VAL A1063 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL A1063 " --> pdb=" O VAL A 720 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLY A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER A1053 " --> pdb=" O GLY A1057 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N VAL A1059 " --> pdb=" O PRO A1051 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A1061 " --> pdb=" O SER A1049 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N SER A1049 " --> pdb=" O LEU A1061 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N VAL A1063 " --> pdb=" O LEU A1047 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 723 through 726 removed outlier: 3.578A pdb=" N THR A1074 " --> pdb=" O SER A1095 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ALA A1076 " --> pdb=" O PHE A1093 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHE A1093 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 731 through 733 removed outlier: 4.218A pdb=" N LYS A 731 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 785 through 786 Processing sheet with id=AC2, first strand: chain 'A' and resid 1118 through 1123 removed outlier: 3.517A pdb=" N SER A1121 " --> pdb=" O ALA A1085 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ALA A1085 " --> pdb=" O SER A1121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 30 through 31 removed outlier: 3.520A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.318A pdb=" N VAL B 36 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 9.537A pdb=" N LEU B 221 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N HIS B 205 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N SER B 203 " --> pdb=" O PRO B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AC6, first strand: chain 'B' and resid 99 through 103 Processing sheet with id=AC7, first strand: chain 'B' and resid 116 through 119 Processing sheet with id=AC8, first strand: chain 'B' and resid 274 through 276 Processing sheet with id=AC9, first strand: chain 'B' and resid 309 through 317 removed outlier: 5.226A pdb=" N ILE B 310 " --> pdb=" O THR B 597 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N THR B 597 " --> pdb=" O ILE B 310 " (cutoff:3.500A) removed outlier: 5.684A pdb=" N GLN B 312 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 595 " --> pdb=" O GLN B 312 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER B 314 " --> pdb=" O VAL B 593 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 323 through 324 removed outlier: 7.828A pdb=" N ILE B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE B 541 " --> pdb=" O LEU B 544 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 323 through 324 removed outlier: 7.828A pdb=" N ILE B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 396 through 400 removed outlier: 3.540A pdb=" N ASP B 396 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL B 510 " --> pdb=" O ASP B 396 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ILE B 400 " --> pdb=" O TYR B 506 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR B 506 " --> pdb=" O ILE B 400 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B 507 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP B 434 " --> pdb=" O ARG B 507 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 471 through 472 Processing sheet with id=AD5, first strand: chain 'B' and resid 563 through 565 removed outlier: 6.581A pdb=" N PHE B 563 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 574 through 575 Processing sheet with id=AD7, first strand: chain 'B' and resid 662 through 665 removed outlier: 6.773A pdb=" N ILE B 668 " --> pdb=" O ILE B 664 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 699 through 702 Processing sheet with id=AD9, first strand: chain 'B' and resid 709 through 720 removed outlier: 6.717A pdb=" N GLN B1069 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 716 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 718 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR B1065 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 720 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1063 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL B1063 " --> pdb=" O LEU B1047 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 709 through 720 removed outlier: 6.717A pdb=" N GLN B1069 " --> pdb=" O THR B 714 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N PHE B 716 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N ILE B 718 " --> pdb=" O TYR B1065 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR B1065 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL B 720 " --> pdb=" O VAL B1063 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N VAL B1063 " --> pdb=" O VAL B 720 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR B1074 " --> pdb=" O SER B1095 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA B1076 " --> pdb=" O PHE B1093 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N PHE B1093 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 723 through 726 Processing sheet with id=AE3, first strand: chain 'B' and resid 731 through 733 removed outlier: 4.308A pdb=" N LYS B 731 " --> pdb=" O LEU B 859 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 1118 through 1123 removed outlier: 3.542A pdb=" N SER B1121 " --> pdb=" O ALA B1085 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA B1085 " --> pdb=" O SER B1121 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AE7, first strand: chain 'C' and resid 222 through 227 removed outlier: 6.135A pdb=" N SER C 203 " --> pdb=" O PRO C 223 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 124 through 127 removed outlier: 6.095A pdb=" N ARG C 100 " --> pdb=" O ASN C 119 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 