Starting phenix.real_space_refine on Fri Mar 6 00:44:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xnq_33323/03_2026/7xnq_33323.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnq_33323/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7xnq_33323/03_2026/7xnq_33323.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnq_33323/03_2026/7xnq_33323.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnq_33323/03_2026/7xnq_33323.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnq_33323/03_2026/7xnq_33323.map" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "C" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Time building chain proxies: 5.70, per 1000 atoms: 0.22 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 1.2 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: 1.19 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: 5.55 Time building geometry restraints manager: 3.01 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 - 22.40: 15814 22.40 - 44.79: 973 44.79 - 67.19: 144 67.19 - 89.59: 45 89.59 - 111.98: 16 Dihedral angle restraints: 16992 sinusoidal: 7479 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 16989 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: 2.010 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.430 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 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 : 14.677 111.983 10776 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 covalent geometry : bond 0.00362 (27087) covalent geometry : angle 0.62737 (36891) SS BOND : bond 0.00620 ( 36) SS BOND : angle 1.70223 ( 72) hydrogen bonds : bond 0.24062 ( 762) hydrogen bonds : angle 8.99694 ( 2061) Misc. bond : bond 0.00088 ( 7) link_BETA1-4 : bond 0.00522 ( 18) link_BETA1-4 : angle 1.62101 ( 54) link_NAG-ASN : bond 0.00694 ( 51) link_NAG-ASN : angle 3.49434 ( 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 : 0.929 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: 0.1627 time to fit residues: 96.2582 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 : 0.802 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 392 ASN C 760 GLN C 893 GLN C 911 GLN C 953 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.169576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109206 restraints weight = 47641.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.112203 restraints weight = 27693.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.113351 restraints weight = 17502.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.113716 restraints weight = 17636.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.113848 restraints weight = 15556.163| |-----------------------------------------------------------------------------| r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.1565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27199 Z= 0.139 Angle : 0.647 13.292 37170 Z= 0.321 Chirality : 0.046 0.457 4356 Planarity : 0.005 0.090 4692 Dihedral : 8.706 97.004 4964 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 1.20 % Allowed : 8.60 % Favored : 90.20 % 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: 0.57 (0.20), residues: 639 sheet: -1.12 (0.21), residues: 552 loop : -1.92 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 455 TYR 0.021 0.001 TYR A 653 PHE 0.025 0.002 PHE C 199 TRP 0.014 0.001 TRP B 631 HIS 0.009 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00321 (27087) covalent geometry : angle 0.61724 (36891) SS BOND : bond 0.00472 ( 36) SS BOND : angle 1.43878 ( 72) hydrogen bonds : bond 0.05137 ( 762) hydrogen bonds : angle 6.33047 ( 2061) Misc. bond : bond 0.00092 ( 7) link_BETA1-4 : bond 0.00526 ( 18) link_BETA1-4 : angle 1.38416 ( 54) link_NAG-ASN : bond 0.00571 ( 51) link_NAG-ASN : angle 2.88512 ( 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 275 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 241 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7849 (m-10) cc_final: 0.7363 (m-80) REVERT: A 151 MET cc_start: 0.5508 (ttt) cc_final: 0.5159 (mmm) REVERT: A 385 LEU cc_start: 0.8546 (mt) cc_final: 0.8214 (mt) REVERT: A 719 SER cc_start: 0.8859 (t) cc_final: 0.8332 (p) REVERT: A 753 GLN cc_start: 0.8621 (tm130) cc_final: 0.7932 (tm-30) REVERT: A 963 GLN cc_start: 0.7848 (tm-30) cc_final: 0.7406 (tm-30) REVERT: A 1120 VAL cc_start: 0.8968 (t) cc_final: 0.8613 (p) REVERT: B 151 MET cc_start: 0.4771 (mmm) cc_final: 0.3684 (mpp) REVERT: B 308 LYS cc_start: 0.9062 (ttmt) cc_final: 0.8829 (tttt) REVERT: B 385 LEU cc_start: 0.8524 (mt) cc_final: 0.8046 (mt) REVERT: B 491 GLN cc_start: 0.7860 (tm-30) cc_final: 0.7502 (tm-30) REVERT: B 608 VAL cc_start: 0.9170 (m) cc_final: 0.8968 (t) REVERT: B 719 SER cc_start: 0.8766 (t) cc_final: 0.8168 (p) REVERT: B 1011 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8858 (mp) REVERT: C 218 PHE cc_start: 0.6790 (t80) cc_final: 0.6173 (t80) REVERT: C 385 LEU cc_start: 0.8611 (mt) cc_final: 0.8172 (mt) REVERT: C 659 GLU cc_start: 0.7643 (tm-30) cc_final: 0.6999 (tm-30) REVERT: C 774 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8522 (ttmm) REVERT: C 852 LYS cc_start: 0.7374 (mmtm) cc_final: 0.7155 (tttp) REVERT: C 1120 VAL cc_start: 0.8901 (t) cc_final: 0.8552 (p) outliers start: 34 outliers final: 20 residues processed: 266 average time/residue: 0.1641 time to fit residues: 71.0562 Evaluate side-chains 193 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.979 ------------------------------------------------------------------------------- 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 974 VAL Chi-restraints excluded: chain B residue 1011 ILE 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 393 VAL Chi-restraints excluded: chain C residue 774 LYS Chi-restraints excluded: chain C residue 910 THR Chi-restraints excluded: chain C residue 974 VAL Chi-restraints excluded: chain C residue 1025 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 166 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 111 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 38 optimal weight: 0.6980 chunk 180 optimal weight: 0.9980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 760 GLN A 911 GLN ** B 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 760 GLN C 119 ASN C 415 ASN C 760 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.168902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107654 restraints weight = 47848.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111144 restraints weight = 30762.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112398 restraints weight = 18687.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112727 restraints weight = 16519.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113139 restraints weight = 15969.210| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 27199 Z= 0.142 Angle : 0.602 12.326 37170 Z= 0.299 Chirality : 0.046 0.437 4356 Planarity : 0.004 0.061 4692 Dihedral : 7.239 92.248 4956 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 1.52 % Allowed : 10.54 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.14), residues: 3249 helix: 0.81 (0.20), residues: 639 sheet: -1.10 (0.21), residues: 537 loop : -1.85 (0.13), residues: 2073 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 455 TYR 0.017 0.001 TYR A1065 PHE 0.016 0.001 PHE C 557 TRP 0.020 0.001 TRP A 884 HIS 0.006 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00332 (27087) covalent geometry : angle 0.57210 (36891) SS BOND : bond 0.00474 ( 36) SS BOND : angle 1.43109 ( 72) hydrogen bonds : bond 0.04702 ( 762) hydrogen bonds : angle 5.87248 ( 2061) Misc. bond : bond 0.00111 ( 7) link_BETA1-4 : bond 0.00453 ( 18) link_BETA1-4 : angle 1.45543 ( 54) link_NAG-ASN : bond 0.00539 ( 51) link_NAG-ASN : angle 2.72242 ( 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 234 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5513 (ttt) cc_final: 0.5138 (mmm) REVERT: A 719 SER cc_start: 0.8885 (t) cc_final: 0.8378 (p) REVERT: A 753 GLN cc_start: 0.8695 (tm130) cc_final: 0.8034 (tm-30) REVERT: A 963 GLN cc_start: 0.7900 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 308 LYS cc_start: 0.9086 (ttmt) cc_final: 0.8866 (tttt) REVERT: B 385 LEU cc_start: 0.8469 (mt) cc_final: 0.8057 (mt) REVERT: B 491 GLN cc_start: 0.7921 (tm-30) cc_final: 0.7595 (tm-30) REVERT: B 1011 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8894 (mp) REVERT: C 385 LEU cc_start: 0.8620 (mt) cc_final: 0.8200 (mt) REVERT: C 659 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7404 (tm-30) REVERT: C 852 LYS cc_start: 0.7383 (mmtm) cc_final: 0.7178 (tttp) REVERT: C 971 ILE cc_start: 0.9032 (mp) cc_final: 0.8788 (mm) REVERT: C 1120 VAL cc_start: 0.8849 (t) cc_final: 0.8542 (p) outliers start: 43 outliers final: 29 residues processed: 221 average time/residue: 0.1576 time to fit residues: 57.6019 Evaluate side-chains 191 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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 523 CYS 