Starting phenix.real_space_refine on Sun Jun 22 21:44:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zy4_60555/06_2025/8zy4_60555.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zy4_60555/06_2025/8zy4_60555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.53 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zy4_60555/06_2025/8zy4_60555.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zy4_60555/06_2025/8zy4_60555.map" model { file = "/net/cci-nas-00/data/ceres_data/8zy4_60555/06_2025/8zy4_60555.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zy4_60555/06_2025/8zy4_60555.cif" } resolution = 2.53 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.031 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 120 5.16 5 C 16620 2.51 5 N 4275 2.21 5 O 5166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26181 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8344 Classifications: {'peptide': 1073} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 47, 'TRANS': 1025} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8350 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 47, 'TRANS': 1025} Chain breaks: 2 Chain: "C" Number of atoms: 8350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1073, 8350 Classifications: {'peptide': 1073} Link IDs: {'PTRANS': 47, 'TRANS': 1025} Chain breaks: 2 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: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLR': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLR': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLR': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 15.82, per 1000 atoms: 0.60 Number of scatterers: 26181 At special positions: 0 Unit cell: (140.16, 146.73, 166.44, 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 120 16.00 O 5166 8.00 N 4275 7.00 C 16620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 16 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 125 " - pdb=" SG CYS A 155 " distance=2.04 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 319 " - pdb=" SG CYS A 344 " distance=2.03 Simple disulfide: pdb=" SG CYS A 362 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 374 " - pdb=" SG CYS A 489 " distance=2.03 Simple disulfide: pdb=" SG CYS A 502 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS A 581 " - pdb=" SG CYS A 613 " distance=2.03 Simple disulfide: pdb=" SG CYS A 626 " - pdb=" SG CYS A 635 " distance=2.03 Simple disulfide: pdb=" SG CYS A 698 " - pdb=" SG CYS A 720 " distance=2.03 Simple disulfide: pdb=" SG CYS A 703 " - pdb=" SG CYS A 709 " distance=2.02 Simple disulfide: pdb=" SG CYS A 800 " - pdb=" SG CYS A 811 " distance=2.03 Simple disulfide: pdb=" SG CYS A 992 " - pdb=" SG CYS A1003 " distance=2.03 Simple disulfide: pdb=" SG CYS A1042 " - pdb=" SG CYS A1086 " distance=2.03 Simple disulfide: pdb=" SG CYS B 16 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 155 " distance=2.04 Simple disulfide: pdb=" SG CYS B 274 " - pdb=" SG CYS B 284 " distance=2.03 Simple disulfide: pdb=" SG CYS B 319 " - pdb=" SG CYS B 344 " distance=2.03 Simple disulfide: pdb=" SG CYS B 362 " - pdb=" SG CYS B 415 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 489 " distance=2.03 Simple disulfide: pdb=" SG CYS B 502 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 581 " - pdb=" SG CYS B 613 " distance=2.03 Simple disulfide: pdb=" SG CYS B 626 " - pdb=" SG CYS B 635 " distance=2.03 Simple disulfide: pdb=" SG CYS B 698 " - pdb=" SG CYS B 720 " distance=2.03 Simple disulfide: pdb=" SG CYS B 703 " - pdb=" SG CYS B 709 " distance=2.03 Simple disulfide: pdb=" SG CYS B 800 " - pdb=" SG CYS B 811 " distance=2.03 Simple disulfide: pdb=" SG CYS B 992 " - pdb=" SG CYS B1003 " distance=2.03 Simple disulfide: pdb=" SG CYS B1042 " - pdb=" SG CYS B1086 " distance=2.03 Simple disulfide: pdb=" SG CYS C 16 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 125 " - pdb=" SG CYS C 155 " distance=2.04 Simple disulfide: pdb=" SG CYS C 274 " - pdb=" SG CYS C 284 " distance=2.03 Simple disulfide: pdb=" SG CYS C 319 " - pdb=" SG CYS C 344 " distance=2.03 Simple disulfide: pdb=" SG CYS C 362 " - pdb=" SG CYS C 415 " distance=2.03 Simple disulfide: pdb=" SG CYS C 374 " - pdb=" SG CYS C 489 " distance=2.03 Simple disulfide: pdb=" SG CYS C 502 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 613 " distance=2.03 Simple disulfide: pdb=" SG CYS C 626 " - pdb=" SG CYS C 635 " distance=2.03 Simple disulfide: pdb=" SG CYS C 698 " - pdb=" SG CYS C 720 " distance=2.03 Simple disulfide: pdb=" SG CYS C 703 " - pdb=" SG CYS C 709 " distance=2.03 Simple disulfide: pdb=" SG CYS C 800 " - pdb=" SG CYS C 811 " distance=2.03 Simple disulfide: pdb=" SG CYS C 992 " - pdb=" SG CYS C1003 " distance=2.03 Simple disulfide: pdb=" SG CYS C1042 " - pdb=" SG CYS C1086 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A1094 " " NAG A1302 " - " ASN A 580 " " NAG A1303 " - " ASN A 62 " " NAG A1304 " - " ASN A 18 " " NAG A1305 " - " ASN A 116 " " NAG A1306 " - " ASN A 141 " " NAG A1307 " - " ASN A 154 " " NAG A1308 " - " ASN A 265 " " NAG A1309 " - " ASN A 314 " " NAG A1310 " - " ASN A 326 " " NAG A1311 " - " ASN A 621 " " NAG A1312 " - " ASN A 669 " " NAG A1313 " - " ASN A1058 " " NAG A1315 " - " ASN A 290 " " NAG B1301 " - " ASN B1094 " " NAG B1302 " - " ASN B 580 " " NAG B1303 " - " ASN B 62 " " NAG B1304 " - " ASN B 18 " " NAG B1305 " - " ASN B 116 " " NAG B1306 " - " ASN B 141 " " NAG B1307 " - " ASN B 154 " " NAG B1308 " - " ASN B 265 " " NAG B1309 " - " ASN B 290 " " NAG B1310 " - " ASN B 314 " " NAG B1311 " - " ASN B 326 " " NAG B1312 " - " ASN B 621 " " NAG B1313 " - " ASN B 669 " " NAG B1314 " - " ASN B1058 " " NAG C1301 " - " ASN C1094 " " NAG C1302 " - " ASN C 580 " " NAG C1303 " - " ASN C 62 " " NAG C1304 " - " ASN C 18 " " NAG C1305 " - " ASN C 116 " " NAG C1306 " - " ASN C 141 " " NAG C1307 " - " ASN C 154 " " NAG C1308 " - " ASN C 265 " " NAG C1309 " - " ASN C 290 " " NAG C1310 " - " ASN C 314 " " NAG C1311 " - " ASN C 326 " " NAG C1312 " - " ASN C 621 " " NAG C1313 " - " ASN C 669 " " NAG C1314 " - " ASN C1058 " " NAG D 1 " - " ASN A 223 " " NAG E 1 " - " ASN A 353 " " NAG F 1 " - " ASN A 677 " " NAG G 1 " - " ASN A 761 " " NAG H 1 " - " ASN A1034 " " NAG I 1 " - " ASN B 223 " " NAG J 1 " - " ASN B 353 " " NAG K 1 " - " ASN B 677 " " NAG L 1 " - " ASN B 761 " " NAG M 1 " - " ASN B1034 " " NAG N 