274 through 276 Processing sheet with id=AF1, first strand: chain 'C' and resid 309 through 317 removed outlier: 5.253A pdb=" N ILE C 310 " --> pdb=" O THR C 597 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N THR C 597 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLN C 312 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL C 595 " --> pdb=" O GLN C 312 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER C 314 " --> pdb=" O VAL C 593 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.508A pdb=" N PHE C 541 " --> pdb=" O LEU C 544 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 396 through 400 removed outlier: 3.562A pdb=" N ASP C 396 " --> pdb=" O VAL C 510 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 510 " --> pdb=" O ASP C 396 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 507 " --> pdb=" O TRP C 434 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP C 434 " --> pdb=" O ARG C 507 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 471 through 472 Processing sheet with id=AF5, first strand: chain 'C' and resid 574 through 575 Processing sheet with id=AF6, first strand: chain 'C' and resid 662 through 665 removed outlier: 6.770A pdb=" N ILE C 668 " --> pdb=" O ILE C 664 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 709 through 720 removed outlier: 6.920A pdb=" N GLN C1069 " --> pdb=" O THR C 714 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE C 716 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 718 " --> pdb=" O TYR C1065 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1065 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 720 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1063 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N VAL C1063 " --> pdb=" O LEU C1047 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 709 through 720 removed outlier: 6.920A pdb=" N GLN C1069 " --> pdb=" O THR C 714 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N PHE C 716 " --> pdb=" O PRO C1067 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 718 " --> pdb=" O TYR C1065 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR C1065 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL C 720 " --> pdb=" O VAL C1063 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL C1063 " --> pdb=" O VAL C 720 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C1074 " --> pdb=" O SER C1095 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 723 through 726 Processing sheet with id=AG1, first strand: chain 'C' and resid 731 through 733 removed outlier: 4.223A pdb=" N LYS C 731 " --> pdb=" O LEU C 859 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 1118 through 1123 removed outlier: 3.552A pdb=" N SER C1121 " --> pdb=" O ALA C1085 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ALA C1085 " --> pdb=" O SER C1121 " (cutoff:3.500A) 772 hydrogen bonds defined for protein. 2061 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 2.97 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: 8357 1.34 - 1.47: 6852 1.47 - 1.59: 11734 1.59 - 1.71: 0 1.71 - 1.84: 144 Bond restraints: 27087 Sorted by residual: bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.489 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" N THR C 331 " pdb=" CA THR C 331 " ideal model delta sigma weight residual 1.459 1.488 -0.028 9.10e-03 1.21e+04 9.70e+00 bond pdb=" N ILE A 330 " pdb=" CA ILE A 330 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.25e-02 6.40e+03 9.02e+00 bond pdb=" N VAL C 360 " pdb=" CA VAL C 360 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.22e-02 6.72e+03 8.46e+00 bond pdb=" N ILE B 330 " pdb=" CA ILE B 330 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.25e-02 6.40e+03 8.38e+00 ... (remaining 27082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 35600 1.56 - 3.13: 1105 3.13 - 4.69: 140 4.69 - 6.26: 37 6.26 - 7.82: 9 Bond angle restraints: 36891 Sorted by residual: angle pdb=" N SER B 528 " pdb=" CA SER B 528 " pdb=" C SER B 528 " ideal model delta sigma weight residual 110.50 104.99 5.51 1.41e+00 5.03e-01 1.53e+01 angle pdb=" N SER C 528 " pdb=" CA SER C 528 " pdb=" C SER C 528 " ideal model delta sigma weight residual 110.53 105.50 5.03 1.32e+00 5.74e-01 1.45e+01 angle pdb=" CA LEU C 333 " pdb=" C LEU C 333 " pdb=" O LEU C 333 " ideal model delta sigma weight residual 121.44 117.51 3.93 1.08e+00 8.57e-01 1.33e+01 angle pdb=" C CYS C 359 " pdb=" CA CYS C 359 " pdb=" CB CYS C 359 " ideal model delta sigma weight residual 114.87 109.38 5.49 1.51e+00 4.39e-01 1.32e+01 angle pdb=" CA LEU B 333 " pdb=" C LEU B 333 " pdb=" O LEU B 333 " ideal model delta sigma weight residual 121.44 117.54 3.90 1.08e+00 8.57e-01 1.30e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 14092 17.99 - 35.99: 1197 35.99 - 53.98: 179 53.98 - 71.98: 44 71.98 - 89.97: 31 Dihedral angle restraints: 15543 sinusoidal: 6030 harmonic: 9513 Sorted by residual: dihedral pdb=" CB CYS B 660 " pdb=" SG CYS B 660 " pdb=" SG CYS B 669 " pdb=" CB CYS B 669 " ideal model delta sinusoidal sigma weight residual 93.00 10.01 82.99 1 1.00e+01 1.00e-02 8.43e+01 dihedral pdb=" CB CYS C 660 " pdb=" SG CYS C 660 " pdb=" SG CYS C 669 " pdb=" CB CYS C 669 " ideal model delta sinusoidal sigma weight residual 93.00 10.22 82.78 1 1.00e+01 1.00e-02 8.39e+01 dihedral pdb=" CB CYS A 660 " pdb=" SG CYS A 660 " pdb=" SG CYS A 669 " pdb=" CB CYS A 669 " ideal model delta sinusoidal sigma weight residual -86.00 -5.22 -80.78 1 1.00e+01 1.00e-02 8.06e+01 ... (remaining 15540 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 4147 0.101 - 0.201: 198 0.201 - 0.302: 5 0.302 - 0.402: 2 0.402 - 0.503: 4 Chirality restraints: 4356 Sorted by residual: chirality pdb=" C1 NAG C1304 " pdb=" ND2 ASN C 147 " pdb=" C2 NAG C1304 " pdb=" O5 NAG C1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.32e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 147 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.24e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 147 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 6.09e+00 ... (remaining 4353 not shown) Planarity restraints: 4743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO B 525 " -0.016 2.00e-02 2.50e+03 3.31e-02 1.10e+01 pdb=" C PRO B 525 " 0.057 2.00e-02 2.50e+03 pdb=" O PRO B 525 " -0.022 2.00e-02 2.50e+03 pdb=" N LYS B 526 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 525 " -0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C PRO C 525 " 0.053 2.00e-02 2.50e+03 pdb=" O PRO C 525 " -0.021 2.00e-02 2.50e+03 pdb=" N LYS C 526 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 525 " 0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C PRO A 525 " -0.049 2.00e-02 2.50e+03 pdb=" O PRO A 525 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS A 526 " 0.017 2.00e-02 2.50e+03 ... (remaining 4740 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 573 2.68 - 3.23: 25833 3.23 - 3.79: 39764 3.79 - 4.34: 53393 4.34 - 4.90: 86984 Nonbonded interactions: 206547 Sorted by model distance: nonbonded pdb=" OG SER A 756 " pdb=" OE1 GLN C 963 " model vdw 2.121 3.040 nonbonded pdb=" OG1 THR A1114 " pdb=" OD1 ASP A1116 " model vdw 2.190 3.040 nonbonded pdb=" OG1 THR B1114 " pdb=" OD1 ASP B1116 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR C1114 " pdb=" OD1 ASP C1116 " model vdw 2.208 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.209 3.040 ... (remaining 206542 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.240 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: 0.460 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.980 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 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 : 0.004 0.083 27199 Z= 0.194 Angle : 0.671 14.660 37170 Z= 0.341 Chirality : 0.049 0.503 4356 Planarity : 0.005 0.069 4692 Dihedral : 13.812 89.974 9327 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.03 % Favored : 93.88 % Rotamer: Outliers : 0.49 % Allowed : 0.35 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.14), residues: 3249 helix: -0.07 (0.20), residues: 630 sheet: -1.00 (0.22), residues: 495 loop : -1.92 (0.13), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 903 TYR 0.026 0.001 TYR A 158 PHE 0.028 0.001 PHE B 65 TRP 0.016 0.001 TRP A 631 HIS 0.013 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.19 (27087) covalent geometry : angle 0.62737 / 0.33 (36891) SS BOND : bond 0.00620 / 0.35 ( 36) SS BOND : angle 1.70223 / 1.21 ( 72) hydrogen bonds : bond 0.24062 / 15.85 ( 762) hydrogen bonds : angle 8.99694 / 6.21 ( 2061) Misc. bond : bond 0.00088 / 0.03 ( 7) link_BETA1-4 : bond 0.00522 / 0.37 ( 18) link_BETA1-4 : angle 1.62101 / 1.08 ( 54) link_NAG-ASN : bond 0.00694 / 0.45 ( 51) link_NAG-ASN : angle 3.49434 / 2.22 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 354 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7562 (m-10) cc_final: 0.7348 (m-80) REVERT: A 151 MET cc_start: 0.5297 (ttt) cc_final: 0.5071 (mmm) REVERT: A 337 ASP cc_start: 0.7916 (p0) cc_final: 0.7566 (p0) REVERT: A 385 LEU cc_start: 0.8482 (mt) cc_final: 0.8104 (mt) REVERT: A 594 SER cc_start: 0.9058 (p) cc_final: 0.8851 (p) REVERT: A 719 SER cc_start: 0.8771 (t) cc_final: 0.8210 (p) REVERT: A 753 GLN cc_start: 0.8570 (tm-30) cc_final: 0.8170 (tm-30) REVERT: A 963 GLN cc_start: 0.7995 (tm-30) cc_final: 0.7484 (tm-30) REVERT: A 1120 VAL cc_start: 0.8972 (t) cc_final: 0.8592 (p) REVERT: B 308 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8717 (tttm) REVERT: B 337 ASP cc_start: 0.7939 (p0) cc_final: 0.7534 (p0) REVERT: B 385 LEU cc_start: 0.8474 (mt) cc_final: 0.8162 (mt) REVERT: B 491 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7621 (tm-30) REVERT: B 719 SER cc_start: 0.8664 (t) cc_final: 0.7962 (p) REVERT: B 852 LYS cc_start: 0.7104 (mmtm) cc_final: 0.6884 (tttm) REVERT: B 1000 GLN cc_start: 0.7853 (tm-30) cc_final: 0.7003 (tm-30) REVERT: B 1027 MET cc_start: 0.8665 (tpp) cc_final: 0.8456 (tpp) REVERT: C 218 PHE cc_start: 0.6757 (t80) cc_final: 0.6311 (t80) REVERT: C 337 ASP cc_start: 0.7957 (p0) cc_final: 0.7734 (p0) REVERT: C 385 LEU cc_start: 0.8593 (mt) cc_final: 0.8156 (mt) REVERT: C 491 GLN cc_start: 0.7787 (tm-30) cc_final: 0.7533 (tm-30) REVERT: C 852 LYS cc_start: 0.7046 (mmtm) cc_final: 0.6809 (tttp) REVERT: C 1048 MET cc_start: 0.7902 (ptm) cc_final: 0.7637 (ptt) outliers start: 14 outliers final: 3 residues processed: 368 average time/residue: 0.1620 time to fit residues: 95.7512 Evaluate side-chains 184 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 LYS Chi-restraints excluded: chain B residue 329 ASN Chi-restraints excluded: chain C residue 392 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 0.0050 chunk 207 optimal weight: 0.0970 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.4980 chunk 298 optimal weight: 2.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 ASN A 753 GLN ** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 ASN A 955 GLN B 753 GLN B 953 ASN B 955 GLN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 194 ASN C 760 GLN C 893 GLN C 911 GLN C 953 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.169687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.109258 restraints weight = 47686.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112297 restraints weight = 27736.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.113510 restraints weight = 17468.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.113832 restraints weight = 17631.