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 1011 ILE 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 119 ASN Chi-restraints excluded: chain C residue 393 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 738 MET 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: 10.0000 chunk 17 optimal weight: 9.9990 chunk 287 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 265 optimal weight: 0.0980 chunk 268 optimal weight: 0.6980 chunk 288 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 19 optimal weight: 20.0000 chunk 170 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 870 GLN C 760 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.169316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108508 restraints weight = 47512.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111856 restraints weight = 31199.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.113091 restraints weight = 18616.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.113283 restraints weight = 15986.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.113847 restraints weight = 16518.998| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2200 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= 0.114 Angle : 0.571 11.587 37170 Z= 0.283 Chirality : 0.045 0.424 4356 Planarity : 0.004 0.060 4692 Dihedral : 6.542 89.049 4956 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 1.52 % Allowed : 12.19 % Favored : 86.29 % 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: -1.58 (0.14), residues: 3249 helix: 1.04 (0.20), residues: 642 sheet: -1.14 (0.21), residues: 546 loop : -1.81 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.017 0.001 TYR B1136 PHE 0.024 0.001 PHE B 199 TRP 0.014 0.001 TRP A 884 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00263 (27087) covalent geometry : angle 0.54344 (36891) SS BOND : bond 0.00384 ( 36) SS BOND : angle 1.30342 ( 72) hydrogen bonds : bond 0.04133 ( 762) hydrogen bonds : angle 5.58416 ( 2061) Misc. bond : bond 0.00089 ( 7) link_BETA1-4 : bond 0.00449 ( 18) link_BETA1-4 : angle 1.42605 ( 54) link_NAG-ASN : bond 0.00511 ( 51) link_NAG-ASN : angle 2.53873 ( 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 226 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 183 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.5534 (ttt) cc_final: 0.5133 (mmm) REVERT: A 523 CYS cc_start: 0.2130 (OUTLIER) cc_final: 0.0241 (p) REVERT: A 719 SER cc_start: 0.8916 (t) cc_final: 0.8445 (p) REVERT: A 753 GLN cc_start: 0.8705 (tm130) cc_final: 0.8112 (tm-30) REVERT: A 867 MET cc_start: 0.8759 (mtp) cc_final: 0.8529 (mtp) REVERT: A 963 GLN cc_start: 0.7862 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 1120 VAL cc_start: 0.8781 (t) cc_final: 0.8490 (p) REVERT: B 272 THR cc_start: 0.8244 (OUTLIER) cc_final: 0.8025 (m) REVERT: B 308 LYS cc_start: 0.9105 (ttmt) cc_final: 0.8865 (tttt) REVERT: B 385 LEU cc_start: 0.8497 (mt) cc_final: 0.8064 (mt) REVERT: B 491 GLN cc_start: 0.7935 (tm-30) cc_final: 0.7652 (tm-30) REVERT: B 1003 GLN cc_start: 0.8060 (tp40) cc_final: 0.7777 (tt0) REVERT: B 1011 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8855 (mp) REVERT: C 272 THR cc_start: 0.8016 (OUTLIER) cc_final: 0.7773 (m) REVERT: C 385 LEU cc_start: 0.8659 (mt) cc_final: 0.8220 (mt) REVERT: C 852 LYS cc_start: 0.7359 (mmtm) cc_final: 0.7144 (tttp) REVERT: C 971 ILE cc_start: 0.9012 (mp) cc_final: 0.8788 (mm) REVERT: C 1120 VAL cc_start: 0.8862 (t) cc_final: 0.8550 (p) outliers start: 43 outliers final: 26 residues processed: 213 average time/residue: 0.1508 time to fit residues: 53.4261 Evaluate side-chains 196 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS 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 920 LEU Chi-restraints excluded: chain B residue 1011 ILE 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 608 VAL Chi-restraints excluded: chain C residue 738 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 241 optimal weight: 8.9990 chunk 224 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 chunk 323 optimal weight: 4.9990 chunk 201 optimal weight: 0.6980 chunk 300 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 304 optimal weight: 0.0010 chunk 255 optimal weight: 3.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 ASN C 415 ASN C 760 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.167362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108071 restraints weight = 47521.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109730 restraints weight = 30602.