1 " - " ASN C 223 " " NAG O 1 " - " ASN C 353 " " NAG P 1 " - " ASN C 677 " " NAG Q 1 " - " ASN C 761 " " NAG R 1 " - " ASN C1034 " Time building additional restraints: 6.18 Conformation dependent library (CDL) restraints added in 3.5 seconds 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6066 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 50 sheets defined 24.8% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 277 through 287 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.946A pdb=" N ILE A 324 " --> pdb=" O PRO A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 336 removed outlier: 3.661A pdb=" N TRP A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 352 removed outlier: 3.760A pdb=" N VAL A 350 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 removed outlier: 4.221A pdb=" N ARG A 391 " --> pdb=" O SER A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 469 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 594 through 599 removed outlier: 3.669A pdb=" N VAL A 599 " --> pdb=" O PRO A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 704 removed outlier: 3.563A pdb=" N GLY A 704 " --> pdb=" O MET A 700 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 713 Processing helix chain 'A' and resid 717 through 743 removed outlier: 3.559A pdb=" N GLU A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASP A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 783 Processing helix chain 'A' and resid 798 through 803 Processing helix chain 'A' and resid 808 through 816 removed outlier: 3.667A pdb=" N ALA A 812 " --> pdb=" O ASP A 808 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 816 " --> pdb=" O ALA A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 844 Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.546A pdb=" N GLY A 849 " --> pdb=" O TRP A 846 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLY A 851 " --> pdb=" O PHE A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 869 removed outlier: 3.652A pdb=" N ILE A 869 " --> pdb=" O ARG A 865 " (cutoff:3.500A) Processing helix chain 'A' and resid 873 through 879 Processing helix chain 'A' and resid 879 through 892 Processing helix chain 'A' and resid 905 through 916 Processing helix chain 'A' and resid 918 through 925 Processing helix chain 'A' and resid 936 through 942 Processing helix chain 'A' and resid 945 through 993 removed outlier: 4.372A pdb=" N VAL A 951 " --> pdb=" O PRO A 947 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLN A 952 " --> pdb=" O GLU A 948 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 956 " --> pdb=" O GLN A 952 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLY A 959 " --> pdb=" O ARG A 955 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N GLN A 962 " --> pdb=" O THR A 958 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 977 " --> pdb=" O ILE A 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 266 No H-bonds generated for 'chain 'B' and resid 264 through 266' Processing helix chain 'B' and resid 277 through 287 Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.670A pdb=" N TRP B 336 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 352 removed outlier: 3.961A pdb=" N VAL B 350 " --> pdb=" O ASP B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 removed outlier: 4.298A pdb=" N ARG B 391 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 469 Processing helix chain 'B' and resid 532 through 536 removed outlier: 3.860A pdb=" N PHE B 536 " --> pdb=" O ALA B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 594 through 599 removed outlier: 3.611A pdb=" N VAL B 599 " --> pdb=" O PRO B 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 703 Processing helix chain 'B' and resid 706 through 713 Processing helix chain 'B' and resid 717 through 730 Processing helix chain 'B' and resid 732 through 743 removed outlier: 3.621A pdb=" N LYS B 736 " --> pdb=" O LEU B 732 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR B 738 " --> pdb=" O GLN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 763 through 766 removed outlier: 3.712A pdb=" N LEU B 766 " --> pdb=" O SER B 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 763 through 766' Processing helix chain 'B' and resid 776 through 783 Processing helix chain 'B' and resid 798 through 803 removed outlier: 4.088A pdb=" N GLY B 802 " --> pdb=" O GLY B 798 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASP B 803 " --> pdb=" O GLU B 799 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 798 through 803' Processing helix chain 'B' and resid 808 through 815 Processing helix chain 'B' and resid 826 through 844 Processing helix chain 'B' and resid 846 through 851 removed outlier: 3.579A pdb=" N GLY B 849 " --> pdb=" O TRP B 846 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLY B 851 " --> pdb=" O PHE B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 869 removed outlier: 3.667A pdb=" N ILE B 869 " --> pdb=" O ARG B 865 " (cutoff:3.500A) Processing helix chain 'B' and resid 872 through 879 removed outlier: 4.359A pdb=" N LEU B 876 " --> pdb=" O THR B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 892 Processing helix chain 'B' and resid 896 through 901 removed outlier: 3.510A pdb=" N THR B 901 " --> pdb=" O SER B 897 " (cutoff:3.500A) Processing helix chain 'B' and resid 905 through 925 removed outlier: 3.565A pdb=" N ALA B 918 " --> pdb=" O GLN B 914 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU B 919 " --> pdb=" O ASN B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 936 through 942 Processing helix chain 'B' and resid 945 through 993 removed outlier: 4.476A pdb=" N VAL B 951 " --> pdb=" O PRO B 947 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLN B 952 " --> pdb=" O GLU B 948 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY B 959 " --> pdb=" O ARG B 955 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N GLN B 962 " --> pdb=" O THR B 958 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU B 977 " --> pdb=" O ILE B 973 " (cutoff:3.500A) Processing helix chain 'B' and resid 1087 through 1089 No H-bonds generated for 'chain 'B' and resid 1087 through 1089' Processing helix chain 'C' and resid 277 through 287 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 332 through 336 removed outlier: 3.709A pdb=" N TRP C 336 " --> pdb=" O VAL