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.114022 restraints weight = 15534.216| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27199 Z= 0.138 Angle : 0.638 13.179 37170 Z= 0.318 Chirality : 0.046 0.440 4356 Planarity : 0.005 0.100 4692 Dihedral : 4.746 65.911 3515 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 1.34 % Allowed : 8.28 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.14), residues: 3249 helix: 0.54 (0.20), residues: 642 sheet: -1.13 (0.21), residues: 552 loop : -1.91 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 455 TYR 0.021 0.001 TYR A 653 PHE 0.027 0.002 PHE B 131 TRP 0.015 0.001 TRP B 631 HIS 0.009 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (27087) covalent geometry : angle 0.60899 / 0.31 (36891) SS BOND : bond 0.00529 / 0.34 ( 36) SS BOND : angle 1.45153 / 1.06 ( 72) hydrogen bonds : bond 0.04894 / 3.20 ( 762) hydrogen bonds : angle 6.36892 / 4.39 ( 2061) Misc. bond : bond 0.00279 / 0.09 ( 7) link_BETA1-4 : bond 0.00545 / 0.37 ( 18) link_BETA1-4 : angle 1.34156 / 0.90 ( 54) link_NAG-ASN : bond 0.00584 / 0.37 ( 51) link_NAG-ASN : angle 2.80092 / 1.79 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 239 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7830 (m-10) cc_final: 0.7359 (m-80) REVERT: A 151 MET cc_start: 0.5489 (ttt) cc_final: 0.5152 (mmm) REVERT: A 385 LEU cc_start: 0.8516 (mt) cc_final: 0.8202 (mt) REVERT: A 719 SER cc_start: 0.8852 (t) cc_final: 0.8338 (p) REVERT: A 753 GLN cc_start: 0.8621 (tm130) cc_final: 0.7957 (tm-30) REVERT: A 963 GLN cc_start: 0.7799 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 1120 VAL cc_start: 0.8943 (t) cc_final: 0.8582 (p) REVERT: B 151 MET cc_start: 0.4758 (mmm) cc_final: 0.3670 (mpp) REVERT: B 308 LYS cc_start: 0.9033 (ttmt) cc_final: 0.8822 (tttt) REVERT: B 385 LEU cc_start: 0.8498 (mt) cc_final: 0.8044 (mt) REVERT: B 491 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7518 (tm-30) REVERT: B 608 VAL cc_start: 0.9191 (m) cc_final: 0.8982 (t) REVERT: B 719 SER cc_start: 0.8763 (t) cc_final: 0.8177 (p) REVERT: C 218 PHE cc_start: 0.6813 (t80) cc_final: 0.6209 (t80) REVERT: C 385 LEU cc_start: 0.8587 (mt) cc_final: 0.8165 (mt) REVERT: C 659 GLU cc_start: 0.7629 (tm-30) cc_final: 0.6993 (tm-30) REVERT: C 1120 VAL cc_start: 0.8868 (t) cc_final: 0.8516 (p) outliers start: 38 outliers final: 20 residues processed: 269 average time/residue: 0.1528 time to fit residues: 66.5913 Evaluate side-chains 192 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 753 GLN Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 974 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 166 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 262 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 256 optimal weight: 20.0000 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 chunk 109 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 180 optimal weight: 0.8980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 760 GLN A 911 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN C 119 ASN C 760 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.163952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.103963 restraints weight = 48195.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.107397 restraints weight = 28859.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.107888 restraints weight = 19030.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.108207 restraints weight = 17050.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.108449 restraints weight = 17707.931| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27199 Z= 0.142 Angle : 0.600 12.399 37170 Z= 0.298 Chirality : 0.045 0.420 4356 Planarity : 0.004 0.061 4692 Dihedral : 4.463 42.637 3509 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.27 % Allowed : 10.61 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.14), residues: 3249 helix: 0.82 (0.20), residues: 639 sheet: -1.13 (0.21), residues: 537 loop : -1.86 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 455 TYR 0.017 0.001 TYR C1136 PHE 0.021 0.001 PHE A 199 TRP 0.021 0.001 TRP A 884 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (27087) covalent geometry : angle 0.57121 / 0.29 (36891) SS BOND : bond 0.00454 / 0.28 ( 36) SS BOND : angle 1.43224 / 1.05 ( 72) hydrogen bonds : bond 0.04675 / 3.04 ( 762) hydrogen bonds : angle 5.89881 / 4.06 ( 2061) Misc. bond : bond 0.00099 / 0.04 ( 7) link_BETA1-4 : bond 0.00439 / 0.30 ( 18) link_BETA1-4 : angle 1.41188 / 0.95 ( 54) link_NAG-ASN : bond 0.00555 / 0.34 ( 51) link_NAG-ASN : angle 2.65138 / 1.70 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5539 (ttt) cc_final: 0.5162 (mmm) REVERT: A 719 SER cc_start: 0.8871 (t) cc_final: 0.8337 (p) REVERT: A 753 GLN cc_start: 0.8719 (tm130) cc_final: 0.8038 (tm-30) REVERT: A 963 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7387 (tm-30) REVERT: B 308 LYS cc_start: 0.9118 (ttmt) cc_final: 0.8866 (tttt) REVERT: B 385 LEU cc_start: 0.8490 (mt) cc_final: 0.8064 (mt) REVERT: B 491 GLN cc_start: 0.7922 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 719 SER cc_start: 0.8794 (t) cc_final: 0.8184 (p) REVERT: C 385 LEU cc_start: 0.8643 (mt) cc_final: 0.8205 (mt) REVERT: C 659 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7430 (tm-30) REVERT: C 738 MET cc_start: 0.7645 (mmm) cc_final: 0.7431 (ttt) outliers start: 36 outliers final: 26 residues processed: 211 average time/residue: 0.1543 time to fit residues: 53.6931 Evaluate side-chains 188 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 119 ASN Chi-restraints excluded: chain C residue 392 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 263 optimal weight: 0.0870 chunk 17 optimal weight: 8.9990 chunk 287 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 265 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 chunk 288 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 170 optimal weight: 0.9990 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 760 GLN A 870 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 392 ASN C 760 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.168917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108048 restraints weight = 47422.