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.109915 restraints weight = 19718.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.110284 restraints weight = 20746.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110448 restraints weight = 18461.690| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 27199 Z= 0.134 Angle : 0.573 10.716 37170 Z= 0.282 Chirality : 0.045 0.398 4356 Planarity : 0.004 0.061 4692 Dihedral : 6.039 85.353 4956 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.66 % Allowed : 14.02 % 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: -1.53 (0.14), residues: 3249 helix: 1.17 (0.20), residues: 639 sheet: -1.16 (0.21), residues: 540 loop : -1.78 (0.13), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 455 TYR 0.018 0.001 TYR A1136 PHE 0.032 0.001 PHE C 199 TRP 0.017 0.001 TRP B 631 HIS 0.005 0.001 HIS A 205 Details of bonding type rmsd covalent geometry : bond 0.00320 (27087) covalent geometry : angle 0.54704 (36891) SS BOND : bond 0.00424 ( 36) SS BOND : angle 1.46671 ( 72) hydrogen bonds : bond 0.04159 ( 762) hydrogen bonds : angle 5.40521 ( 2061) Misc. bond : bond 0.00092 ( 7) link_BETA1-4 : bond 0.00440 ( 18) link_BETA1-4 : angle 1.45092 ( 54) link_NAG-ASN : bond 0.00492 ( 51) link_NAG-ASN : angle 2.42277 ( 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 227 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 180 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 491 GLN cc_start: 0.7412 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 523 CYS cc_start: 0.2145 (OUTLIER) cc_final: 0.0578 (p) REVERT: A 527 LYS cc_start: 0.9041 (ttpp) cc_final: 0.8401 (tppt) REVERT: A 719 SER cc_start: 0.8842 (t) cc_final: 0.8294 (p) REVERT: A 753 GLN cc_start: 0.8705 (tm130) cc_final: 0.8232 (tm-30) REVERT: A 963 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7373 (tm-30) REVERT: B 308 LYS cc_start: 0.9135 (ttmt) cc_final: 0.8916 (tttt) REVERT: B 385 LEU cc_start: 0.8499 (mt) cc_final: 0.8117 (mt) REVERT: B 1011 ILE cc_start: 0.9083 (OUTLIER) cc_final: 0.8866 (mp) REVERT: C 385 LEU cc_start: 0.8641 (mt) cc_final: 0.8230 (mt) REVERT: C 971 ILE cc_start: 0.9030 (mp) cc_final: 0.8734 (mm) REVERT: C 1120 VAL cc_start: 0.8883 (t) cc_final: 0.8579 (p) outliers start: 47 outliers final: 36 residues processed: 210 average time/residue: 0.1471 time to fit residues: 51.6223 Evaluate side-chains 206 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 0.922 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR 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 198 TYR Chi-restraints excluded: chain B residue 284 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 1011 ILE 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 393 VAL Chi-restraints excluded: chain C residue 608 VAL Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 738 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 88 optimal weight: 0.0270 chunk 149 optimal weight: 0.7980 chunk 152 optimal weight: 0.0570 chunk 137 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 67 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 194 optimal weight: 2.9990 chunk 139 optimal weight: 20.0000 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 415 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.168225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.108395 restraints weight = 47488.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.110741 restraints weight = 28605.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111185 restraints weight = 19267.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112362 restraints weight = 17645.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.112294 restraints weight = 16288.261| |-----------------------------------------------------------------------------| r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 27199 Z= 0.113 Angle : 0.556 10.436 37170 Z= 0.274 Chirality : 0.044 0.393 4356 Planarity : 0.004 0.061 4692 Dihedral : 5.756 81.905 4956 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.41 % Allowed : 14.62 % Favored : 83.97 % 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: -1.46 (0.14), residues: 3249 helix: 1.39 (0.21), residues: 636 sheet: -1.17 (0.21), residues: 549 loop : -1.78 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1105 TYR 0.022 0.001 TYR B 198 PHE 0.026 0.001 PHE B 199 TRP 0.020 0.001 TRP B 631 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00265 (27087) covalent geometry : angle 0.53150 (36891) SS BOND : bond 0.00332 ( 36) SS BOND : angle 1.31522 ( 72) hydrogen bonds : bond 0.03888 ( 762) hydrogen bonds : angle 5.29379 ( 2061) Misc. bond : bond 0.00079 ( 7) link_BETA1-4 : bond 0.00469 ( 18) link_BETA1-4 : angle 1.42002 ( 54) link_NAG-ASN : bond 0.00472 ( 51) link_NAG-ASN : angle 2.35119 ( 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 211 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 171 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 MET cc_start: 0.4339 (mmm) cc_final: 0.3493 (mpp) REVERT: A 385 LEU cc_start: 0.8642 (mt) cc_final: 0.8231 (mt) REVERT: A 491 GLN cc_start: 0.7271 (tm-30) cc_final: 0.6995 (tm-30) REVERT: A 523 CYS cc_start: 0.2070 (OUTLIER) cc_final: 0.0445 (p) REVERT: A 527 LYS cc_start: 0.8978 (ttpp) cc_final: 0.8340 (tppt) REVERT: A 719 SER cc_start: 0.8897 (t) cc_final: 0.8399 (p) REVERT: A 753 GLN cc_start: 0.8652 (tm130) cc_final: 0.8231 (tm-30) REVERT: A 963 GLN cc_start: 0.7931 (tm-30) cc_final: 0.7327 (tm-30) REVERT: B 385 LEU cc_start: 0.8518 (mt) cc_final: 0.8128 (mt) REVERT: B 1003 GLN cc_start: 0.8052 (tp40) cc_final: 0.7759 (tt0) REVERT: B 1011 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8870 (mp) REVERT: C 168 TYR cc_start: 0.8154 (m-80) cc_final: 0.7790 (m-80) REVERT: C 272 THR cc_start: 0.8064 (OUTLIER) cc_final: 0.7841 (m) REVERT: C 385 LEU cc_start: 0.8682 (mt) cc_final: 0.8268 (mt) REVERT: C 1120 VAL cc_start: 0.8869 (t) cc_final: 0.8562 (p) outliers start: 40 outliers final: 31 residues processed: 195 average time/residue: 0.1471 time to fit residues: 47.9333 Evaluate side-chains 194 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 160 time to evaluate : 0.816 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 910 THR 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 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 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1011 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 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 608 VAL Chi-restraints excluded: chain C residue 695 MET Chi-restraints excluded: chain C residue 738 MET 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: 7.9990 chunk 150 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 31 optimal weight: 20.0000 chunk 293 optimal weight: 0.8980 chunk 259 optimal weight: 10.0000 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 227 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.163013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.100659 restraints weight = 46973.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.103986 restraints weight = 25030.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106124 restraints weight = 17390.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.107257 restraints weight = 14185.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108041 restraints weight = 12708.190| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 27199 Z= 0.245 Angle : 0.661 10.757 37170 Z= 0.328 Chirality : 0.047 0.370 4356 Planarity : 0.004 0.061 4692 Dihedral : 6.028 77.723 4956 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % Rotamer: Outliers : 2.26 % Allowed : 14.06 % Favored : 83.69 % 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: -1.78 (0.14), residues: 3249 helix: 0.97 (0.20), residues: 645 sheet: -1.58 (0.19), residues: 612 loop : -1.87 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 813 TYR 0.019 0.002 TYR B 198 PHE 0.029 0.002 PHE C 199 TRP 0.021 0.002 TRP B 631 HIS 0.006 0.001 HIS B1046 Details of bonding type rmsd covalent geometry : bond 0.00589 (27087) covalent geometry : angle 0.63641 (36891) SS BOND : bond 0.00542 ( 36) SS BOND : angle 1.92541 ( 72) hydrogen bonds : bond 0.04931 ( 762) hydrogen bonds : angle 5.56759 ( 2061) Misc. bond : bond 0.00146 ( 7) link_BETA1-4 : bond 0.00449 ( 18) link_BETA1-4 : angle 1.55555 ( 54) link_NAG-ASN : bond 0.00508 ( 51) link_NAG-ASN : angle 2.43640 ( 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 237 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 173 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.7440 (m-80) cc_final: 0.7130 (m-80) REVERT: A 385 LEU cc_start: 0.8592 (mt) cc_final: 0.8299 (tt) REVERT: A 491 GLN cc_start: 0.7288 (tm-30) cc_final: 0.7025 (tm-30) REVERT: A 523 CYS cc_start: 0.2450 (OUTLIER) cc_final: 0.1584 (p) REVERT: A 719 SER cc_start: 0.8776 (t) cc_final: 0.8240 (p) REVERT: B 90 PHE cc_start: 0.8311 (t80) cc_final: 0.8095 (t80) REVERT: B 385 LEU cc_start: 0.8522 (mt) cc_final: 0.8197 (mt) REVERT: B 527 LYS cc_start: 0.8977 (ttpp) cc_final: 0.8389 (tppt) REVERT: C 168 TYR cc_start: 0.8183 (m-80) cc_final: 0.7898 (m-80) REVERT: C 385 LEU cc_start: 0.8661 (mt) cc_final: 0.8277 (mt) REVERT: C 513 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7208 (p90) REVERT: C 902 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.5910 (m-80) REVERT: C 1120 VAL cc_start: 0.8906 (t) cc_final: 0.8650 (p) outliers start: 64 outliers final: 38 residues processed: 218 average time/residue: 0.1438 time to fit residues: 53.3828 Evaluate side-chains 202 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.923 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 971 ILE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 175 MET 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 745 THR Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 974 VAL Chi-restraints excluded: chain B residue 991 ILE Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1112 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 513 PHE Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 738 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 971 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 227 optimal weight: 1.9990 chunk 272 optimal weight: 0.6980 chunk 155 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 233 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 266 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 chunk 292 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.167261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 108)---------------| | r_work = 0.3450 r_free = 0.3450 target = 0.110553 restraints weight = 47182.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111725 restraints weight = 32666.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.110822 restraints weight = 26760.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111129 restraints weight = 27987.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111265 restraints weight = 25368.682| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 27199 Z= 0.116 Angle : 0.586 10.936 37170 Z= 0.287 Chirality : 0.045 0.380 4356 Planarity : 0.004 0.061 4692 Dihedral : 5.647 75.148 4956 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 1.59 % Allowed : 14.98 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.14), residues: 3249 helix: 1.37 (0.21), residues: 642 sheet: -1.46 (0.20), residues: 624 loop : -1.79 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1105 TYR 0.020 0.001 TYR B 198 PHE 0.026 0.001 PHE A 90 TRP 0.019 0.001 TRP B 631 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00273 (27087) covalent geometry : angle 0.56289 (36891) SS BOND : bond 0.00342 ( 36) SS BOND : angle 1.40167 ( 72) hydrogen bonds : bond 0.04022 ( 762) hydrogen bonds : angle 5.31961 ( 2061) Misc. bond : bond 0.00078 ( 7) link_BETA1-4 : bond 0.00452 ( 18) link_BETA1-4 : angle 1.43282 ( 54) link_NAG-ASN : bond 0.00455 ( 51) link_NAG-ASN : angle 2.34019 ( 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 213 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 168 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.7417 (m-80) cc_final: 0.7052 (m-80) REVERT: A 385 LEU cc_start: 0.8432 (mt) cc_final: 0.8141 (tt) REVERT: A 523 CYS cc_start: 0.2468 (OUTLIER) cc_final: 0.1078 (p) REVERT: A 719 SER cc_start: 0.8854 (t) cc_final: 0.8415 (p) REVERT: A 963 GLN cc_start: 0.8017 (tm-30) cc_final: 0.7375 (tm-30) REVERT: B 385 LEU cc_start: 0.8373 (mt) cc_final: 0.8092 (mt) REVERT: C 168 TYR cc_start: 0.8121 (m-80) cc_final: 0.7869 (m-80) REVERT: C 385 LEU cc_start: 0.8471 (mt) cc_final: 0.8180 (mt) REVERT: C 719 SER cc_start: 0.8820 (t) cc_final: 0.8355 (p) REVERT: C 902 TYR cc_start: 0.6646 (OUTLIER) cc_final: 0.5961 (m-80) REVERT: C 1120 VAL cc_start: 0.8602 (t) cc_final: 0.8328 (p) outliers start: 45 outliers final: 36 residues processed: 195 average time/residue: 0.1446 time to fit residues: 47.8271 Evaluate side-chains 191 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 153 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 TYR 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 753 GLN Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 201 ILE 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 631 TRP Chi-restraints excluded: chain B residue 745 THR 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 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 738 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 971 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 27 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 39 optimal weight: 0.0030 chunk 119 optimal weight: 0.9990 chunk 161 optimal weight: 0.9990 chunk 112 optimal weight: 4.9990 chunk 133 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 753 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.164800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.104501 restraints weight = 47398.