C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 removed outlier: 3.971A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 351 " --> pdb=" O TYR C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 372 Processing helix chain 'C' and resid 388 through 393 removed outlier: 4.305A pdb=" N ARG C 391 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 405 removed outlier: 3.599A pdb=" N ASP C 403 " --> pdb=" O GLY C 399 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 466 through 469 Processing helix chain 'C' and resid 583 through 588 Processing helix chain 'C' and resid 589 through 593 Processing helix chain 'C' and resid 594 through 599 removed outlier: 3.625A pdb=" N VAL C 599 " --> pdb=" O PRO C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 697 through 704 Processing helix chain 'C' and resid 706 through 713 Processing helix chain 'C' and resid 717 through 730 Processing helix chain 'C' and resid 732 through 743 removed outlier: 3.568A pdb=" N LYS C 736 " --> pdb=" O LEU C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 763 through 766 removed outlier: 3.693A pdb=" N LEU C 766 " --> pdb=" O SER C 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 763 through 766' Processing helix chain 'C' and resid 776 through 783 Processing helix chain 'C' and resid 803 through 807 removed outlier: 3.681A pdb=" N ALA C 806 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 808 through 816 removed outlier: 3.640A pdb=" N ASN C 816 " --> pdb=" O ALA C 812 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 844 Processing helix chain 'C' and resid 846 through 851 removed outlier: 3.561A pdb=" N GLY C 849 " --> pdb=" O TRP C 846 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLY C 851 " --> pdb=" O PHE C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 868 Processing helix chain 'C' and resid 872 through 879 removed outlier: 4.347A pdb=" N LEU C 876 " --> pdb=" O THR C 872 " (cutoff:3.500A) Processing helix chain 'C' and resid 879 through 892 Processing helix chain 'C' and resid 896 through 901 removed outlier: 3.640A pdb=" N THR C 900 " --> pdb=" O GLU C 896 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR C 901 " --> pdb=" O SER C 897 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 896 through 901' Processing helix chain 'C' and resid 905 through 916 Processing helix chain 'C' and resid 918 through 925 Processing helix chain 'C' and resid 936 through 942 Processing helix chain 'C' and resid 945 through 993 removed outlier: 4.368A pdb=" N VAL C 951 " --> pdb=" O PRO C 947 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 952 " --> pdb=" O GLU C 948 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG C 955 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 956 " --> pdb=" O GLN C 952 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLY C 959 " --> pdb=" O ARG C 955 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN C 962 " --> pdb=" O THR C 958 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU C 977 " --> pdb=" O ILE C 973 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA C 980 " --> pdb=" O ALA C 976 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 993 " --> pdb=" O MET C 989 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.923A pdb=" N ASN A 28 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 8.120A pdb=" N ASN A 62 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N TYR A 252 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 247 " --> pdb=" O THR A 89 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N VAL A 176 " --> pdb=" O ILE A 199 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 199 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N LEU A 190 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LYS A 217 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ILE A 192 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N TYR A 196 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL A 211 " --> pdb=" O TYR A 196 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 37 " --> pdb=" O LEU A 212 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 56 removed outlier: 4.062A pdb=" N ASN A 270 " --> pdb=" O SER A 261 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 79 removed outlier: 3.655A pdb=" N GLY A 97 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE A 157 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 144 through 151 removed outlier: 10.081A pdb=" N GLN A 144 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 11.605A pdb=" N LEU A 134 " --> pdb=" O GLN A 144 " (cutoff:3.500A) removed outlier: 10.183A pdb=" N SER A 146 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 11.425A pdb=" N VAL A 132 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N LEU A 148 " --> pdb=" O CYS A 130 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS A 130 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU A 128 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 12.561A pdb=" N LEU A 129 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 12.779A pdb=" N THR A 229 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 10.747A pdb=" N LYS A 131 " --> pdb=" O THR A 229 " (cutoff:3.500A) removed outlier: 10.041A pdb=" N LEU A 231 " --> pdb=" O LYS A 131 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N VAL A 233 " --> pdb=" O PRO A 133 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N PHE A 135 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ARG A 235 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL A 137 " --> pdb=" O ARG A 235 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 294 through 297 Processing sheet with id=AA6, first strand: chain 'A' and resid 307 through 310 removed outlier: 4.426A pdb=" N ARG A 307 " --> pdb=" O CYS A 502 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASN A 504 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 337 through 341 removed outlier: 3.527A pdb=" N GLU A 337 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL A 378 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 344 through 345 removed outlier: 6.473A pdb=" N CYS A 344 " --> pdb=" O CYS A 489 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 488 " --> pdb=" O PHE A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 428 through 432 Processing sheet with id=AB1, first strand: chain 'A' and resid 