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111389 restraints weight = 31525.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112474 restraints weight = 18803.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.112894 restraints weight = 16295.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.113362 restraints weight = 16472.350| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27199 Z= 0.117 Angle : 0.573 11.649 37170 Z= 0.283 Chirality : 0.045 0.409 4356 Planarity : 0.004 0.060 4692 Dihedral : 4.330 29.985 3509 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 1.41 % Allowed : 12.09 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.14), residues: 3249 helix: 1.04 (0.20), residues: 642 sheet: -1.12 (0.21), residues: 543 loop : -1.80 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 455 TYR 0.018 0.001 TYR B1136 PHE 0.015 0.001 PHE A 199 TRP 0.015 0.001 TRP B 631 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (27087) covalent geometry : angle 0.54600 / 0.28 (36891) SS BOND : bond 0.00375 / 0.23 ( 36) SS BOND : angle 1.34568 / 0.96 ( 72) hydrogen bonds : bond 0.04165 / 2.71 ( 762) hydrogen bonds : angle 5.61380 / 3.86 ( 2061) Misc. bond : bond 0.00086 / 0.04 ( 7) link_BETA1-4 : bond 0.00430 / 0.30 ( 18) link_BETA1-4 : angle 1.38665 / 0.94 ( 54) link_NAG-ASN : bond 0.00524 / 0.33 ( 51) link_NAG-ASN : angle 2.50404 / 1.61 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 182 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5549 (ttt) cc_final: 0.5136 (mmm) REVERT: A 719 SER cc_start: 0.8897 (t) cc_final: 0.8387 (p) REVERT: A 753 GLN cc_start: 0.8702 (tm130) cc_final: 0.8114 (tm-30) REVERT: A 963 GLN cc_start: 0.7871 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 1120 VAL cc_start: 0.8786 (t) cc_final: 0.8495 (p) REVERT: B 272 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8031 (m) REVERT: B 308 LYS cc_start: 0.9108 (ttmt) cc_final: 0.8867 (tttt) REVERT: B 385 LEU cc_start: 0.8496 (mt) cc_final: 0.8066 (mt) REVERT: B 1003 GLN cc_start: 0.8090 (tp40) cc_final: 0.7778 (tt0) REVERT: C 272 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7778 (m) REVERT: C 385 LEU cc_start: 0.8641 (mt) cc_final: 0.8205 (mt) REVERT: C 971 ILE cc_start: 0.9033 (mp) cc_final: 0.8779 (mm) REVERT: C 1120 VAL cc_start: 0.8869 (t) cc_final: 0.8555 (p) outliers start: 40 outliers final: 27 residues processed: 210 average time/residue: 0.1425 time to fit residues: 49.6313 Evaluate side-chains 189 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 604 ASN Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 241 optimal weight: 8.9990 chunk 224 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 201 optimal weight: 2.9990 chunk 300 optimal weight: 2.9990 chunk 315 optimal weight: 0.9990 chunk 304 optimal weight: 0.0670 chunk 255 optimal weight: 8.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 760 GLN C1052 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.164862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102916 restraints weight = 47084.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.106337 restraints weight = 24859.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.108406 restraints weight = 17177.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.109800 restraints weight = 13972.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110383 restraints weight = 12404.756| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 27199 Z= 0.185 Angle : 0.615 10.790 37170 Z= 0.303 Chirality : 0.046 0.380 4356 Planarity : 0.004 0.060 4692 Dihedral : 4.399 21.867 3507 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.04 % Allowed : 13.64 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.14), residues: 3249 helix: 1.01 (0.20), residues: 642 sheet: -1.29 (0.21), residues: 543 loop : -1.83 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 455 TYR 0.019 0.001 TYR A1136 PHE 0.031 0.002 PHE C 199 TRP 0.021 0.002 TRP B 631 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.18 (27087) covalent geometry : angle 0.58921 / 0.30 (36891) SS BOND : bond 0.00474 / 0.28 ( 36) SS BOND : angle 1.65959 / 1.21 ( 72) hydrogen bonds : bond 0.04614 / 2.99 ( 762) hydrogen bonds : angle 5.54992 / 3.82 ( 2061) Misc. bond : bond 0.00111 / 0.05 ( 7) link_BETA1-4 : bond 0.00425 / 0.30 ( 18) link_BETA1-4 : angle 1.46394 / 0.99 ( 54) link_NAG-ASN : bond 0.00504 / 0.30 ( 51) link_NAG-ASN : angle 2.45886 / 1.60 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 180 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 719 SER cc_start: 0.8871 (t) cc_final: 0.8339 (p) REVERT: B 272 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7768 (m) REVERT: B 385 LEU cc_start: 0.8461 (mt) cc_final: 0.8113 (mt) REVERT: C 168 TYR cc_start: 0.7999 (m-80) cc_final: 0.7740 (m-80) REVERT: C 272 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7852 (m) REVERT: C 385 LEU cc_start: 0.8623 (mt) cc_final: 0.8229 (mt) REVERT: C 513 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7009 (p90) outliers start: 58 outliers final: 39 residues processed: 221 average time/residue: 0.1401 time to fit residues: 52.3344 Evaluate side-chains 210 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 168 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 226 ASP Chi-restraints excluded: chain B residue 272 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 ILE Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 513 PHE Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 545 THR Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 991 ILE Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 88 optimal weight: 0.3980 chunk 149 optimal weight: 7.9990 chunk 152 optimal weight: 6.9990 chunk 137 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 41 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 194 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.167320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.106749 restraints weight = 47603.