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.105975 restraints weight = 32176.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.106150 restraints weight = 24848.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106288 restraints weight = 25575.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.106610 restraints weight = 23449.190| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3066 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= 0.129 Angle : 0.588 11.126 37170 Z= 0.288 Chirality : 0.045 0.373 4356 Planarity : 0.004 0.061 4692 Dihedral : 5.466 71.694 4956 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.59 % Allowed : 15.29 % Favored : 83.12 % 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: -1.48 (0.15), residues: 3249 helix: 1.43 (0.21), residues: 642 sheet: -1.39 (0.20), residues: 618 loop : -1.75 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1105 TYR 0.018 0.001 TYR C1136 PHE 0.032 0.001 PHE C 199 TRP 0.018 0.001 TRP B 631 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00308 (27087) covalent geometry : angle 0.56474 (36891) SS BOND : bond 0.00380 ( 36) SS BOND : angle 1.46061 ( 72) hydrogen bonds : bond 0.03986 ( 762) hydrogen bonds : angle 5.27076 ( 2061) Misc. bond : bond 0.00085 ( 7) link_BETA1-4 : bond 0.00453 ( 18) link_BETA1-4 : angle 1.43724 ( 54) link_NAG-ASN : bond 0.00449 ( 51) link_NAG-ASN : angle 2.31546 ( 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 209 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 164 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.7542 (m-80) cc_final: 0.7275 (m-80) REVERT: A 385 LEU cc_start: 0.8484 (mt) cc_final: 0.8177 (tt) REVERT: A 523 CYS cc_start: 0.2454 (OUTLIER) cc_final: 0.1031 (p) REVERT: A 719 SER cc_start: 0.8776 (t) cc_final: 0.8308 (p) REVERT: A 963 GLN cc_start: 0.8013 (tm-30) cc_final: 0.7405 (tm-30) REVERT: B 385 LEU cc_start: 0.8417 (mt) cc_final: 0.8109 (mt) REVERT: C 168 TYR cc_start: 0.8168 (m-80) cc_final: 0.7893 (m-80) REVERT: C 385 LEU cc_start: 0.8511 (mt) cc_final: 0.8158 (mt) REVERT: C 719 SER cc_start: 0.8803 (t) cc_final: 0.8343 (p) REVERT: C 902 TYR cc_start: 0.6699 (OUTLIER) cc_final: 0.5989 (m-80) REVERT: C 1120 VAL cc_start: 0.8642 (t) cc_final: 0.8385 (p) outliers start: 45 outliers final: 37 residues processed: 192 average time/residue: 0.1431 time to fit residues: 46.9767 Evaluate side-chains 193 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 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 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 757 PHE 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 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 615 CYS Chi-restraints excluded: chain C residue 738 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 971 ILE 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: 2.9990 chunk 117 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 317 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.164879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.115392 restraints weight = 47222.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.113968 restraints weight = 49734.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.110078 restraints weight = 35045.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109393 restraints weight = 33794.