618 through 624 removed outlier: 6.342A pdb=" N GLU A 618 " --> pdb=" O ALA A 654 " (cutoff:3.500A) removed outlier: 8.537A pdb=" N THR A 656 " --> pdb=" O GLU A 618 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL A 620 " --> pdb=" O THR A 656 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 634 " --> pdb=" O ILE A 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 661 through 663 removed outlier: 6.768A pdb=" N ALA A 661 " --> pdb=" O MET B 748 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 672 through 675 removed outlier: 3.716A pdb=" N THR A1036 " --> pdb=" O SER A1057 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1038 " --> pdb=" O PHE A1055 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N PHE A1055 " --> pdb=" O ALA A1038 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 678 through 688 removed outlier: 3.520A pdb=" N MET A1010 " --> pdb=" O VAL A1025 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR A1027 " --> pdb=" O HIS A1008 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N HIS A1008 " --> pdb=" O TYR A1027 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 693 through 696 removed outlier: 4.517A pdb=" N LYS A 693 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 747 through 749 Processing sheet with id=AB7, first strand: chain 'A' and resid 756 through 757 Processing sheet with id=AB8, first strand: chain 'A' and resid 1080 through 1085 removed outlier: 6.548A pdb=" N ALA A1047 " --> pdb=" O ALA A1083 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.900A pdb=" N ASN B 28 " --> pdb=" O GLN B 65 " (cutoff:3.500A) removed outlier: 8.192A pdb=" N ASN B 62 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR B 252 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N VAL B 176 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LEU B 190 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS B 217 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE B 192 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N TYR B 196 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 211 " --> pdb=" O TYR B 196 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 37 " --> pdb=" O LEU B 212 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 49 through 56 removed outlier: 3.516A pdb=" N HIS B 50 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN B 270 " --> pdb=" O SER B 261 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 78 through 79 removed outlier: 3.750A pdb=" N GLY B 97 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASN B 126 " --> pdb=" O PHE B 153 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N PHE B 153 " --> pdb=" O ASN B 126 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ASP B 151 " --> pdb=" O GLU B 128 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.027A pdb=" N PHE B 135 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG B 235 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 137 " --> pdb=" O ARG B 235 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 294 through 298 removed outlier: 4.899A pdb=" N VAL B 559 " --> pdb=" O THR B 298 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 309 through 310 removed outlier: 7.410A pdb=" N VAL B 309 " --> pdb=" O ASN B 506 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 337 through 341 removed outlier: 3.555A pdb=" N GLU B 337 " --> pdb=" O THR B 382 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL B 378 " --> pdb=" O ILE B 341 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 344 through 345 removed outlier: 6.741A pdb=" N CYS B 344 " --> pdb=" O CYS B 489 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 429 through 432 Processing sheet with id=AC9, first strand: chain 'B' and resid 514 through 517 removed outlier: 3.666A pdb=" N LEU B 516 " --> pdb=" O ASP B 550 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 618 through 624 removed outlier: 6.193A pdb=" N GLU B 618 " --> pdb=" O ALA B 654 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N THR B 656 " --> pdb=" O GLU B 618 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N VAL B 620 " --> pdb=" O THR B 656 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE B 634 " --> pdb=" O ILE B 630 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 661 through 663 removed outlier: 6.736A pdb=" N ALA B 661 " --> pdb=" O MET C 748 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'B' and resid 672 through 675 removed outlier: 3.771A pdb=" N THR B1036 " --> pdb=" O SER B1057 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA B1038 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N PHE B1055 " --> pdb=" O ALA B1038 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 678 through 688 removed outlier: 3.552A pdb=" N MET B1010 " --> pdb=" O VAL B1025 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N TYR B1027 " --> pdb=" O HIS B1008 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N HIS B1008 " --> pdb=" O TYR B1027 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 693 through 696 removed outlier: 4.376A pdb=" N LYS B 693 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 756 through 757 Processing sheet with id=AD7, first strand: chain 'B' and resid 1080 through 1085 removed outlier: 6.586A pdb=" N ALA B1047 " --> pdb=" O ALA B1083 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.891A pdb=" N ASN C 28 " --> pdb=" O GLN C 65 " (cutoff:3.500A) removed outlier: 8.189A pdb=" N ASN C 62 " --> pdb=" O TYR C 252 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N TYR C 252 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 247 " --> pdb=" O THR C 89 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N VAL C 176 " --> pdb=" O ILE C 199 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 199 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU C 190 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS C 217 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 192 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N TYR C 196 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 7.954A pdb=" N VAL C 211 " --> pdb=" O TYR C 196 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL C 37 " --> pdb=" O LEU C 212 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 49 through 56 removed outlier: 4.360A pdb=" N ASN C 270 " --> pdb=" O SER C 261 