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.110001 restraints weight = 28367.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.109808 restraints weight = 18291.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.110569 restraints weight = 18197.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.110863 restraints weight = 16419.298| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 27199 Z= 0.113 Angle : 0.571 10.466 37170 Z= 0.280 Chirality : 0.045 0.379 4356 Planarity : 0.004 0.060 4692 Dihedral : 4.223 20.083 3507 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 1.66 % Allowed : 14.45 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.15), residues: 3249 helix: 1.37 (0.21), residues: 636 sheet: -1.41 (0.20), residues: 618 loop : -1.76 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1105 TYR 0.019 0.001 TYR B1136 PHE 0.013 0.001 PHE B 218 TRP 0.020 0.001 TRP B 631 HIS 0.004 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 (27087) covalent geometry : angle 0.54714 / 0.27 (36891) SS BOND : bond 0.00328 / 0.20 ( 36) SS BOND : angle 1.32364 / 0.94 ( 72) hydrogen bonds : bond 0.03981 / 2.58 ( 762) hydrogen bonds : angle 5.36344 / 3.69 ( 2061) Misc. bond : bond 0.00076 / 0.03 ( 7) link_BETA1-4 : bond 0.00441 / 0.30 ( 18) link_BETA1-4 : angle 1.36454 / 0.94 ( 54) link_NAG-ASN : bond 0.00471 / 0.29 ( 51) link_NAG-ASN : angle 2.34351 / 1.52 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.4273 (mmm) cc_final: 0.3450 (mpp) REVERT: A 491 GLN cc_start: 0.7251 (tm-30) cc_final: 0.6965 (tm-30) REVERT: A 719 SER cc_start: 0.8882 (t) cc_final: 0.8375 (p) REVERT: A 963 GLN cc_start: 0.7954 (tm-30) cc_final: 0.7334 (tm-30) REVERT: B 199 PHE cc_start: 0.6954 (t80) cc_final: 0.6690 (t80) REVERT: B 385 LEU cc_start: 0.8535 (mt) cc_final: 0.8136 (mt) REVERT: C 385 LEU cc_start: 0.8646 (mt) cc_final: 0.8204 (mt) REVERT: C 971 ILE cc_start: 0.9050 (mp) cc_final: 0.8843 (mm) outliers start: 47 outliers final: 39 residues processed: 202 average time/residue: 0.1375 time to fit residues: 46.5114 Evaluate side-chains 200 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 198 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 745 THR Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 778 GLU Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 114 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 293 optimal weight: 0.7980 chunk 259 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 chunk 227 optimal weight: 6.9990 chunk 130 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.166803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106540 restraints weight = 47380.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.109751 restraints weight = 28377.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.109301 restraints weight = 18926.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.110107 restraints weight = 18582.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110184 restraints weight = 17357.818| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27199 Z= 0.124 Angle : 0.572 10.063 37170 Z= 0.281 Chirality : 0.045 0.366 4356 Planarity : 0.004 0.060 4692 Dihedral : 4.160 20.347 3507 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.90 % Allowed : 14.34 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3249 helix: 1.45 (0.21), residues: 636 sheet: -1.44 (0.20), residues: 588 loop : -1.77 (0.13), residues: 2025 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1105 TYR 0.025 0.001 TYR B 198 PHE 0.031 0.001 PHE C 199 TRP 0.018 0.001 TRP B 631 HIS 0.004 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.12 (27087) covalent geometry : angle 0.54863 / 0.28 (36891) SS BOND : bond 0.00360 / 0.22 ( 36) SS BOND : angle 1.38811 / 1.00 ( 72) hydrogen bonds : bond 0.03933 / 2.56 ( 762) hydrogen bonds : angle 5.25364 / 3.62 ( 2061) Misc. bond : bond 0.00079 / 0.03 ( 7) link_BETA1-4 : bond 0.00430 / 0.30 ( 18) link_BETA1-4 : angle 1.38760 / 0.95 ( 54) link_NAG-ASN : bond 0.00451 / 0.28 ( 51) link_NAG-ASN : angle 2.27769 / 1.48 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.4175 (mmm) cc_final: 0.3223 (mpp) REVERT: A 491 GLN cc_start: 0.7233 (tm-30) cc_final: 0.6971 (tm-30) REVERT: A 719 SER cc_start: 0.8899 (t) cc_final: 0.8379 (p) REVERT: A 963 GLN cc_start: 0.7988 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 385 LEU cc_start: 0.8576 (mt) cc_final: 0.8241 (mt) REVERT: C 168 TYR cc_start: 0.8062 (m-80) cc_final: 0.7759 (m-80) REVERT: C 272 THR cc_start: 0.8008 (OUTLIER) cc_final: 0.7784 (m) REVERT: C 385 LEU cc_start: 0.8605 (mt) cc_final: 0.8175 (mt) REVERT: C 971 ILE cc_start: 0.9019 (mp) cc_final: 0.8798 (mm) outliers start: 54 outliers final: 39 residues processed: 212 average time/residue: 0.1376 time to fit residues: 49.5561 Evaluate side-chains 201 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 991 ILE Chi-restraints excluded: chain B residue 1048 MET Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 272 THR Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 0.1980 chunk 272 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 233 optimal weight: 3.9990 chunk 99 optimal weight: 0.6980 chunk 266 optimal weight: 8.9990 chunk 156 optimal weight: 0.2980 chunk 292 optimal weight: 0.7980 chunk 192 optimal weight: 0.6980 chunk 12 optimal weight: 8.