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.109649 restraints weight = 34062.799| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 27199 Z= 0.211 Angle : 0.646 11.341 37170 Z= 0.318 Chirality : 0.046 0.363 4356 Planarity : 0.004 0.061 4692 Dihedral : 5.551 62.846 4956 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.59 % Allowed : 15.54 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3249 helix: 1.20 (0.20), residues: 648 sheet: -1.52 (0.19), residues: 642 loop : -1.80 (0.14), residues: 1959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 813 TYR 0.019 0.001 TYR B1065 PHE 0.028 0.002 PHE A 90 TRP 0.017 0.002 TRP B 631 HIS 0.005 0.001 HIS A1046 Details of bonding type rmsd covalent geometry : bond 0.00513 (27087) covalent geometry : angle 0.62170 (36891) SS BOND : bond 0.00488 ( 36) SS BOND : angle 1.82956 ( 72) hydrogen bonds : bond 0.04534 ( 762) hydrogen bonds : angle 5.41039 ( 2061) Misc. bond : bond 0.00120 ( 7) link_BETA1-4 : bond 0.00410 ( 18) link_BETA1-4 : angle 1.53550 ( 54) link_NAG-ASN : bond 0.00486 ( 51) link_NAG-ASN : angle 2.40014 ( 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 207 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 162 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 363 TYR cc_start: 0.7374 (m-80) cc_final: 0.7131 (m-80) REVERT: A 385 LEU cc_start: 0.8367 (mt) cc_final: 0.8070 (tt) REVERT: A 523 CYS cc_start: 0.2668 (OUTLIER) cc_final: 0.1355 (p) REVERT: A 719 SER cc_start: 0.8750 (t) cc_final: 0.8289 (p) REVERT: B 385 LEU cc_start: 0.8288 (mt) cc_final: 0.8076 (mt) REVERT: C 385 LEU cc_start: 0.8429 (mt) cc_final: 0.8195 (mt) REVERT: C 513 PHE cc_start: 0.8317 (OUTLIER) cc_final: 0.7304 (p90) REVERT: C 719 SER cc_start: 0.8780 (t) cc_final: 0.8308 (p) REVERT: C 902 TYR cc_start: 0.6991 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: C 1120 VAL cc_start: 0.8648 (t) cc_final: 0.8444 (p) outliers start: 45 outliers final: 38 residues processed: 193 average time/residue: 0.1423 time to fit residues: 46.8512 Evaluate side-chains 198 residues out of total 2853 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 157 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 TYR 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 522 VAL Chi-restraints excluded: chain A residue 523 CYS Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 784 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1095 SER Chi-restraints excluded: chain B residue 175 MET Chi-restraints excluded: chain B residue 201 ILE 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 757 PHE Chi-restraints excluded: chain B residue 910 THR Chi-restraints excluded: chain B residue 920 LEU Chi-restraints excluded: chain B residue 1095 SER 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 513 PHE Chi-restraints excluded: chain C residue 517 HIS Chi-restraints excluded: chain C residue 522 VAL Chi-restraints excluded: chain C residue 523 CYS Chi-restraints excluded: chain C residue 615 CYS Chi-restraints excluded: chain C residue 738 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 971 ILE 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: 0.6980 chunk 194 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 248 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 173 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 321 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 244 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 642 GLN ** C 753 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.162781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.103685 restraints weight = 47385.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.105306 restraints weight = 33134.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.105978 restraints weight = 24486.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.106021 restraints weight = 22742.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.106152 restraints weight = 22158.355| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3295 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= 0.129 Angle : 0.599 11.270 37170 Z= 0.292 Chirality : 0.045 0.366 4356 Planarity : 0.004 0.061 4692 Dihedral : 5.302 55.978 4956 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 1.52 % Allowed : 15.75 % Favored : 82.73 % 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: -1.50 (0.14), residues: 3249 helix: 1.43 (0.21), residues: 642 sheet: -1.43 (0.20), residues: 618 loop : -1.76 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1105 TYR 0.017 0.001 TYR C1136 PHE 0.032 0.001 PHE C 199 TRP 0.016 0.001 TRP B 631 HIS 0.004 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00308 (27087) covalent geometry : angle 0.57514 (36891) SS BOND : bond 0.00395 ( 36) SS BOND : angle 1.51548 ( 72) hydrogen bonds : bond 0.03996 ( 762) hydrogen bonds : angle 5.24541 ( 2061) Misc. bond : bond 0.00083 ( 7) link_BETA1-4 : bond 0.00434 ( 18) link_BETA1-4 : angle 1.45693 ( 54) link_NAG-ASN : bond 0.00443 ( 51) link_NAG-ASN : angle 2.36601 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4357.08 seconds wall clock time: 76 minutes 11.05 seconds (4571.05 seconds total)