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 78 through 79 removed outlier: 3.775A pdb=" N GLY C 97 " --> pdb=" O PHE C 230 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL C 124 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N PHE C 157 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 134 through 138 removed outlier: 5.681A pdb=" N PHE C 135 " --> pdb=" O VAL C 233 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ARG C 235 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N VAL C 137 " --> pdb=" O ARG C 235 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 294 through 298 removed outlier: 4.932A pdb=" N VAL C 559 " --> pdb=" O THR C 298 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY C 612 " --> pdb=" O THR C 609 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 308 through 309 removed outlier: 3.523A pdb=" N LYS C 511 " --> pdb=" O PHE C 505 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 337 through 341 removed outlier: 3.548A pdb=" N GLU C 337 " --> pdb=" O THR C 382 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 378 " --> pdb=" O ILE C 341 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 344 through 345 removed outlier: 6.515A pdb=" N CYS C 344 " --> pdb=" O CYS C 489 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 428 through 432 Processing sheet with id=AE8, first strand: chain 'C' and resid 623 through 624 removed outlier: 3.801A pdb=" N TYR C 624 " --> pdb=" O THR C 656 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 634 " --> pdb=" O ILE C 630 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 638 through 639 Processing sheet with id=AF1, first strand: chain 'C' and resid 672 through 675 removed outlier: 3.669A pdb=" N THR C1036 " --> pdb=" O SER C1057 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA C1038 " --> pdb=" O PHE C1055 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE C1055 " --> pdb=" O ALA C1038 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 678 through 688 removed outlier: 3.596A pdb=" N MET C1010 " --> pdb=" O VAL C1025 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR C1027 " --> pdb=" O HIS C1008 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N HIS C1008 " --> pdb=" O TYR C1027 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 693 through 696 removed outlier: 4.402A pdb=" N LYS C 693 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 756 through 757 Processing sheet with id=AF5, first strand: chain 'C' and resid 1080 through 1085 removed outlier: 5.825A pdb=" N VAL C1082 " --> pdb=" O PHE C1049 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N PHE C1049 " --> pdb=" O VAL C1082 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N GLY C1084 " --> pdb=" O ALA C1047 " (cutoff:3.500A) 932 hydrogen bonds defined for protein. 2526 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: 12.12 Time building geometry restraints manager: 7.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8086 1.34 - 1.46: 6914 1.46 - 1.59: 11589 1.59 - 1.72: 0 1.72 - 1.84: 156 Bond restraints: 26745 Sorted by residual: bond pdb=" C4D BLR B1315 " pdb=" CHA BLR B1315 " ideal model delta sigma weight residual 1.496 1.374 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C4D BLR C1315 " pdb=" CHA BLR C1315 " ideal model delta sigma weight residual 1.496 1.376 0.120 2.00e-02 2.50e+03 3.60e+01 bond pdb=" C4D BLR A1314 " pdb=" CHA BLR A1314 " ideal model delta sigma weight residual 1.496 1.376 0.120 2.00e-02 2.50e+03 3.57e+01 bond pdb=" C1A BLR B1315 " pdb=" CHA BLR B1315 " ideal model delta sigma weight residual 1.498 1.417 0.081 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C1A BLR A1314 " pdb=" CHA BLR A1314 " ideal model delta sigma weight residual 1.498 1.418 0.080 2.00e-02 2.50e+03 1.59e+01 ... (remaining 26740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.74: 36100 2.74 - 5.48: 251 5.48 - 8.22: 44 8.22 - 10.96: 6 10.96 - 13.70: 3 Bond angle restraints: 36404 Sorted by residual: angle pdb=" CA GLU C 948 " pdb=" CB GLU C 948 " pdb=" CG GLU C 948 " ideal model delta sigma weight residual 114.10 124.03 -9.93 2.00e+00 2.50e-01 2.47e+01 angle pdb=" C1A BLR C1315 " pdb=" CHA BLR C1315 " pdb=" C4D BLR C1315 " ideal model delta sigma weight residual 114.18 127.88 -13.70 3.00e+00 1.11e-01 2.08e+01 angle pdb=" C1A BLR B1315 " pdb=" CHA BLR B1315 " pdb=" C4D BLR B1315 " ideal model delta sigma weight residual 114.18 127.77 -13.59 3.00e+00 1.11e-01 2.05e+01 angle pdb=" N VAL C 426 " pdb=" CA VAL C 426 " pdb=" C VAL C 426 " ideal model delta sigma weight residual 113.53 109.10 4.43 9.80e-01 1.04e+00 2.04e+01 angle pdb=" C1A BLR A1314 " pdb=" CHA BLR A1314 " pdb=" C4D BLR A1314 " ideal model delta sigma weight residual 114.18 127.68 -13.50 3.00e+00 1.11e-01 2.03e+01 ... (remaining 36399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 14770 17.81 - 35.62: 1576 35.62 - 53.42: 402 53.42 - 71.23: 81 71.23 - 89.04: 38 Dihedral angle restraints: 16867 sinusoidal: 7459 harmonic: 9408 Sorted by residual: dihedral pdb=" CB CYS C1042 " pdb=" SG CYS C1042 " pdb=" SG CYS C1086 " pdb=" CB CYS C1086 " ideal model delta sinusoidal sigma weight residual 93.00 26.38 66.62 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CB CYS B 800 " pdb=" SG CYS B 800 " pdb=" SG CYS B 811 " pdb=" CB CYS B 811 " ideal model delta sinusoidal sigma weight residual 93.00 148.66 -55.66 1 1.00e+01 1.00e-02 4.18e+01 dihedral pdb=" CB CYS C 125 " pdb=" SG CYS C 125 " pdb=" SG CYS C 155 " pdb=" CB CYS C 155 " ideal model delta sinusoidal sigma weight residual 93.00 38.77 54.23 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 16864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 4096 0.103 - 0.205: 245 0.205 - 0.308: 5 0.308 - 0.411: 0 0.411 - 0.514: 1 Chirality restraints: 4347 Sorted by residual: chirality pdb=" C1 NAG C1309 " pdb=" ND2 ASN C 290 " pdb=" C2 NAG C1309 " pdb=" O5 NAG C1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.89 -0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CB ILE C 199 " pdb=" CA ILE C 199 " pdb=" CG1 ILE C 199 " pdb=" CG2 ILE C 199 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG C1310 " pdb=" ND2 ASN C 314 " pdb=" C2 NAG C1310 " pdb=" O5 NAG C1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 4344 not shown) Planarity restraints: 4673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1309 " 0.051 