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 GLN ** 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 = 0.4252 r_free = 0.4252 target = 0.169167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.120447 restraints weight = 47283.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.114888 restraints weight = 44517.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.113961 restraints weight = 37869.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.113548 restraints weight = 28559.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.114024 restraints weight = 28049.695| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 27199 Z= 0.105 Angle : 0.572 15.016 37170 Z= 0.280 Chirality : 0.044 0.365 4356 Planarity : 0.004 0.061 4692 Dihedral : 4.068 19.478 3507 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.44 % Allowed : 14.94 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.15), residues: 3249 helix: 1.57 (0.21), residues: 642 sheet: -1.35 (0.20), residues: 624 loop : -1.75 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1105 TYR 0.022 0.001 TYR B 198 PHE 0.025 0.001 PHE A 90 TRP 0.015 0.001 TRP B 631 HIS 0.004 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (27087) covalent geometry : angle 0.55074 / 0.27 (36891) SS BOND : bond 0.00282 / 0.18 ( 36) SS BOND : angle 1.24204 / 0.88 ( 72) hydrogen bonds : bond 0.03678 / 2.41 ( 762) hydrogen bonds : angle 5.15083 / 3.56 ( 2061) Misc. bond : bond 0.00066 / 0.03 ( 7) link_BETA1-4 : bond 0.00417 / 0.28 ( 18) link_BETA1-4 : angle 1.36471 / 0.94 ( 54) link_NAG-ASN : bond 0.00441 / 0.27 ( 51) link_NAG-ASN : angle 2.22353 / 1.44 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.3922 (mmm) cc_final: 0.3699 (mmm) REVERT: A 523 CYS cc_start: 0.2947 (OUTLIER) cc_final: 0.1310 (p) REVERT: A 550 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7747 (mm) REVERT: A 719 SER cc_start: 0.8821 (t) cc_final: 0.8403 (p) REVERT: B 385 LEU cc_start: 0.8298 (mt) cc_final: 0.8097 (mt) REVERT: C 385 LEU cc_start: 0.8335 (mt) cc_final: 0.8036 (mt) REVERT: C 902 TYR cc_start: 0.6529 (OUTLIER) cc_final: 0.5778 (m-80) REVERT: C 971 ILE cc_start: 0.8863 (mp) cc_final: 0.8658 (mm) outliers start: 41 outliers final: 30 residues processed: 188 average time/residue: 0.1310 time to fit residues: 41.9750 Evaluate side-chains 182 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 149 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 757 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 27 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 141 optimal weight: 7.9990 chunk 190 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 119 optimal weight: 0.0270 chunk 161 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.0844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 963 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1003 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.165416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.106025 restraints weight = 47451.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.107203 restraints weight = 33956.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107068 restraints weight = 28254.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.107355 restraints weight = 26446.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107527 restraints weight = 24444.194| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 27199 Z= 0.132 Angle : 0.578 12.023 37170 Z= 0.283 Chirality : 0.045 0.353 4356 Planarity : 0.004 0.061 4692 Dihedral : 4.071 20.218 3507 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 1.44 % Allowed : 15.19 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.15), residues: 3249 helix: 1.54 (0.21), residues: 642 sheet: -1.30 (0.20), residues: 618 loop : -1.72 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.022 0.001 TYR B 198 PHE 0.032 0.001 PHE C 199 TRP 0.016 0.001 TRP B 631 HIS 0.003 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.13 (27087) covalent geometry : angle 0.55674 / 0.28 (36891) SS BOND : bond 0.00380 / 0.23 ( 36) SS BOND : angle 1.43289 / 1.05 ( 72) hydrogen bonds : bond 0.03882 / 2.52 ( 762) hydrogen bonds : angle 5.15134 / 3.56 ( 2061) Misc. bond : bond 0.00082 / 0.04 ( 7) link_BETA1-4 : bond 0.00426 / 0.30 ( 18) link_BETA1-4 : angle 1.38238 / 0.95 ( 54) link_NAG-ASN : bond 0.00436 / 0.27 ( 51) link_NAG-ASN : angle 2.19350 / 1.43 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 165 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.4125 (mmm) cc_final: 0.3914 (mmm) REVERT: A 550 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7853 (mm) REVERT: A 719 SER cc_start: 0.8825 (t) cc_final: 0.8362 (p) REVERT: B 385 LEU cc_start: 0.8405 (mt) cc_final: 0.8108 (mt) REVERT: C 385 LEU cc_start: 0.8481 (mt) cc_final: 0.8121 (mt) REVERT: C 902 TYR cc_start: 0.6744 (OUTLIER) cc_final: 0.6017 (m-80) REVERT: C 971 ILE cc_start: 0.8928 (mp) cc_final: 0.8720 (mm) outliers start: 41 outliers final: 35 residues processed: 189 average time/residue: 0.1512 time to fit residues: 48.8736 Evaluate side-chains 195 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 158 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 MET Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain A residue 1048 MET Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 695 MET Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 48 optimal weight: 0.6980 chunk 117 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 222 optimal weight: 3.9990 chunk 3 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 317 optimal weight: 1.9990 chunk 265 optimal weight: 0.3980 chunk 160 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 760 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.164723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108333 restraints weight = 47538.