2.00e-02 2.50e+03 4.19e-02 2.19e+01 pdb=" C7 NAG C1309 " -0.016 2.00e-02 2.50e+03 pdb=" C8 NAG C1309 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG C1309 " -0.066 2.00e-02 2.50e+03 pdb=" O7 NAG C1309 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE B 856 " 0.046 5.00e-02 4.00e+02 7.04e-02 7.92e+00 pdb=" N PRO B 857 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO B 857 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO B 857 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 856 " -0.044 5.00e-02 4.00e+02 6.68e-02 7.14e+00 pdb=" N PRO A 857 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO A 857 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 857 " -0.037 5.00e-02 4.00e+02 ... (remaining 4670 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3343 2.76 - 3.29: 22556 3.29 - 3.83: 41864 3.83 - 4.36: 48016 4.36 - 4.90: 85938 Nonbonded interactions: 201717 Sorted by model distance: nonbonded pdb=" OG SER C 447 " pdb=" OE2 GLU C 450 " model vdw 2.222 3.040 nonbonded pdb=" O SER A1071 " pdb=" OG SER A1071 " model vdw 2.274 3.040 nonbonded pdb=" O ILE B 168 " pdb=" OH TYR B 234 " model vdw 2.275 3.040 nonbonded pdb=" O SER C1071 " pdb=" OG SER C1071 " model vdw 2.289 3.040 nonbonded pdb=" O ASP C 74 " pdb=" OH TYR C 248 " model vdw 2.294 3.040 ... (remaining 201712 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 1100 or resid 1301 through 1313)) selection = (chain 'B' and (resid 15 through 317 or (resid 318 and (name N or name CA or nam \ e C or name O or name CB )) or resid 319 through 1100 or resid 1301 through 1313 \ )) selection = (chain 'C' and (resid 15 through 317 or (resid 318 and (name N or name CA or nam \ e C or name O or name CB )) or resid 319 through 1100 or resid 1301 through 1313 \ )) } 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 61.500 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 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 0.122 26859 Z= 0.179 Angle : 0.688 13.697 36704 Z= 0.358 Chirality : 0.048 0.514 4347 Planarity : 0.005 0.075 4616 Dihedral : 15.747 89.041 10675 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.47 % Allowed : 23.13 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.14), residues: 3201 helix: -0.92 (0.18), residues: 681 sheet: 0.09 (0.18), residues: 870 loop : -1.82 (0.14), residues: 1650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 846 HIS 0.004 0.001 HIS C 434 PHE 0.035 0.001 PHE C 507 TYR 0.019 0.001 TYR B 159 ARG 0.018 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00316 ( 57) link_NAG-ASN : angle 2.15165 ( 171) link_BETA1-4 : bond 0.00440 ( 15) link_BETA1-4 : angle 1.27292 ( 45) hydrogen bonds : bond 0.23167 ( 932) hydrogen bonds : angle 7.87836 ( 2526) SS BOND : bond 0.00286 ( 42) SS BOND : angle 1.36769 ( 84) covalent geometry : bond 0.00355 (26745) covalent geometry : angle 0.67067 (36404) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 90 time to evaluate : 3.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8526 (m-80) cc_final: 0.8161 (m-80) REVERT: A 153 PHE cc_start: 0.8377 (m-10) cc_final: 0.7914 (m-10) REVERT: A 508 ASN cc_start: 0.5306 (OUTLIER) cc_final: 0.5079 (m-40) REVERT: A 687 MET cc_start: 0.9573 (mtp) cc_final: 0.9340 (mtm) REVERT: A 715 GLN cc_start: 0.8246 (mt0) cc_final: 0.7988 (mp10) REVERT: A 793 PHE cc_start: 0.6942 (m-80) cc_final: 0.6452 (t80) REVERT: A 804 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.7263 (mm) REVERT: B 497 LEU cc_start: 0.5711 (OUTLIER) cc_final: 0.5092 (pp) REVERT: B 522 ARG cc_start: 0.6032 (OUTLIER) cc_final: 0.5390 (ppt170) REVERT: B 549 LEU cc_start: 0.7779 (mt) cc_final: 0.7559 (mm) REVERT: B 687 MET cc_start: 0.9590 (mtp) cc_final: 0.9199 (mtp) REVERT: C 153 PHE cc_start: 0.8059 (m-10) cc_final: 0.7546 (m-10) REVERT: C 516 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7522 (tp) REVERT: C 522 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6578 (tpt90) REVERT: C 893 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8228 (pp30) REVERT: C 1085 ASN cc_start: 0.8849 (OUTLIER) cc_final: 0.8163 (p0) outliers start: 69 outliers final: 49 residues processed: 153 average time/residue: 1.2597 time to fit residues: 235.0808 Evaluate side-chains 141 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 84 time to evaluate : 3.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 62 ASN Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 303 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 372 ASP Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 478 SER Chi-restraints excluded: chain A residue 508 ASN Chi-restraints excluded: chain A residue 545 THR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 725 ARG Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 954 ASP Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 42 ASP Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 99 ILE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 522 ARG Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 1042 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 62 ASN Chi-restraints excluded: chain C residue 130 CYS Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 372 ASP Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 893 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1078 ASP Chi-restraints excluded: chain C residue 1085 ASN Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 3.9990 chunk 243 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 251 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 187 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 861 GLN B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.053441 restraints weight = 58646.324| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 3.32 r_work: 0.2625 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 26859 Z= 0.136 Angle : 0.569 10.200 36704 Z= 0.295 Chirality : 0.044 0.236 4347 Planarity : 0.004 0.061 4616 Dihedral : 7.651 86.577 5122 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.01 % Allowed : 20.15 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.15), residues: 3201 helix: -0.01 (0.20), residues: 717 sheet: 0.28 (0.18), residues: 837 loop : -1.55 (0.14), residues: 1647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 419 HIS 0.002 0.001 HIS B 147 PHE 0.015 0.001 PHE C 507 TYR 0.016 0.001 TYR B1027 ARG 0.006 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00241 ( 57) link_NAG-ASN : angle 2.04969 ( 171) link_BETA1-4 : bond 0.00302 ( 15) link_BETA1-4 : angle 1.30715 ( 45) hydrogen bonds : bond 0.05075 ( 932) hydrogen bonds : angle 5.80614 ( 2526) SS BOND : bond 0.00301 ( 42) SS BOND : angle 1.14411 ( 84) covalent geometry : bond 0.00308 (26745) covalent geometry : angle 0.54951 (36404) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 82 time to evaluate : 2.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8556 (m-80) cc_final: 0.8188 (m-80) REVERT: A 153 PHE cc_start: 0.8253 (m-10) cc_final: 0.7739 (m-10) REVERT: A 516 LEU cc_start: 0.7917 (tp) cc_final: 0.7680 (tm) REVERT: B 45 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7440 (mtt180) REVERT: B 168 ILE cc_start: 0.9208 (OUTLIER) cc_final: 0.8968 (mt) REVERT: B 497 LEU cc_start: 0.5794 (OUTLIER) cc_final: 0.5147 (pp) REVERT: B 809 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8115 (mt) REVERT: B 893 GLN cc_start: 0.8597 (OUTLIER) cc_final: 0.8315 (pp30) REVERT: C 153 PHE cc_start: 0.7938 (m-10) cc_final: 0.7429 (m-10) REVERT: C 522 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6471 (tpt90) REVERT: C 547 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7226 (tt0) REVERT: C 893 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8341 (pp30) outliers start: 84 outliers final: 46 residues processed: 162 average time/residue: 1.1570 time to fit residues: 226.6694 Evaluate side-chains 132 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 78 time to evaluate : 2.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 1042 CYS Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 521 LYS Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 809 LEU Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1042 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 547 GLU Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 893 GLN Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 917 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 292 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 129 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 123 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 262 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 895 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.072412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.050731 restraints weight = 58931.963| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 3.29 r_work: 0.2559 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 26859 Z= 0.251 Angle : 0.645 10.158 36704 Z= 0.333 Chirality : 0.047 0.239 4347 Planarity : 0.004 0.064 4616 Dihedral : 7.488 88.807 5068 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.94 % Allowed : 19.25 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.15), residues: 3201 helix: 0.18 (0.20), residues: 702 sheet: 0.13 (0.18), residues: 882 loop : -1.58 (0.15), residues: 1617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 846 HIS 0.005 0.001 HIS C1024 PHE 0.026 0.002 PHE C 526 TYR 0.017 0.001 TYR B1027 ARG 0.005 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 57) link_NAG-ASN : angle 2.23337 ( 171) link_BETA1-4 : bond 0.00226 ( 15) link_BETA1-4 : angle 1.34689 ( 45) hydrogen bonds : bond 0.05811 ( 932) hydrogen bonds : angle 5.59081 ( 2526) SS BOND : bond 0.00439 ( 42) SS BOND : angle 1.58263 ( 84) covalent geometry : bond 0.00603 (26745) covalent geometry : angle 0.62340 (36404) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 79 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8570 (m-80) cc_final: 0.8129 (m-80) REVERT: A 153 PHE cc_start: 0.8245 (m-10) cc_final: 0.7649 (m-10) REVERT: A 542 ASP cc_start: 0.5910 (OUTLIER) cc_final: 0.5693 (t0) REVERT: A 546 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6208 (tm) REVERT: A 549 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7243 (mm) REVERT: A 804 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7914 (mm) REVERT: B 168 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9028 (mt) REVERT: B 497 LEU cc_start: 0.5602 (OUTLIER) cc_final: 0.5168 (pp) REVERT: C 90 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7525 (pp20) REVERT: C 153 PHE cc_start: 0.7988 (m-10) cc_final: 0.7485 (m-10) REVERT: C 522 ARG cc_start: 0.7194 (OUTLIER) cc_final: 0.6473 (tpt90) REVERT: C 948 GLU cc_start: 0.8660 (tp30) cc_final: 0.8284 (tp30) outliers start: 110 outliers final: 63 residues processed: 179 average time/residue: 1.0599 time to fit residues: 233.9485 Evaluate side-chains 145 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 74 time to evaluate : 2.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 559 VAL Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 703 CYS Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 508 ASN Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 917 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 107 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 307 optimal weight: 1.9990 chunk 299 optimal weight: 3.9990 chunk 242 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 184 optimal weight: 8.9990 chunk 248 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 592 GLN B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 GLN C 915 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.074528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.052835 restraints weight = 59086.258| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 3.33 r_work: 0.2610 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 26859 Z= 0.119 Angle : 0.553 9.713 36704 Z= 0.283 Chirality : 0.044 0.251 4347 Planarity : 0.004 0.057 4616 Dihedral : 7.056 88.267 5062 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.16 % Allowed : 19.79 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.15), residues: 3201 helix: 0.41 (0.21), residues: 699 sheet: 0.19 (0.18), residues: 882 loop : -1.47 (0.15), residues: 1620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 846 HIS 0.003 0.001 HIS B 147 PHE 0.016 0.001 PHE B 153 TYR 0.014 0.001 TYR B1027 ARG 0.003 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00248 ( 57) link_NAG-ASN : angle 2.09241 ( 171) link_BETA1-4 : bond 0.00307 ( 15) link_BETA1-4 : angle 1.19521 ( 45) hydrogen bonds : bond 0.04357 ( 932) hydrogen bonds : angle 5.28185 ( 2526) SS BOND : bond 0.00442 ( 42) SS BOND : angle 1.26080 ( 84) covalent geometry : bond 0.00268 (26745) covalent geometry : angle 0.53097 (36404) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 76 time to evaluate : 3.