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.110086 restraints weight = 31793.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.109935 restraints weight = 24342.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.110122 restraints weight = 26852.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.110254 restraints weight = 23223.724| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27199 Z= 0.124 Angle : 0.580 11.210 37170 Z= 0.284 Chirality : 0.044 0.353 4356 Planarity : 0.004 0.061 4692 Dihedral : 4.051 19.935 3507 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.37 % Allowed : 15.40 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.15), residues: 3249 helix: 1.66 (0.21), residues: 639 sheet: -1.28 (0.20), residues: 618 loop : -1.70 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 813 TYR 0.018 0.001 TYR A1136 PHE 0.026 0.001 PHE A 90 TRP 0.015 0.001 TRP B 631 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (27087) covalent geometry : angle 0.55913 / 0.28 (36891) SS BOND : bond 0.00312 / 0.19 ( 36) SS BOND : angle 1.36750 / 0.99 ( 72) hydrogen bonds : bond 0.03797 / 2.47 ( 762) hydrogen bonds : angle 5.09910 / 3.53 ( 2061) Misc. bond : bond 0.00076 / 0.03 ( 7) link_BETA1-4 : bond 0.00445 / 0.31 ( 18) link_BETA1-4 : angle 1.36145 / 0.94 ( 54) link_NAG-ASN : bond 0.00428 / 0.27 ( 51) link_NAG-ASN : angle 2.17156 / 1.41 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6498 Ramachandran restraints generated. 3249 Oldfield, 0 Emsley, 3249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 161 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 CYS cc_start: 0.3056 (OUTLIER) cc_final: 0.1361 (p) REVERT: A 550 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7893 (mm) REVERT: A 719 SER cc_start: 0.8836 (t) cc_final: 0.8377 (p) REVERT: B 385 LEU cc_start: 0.8322 (mt) cc_final: 0.8056 (mt) REVERT: C 385 LEU cc_start: 0.8374 (mt) cc_final: 0.8098 (mt) REVERT: C 719 SER cc_start: 0.8773 (t) cc_final: 0.8265 (p) REVERT: C 902 TYR cc_start: 0.6735 (OUTLIER) cc_final: 0.5912 (m-80) REVERT: C 971 ILE cc_start: 0.8903 (mp) cc_final: 0.8700 (mm) outliers start: 39 outliers final: 34 residues processed: 185 average time/residue: 0.1592 time to fit residues: 50.1213 Evaluate side-chains 192 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 155 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 GLU Chi-restraints excluded: chain A residue 331 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 428 THR Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 938 SER Chi-restraints excluded: chain B residue 46 SER Chi-restraints excluded: chain B residue 158 TYR Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 523 CYS Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 615 CYS Chi-restraints excluded: chain B residue 631 TRP Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 991 ILE Chi-restraints excluded: chain C residue 158 TYR Chi-restraints excluded: chain C residue 175 MET Chi-restraints excluded: chain C residue 333 LEU Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 789 THR Chi-restraints excluded: chain C residue 902 TYR Chi-restraints excluded: chain C residue 938 SER Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Chi-restraints excluded: chain C residue 1095 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 318 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 76 optimal weight: 0.0270 chunk 248 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 173 optimal weight: 6.9990 chunk 174 optimal weight: 7.9990 chunk 321 optimal weight: 0.0870 chunk 51 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 760 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.165802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111401 restraints weight = 47270.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111467 restraints weight = 31759.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110929 restraints weight = 25220.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111764 restraints weight = 27524.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.111562 restraints weight = 24300.436| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 27199 Z= 0.103 Angle : 0.564 10.646 37170 Z= 0.276 Chirality : 0.044 0.349 4356 Planarity : 0.004 0.061 4692 Dihedral : 3.960 19.166 3507 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.30 % Allowed : 15.61 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.15), residues: 3249 helix: 1.75 (0.21), residues: 639 sheet: -1.26 (0.20), residues: 627 loop : -1.70 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 455 TYR 0.021 0.001 TYR A1136 PHE 0.032 0.001 PHE C 199 TRP 0.013 0.001 TRP B 631 HIS 0.003 0.001 HIS B 517 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (27087) covalent geometry : angle 0.54368 / 0.27 (36891) SS BOND : bond 0.00317 / 0.20 ( 36) SS BOND : angle 1.28209 / 0.93 ( 72) hydrogen bonds : bond 0.03578 / 2.32 ( 762) hydrogen bonds : angle 5.01407 / 3.48 ( 2061) Misc. bond : bond 0.00065 / 0.03 ( 7) link_BETA1-4 : bond 0.00448 / 0.31 ( 18) link_BETA1-4 : angle 1.34467 / 0.93 ( 54) link_NAG-ASN : bond 0.00428 / 0.27 ( 51) link_NAG-ASN : angle 2.11493 / 1.37 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4328.07 seconds wall clock time: 91 minutes 15.64 seconds (5475.64 seconds total)