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8533 (m-80) cc_final: 0.8094 (m-80) REVERT: A 153 PHE cc_start: 0.8293 (m-10) cc_final: 0.7818 (m-10) REVERT: A 522 ARG cc_start: 0.7186 (ttt-90) cc_final: 0.6615 (ttp80) REVERT: A 550 ASP cc_start: 0.8862 (OUTLIER) cc_final: 0.8470 (m-30) REVERT: A 804 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7837 (mm) REVERT: B 45 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7523 (mtt180) REVERT: B 168 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8971 (mt) REVERT: B 497 LEU cc_start: 0.5663 (OUTLIER) cc_final: 0.5178 (pp) REVERT: B 894 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8873 (tt) REVERT: C 90 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: C 153 PHE cc_start: 0.7942 (m-10) cc_final: 0.7396 (m-10) REVERT: C 522 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.6493 (tpt90) REVERT: C 948 GLU cc_start: 0.8740 (tp30) cc_final: 0.8290 (tp30) outliers start: 88 outliers final: 51 residues processed: 156 average time/residue: 1.1281 time to fit residues: 212.9915 Evaluate side-chains 131 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 72 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 168 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 545 THR Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 297 GLN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 770 SER Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 73 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 268 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 241 optimal weight: 6.9990 chunk 263 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 126 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.072448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.050876 restraints weight = 59107.917| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.28 r_work: 0.2563 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 26859 Z= 0.228 Angle : 0.623 11.531 36704 Z= 0.319 Chirality : 0.047 0.239 4347 Planarity : 0.004 0.061 4616 Dihedral : 7.222 88.332 5061 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.51 % Allowed : 19.51 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 3201 helix: 0.37 (0.20), residues: 720 sheet: 0.11 (0.17), residues: 897 loop : -1.44 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 846 HIS 0.004 0.001 HIS C1018 PHE 0.025 0.001 PHE C 526 TYR 0.016 0.001 TYR A 459 ARG 0.004 0.000 ARG A 541 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 57) link_NAG-ASN : angle 2.21992 ( 171) link_BETA1-4 : bond 0.00255 ( 15) link_BETA1-4 : angle 1.29397 ( 45) hydrogen bonds : bond 0.05295 ( 932) hydrogen bonds : angle 5.33606 ( 2526) SS BOND : bond 0.00442 ( 42) SS BOND : angle 1.68828 ( 84) covalent geometry : bond 0.00550 (26745) covalent geometry : angle 0.60010 (36404) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 77 time to evaluate : 2.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8581 (m-80) cc_final: 0.8096 (m-80) REVERT: A 153 PHE cc_start: 0.8242 (m-10) cc_final: 0.7688 (m-10) REVERT: A 517 THR cc_start: 0.8616 (m) cc_final: 0.8300 (t) REVERT: A 547 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.6753 (tt0) REVERT: A 549 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7282 (mm) REVERT: A 550 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: A 804 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.8009 (mm) REVERT: B 259 MET cc_start: 0.9530 (ttp) cc_final: 0.9152 (ttt) REVERT: B 497 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5382 (pp) REVERT: B 894 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8878 (tt) REVERT: C 90 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7313 (pp20) REVERT: C 153 PHE cc_start: 0.7944 (m-10) cc_final: 0.7417 (m-10) REVERT: C 522 ARG cc_start: 0.7148 (OUTLIER) cc_final: 0.6472 (tpt90) REVERT: C 948 GLU cc_start: 0.8753 (tp30) cc_final: 0.8300 (tp30) outliers start: 98 outliers final: 63 residues processed: 165 average time/residue: 1.0238 time to fit residues: 208.0856 Evaluate side-chains 146 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 75 time to evaluate : 2.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 599 VAL Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 894 ILE Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 917 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 297 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 219 optimal weight: 7.9990 chunk 294 optimal weight: 0.8980 chunk 272 optimal weight: 0.0770 chunk 271 optimal weight: 0.0050 chunk 152 optimal weight: 6.9990 chunk 101 optimal weight: 1.9990 chunk 298 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN B 861 GLN B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 GLN C 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.053820 restraints weight = 58560.564| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.31 r_work: 0.2635 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 26859 Z= 0.095 Angle : 0.529 10.358 36704 Z= 0.269 Chirality : 0.043 0.257 4347 Planarity : 0.004 0.054 4616 Dihedral : 6.801 87.352 5061 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.72 % Allowed : 20.11 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.15), residues: 3201 helix: 0.64 (0.21), residues: 699 sheet: 0.31 (0.18), residues: 849 loop : -1.35 (0.15), residues: 1653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 846 HIS 0.002 0.000 HIS B 147 PHE 0.013 0.001 PHE C 507 TYR 0.014 0.001 TYR A1027 ARG 0.002 0.000 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 57) link_NAG-ASN : angle 2.03206 ( 171) link_BETA1-4 : bond 0.00346 ( 15) link_BETA1-4 : angle 1.12950 ( 45) hydrogen bonds : bond 0.03855 ( 932) hydrogen bonds : angle 5.05226 ( 2526) SS BOND : bond 0.00251 ( 42) SS BOND : angle 1.16013 ( 84) covalent geometry : bond 0.00202 (26745) covalent geometry : angle 0.50788 (36404) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 79 time to evaluate : 2.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8530 (m-80) cc_final: 0.8081 (m-80) REVERT: A 153 PHE cc_start: 0.8244 (m-10) cc_final: 0.7751 (m-10) REVERT: A 511 LYS cc_start: 0.8119 (tptt) cc_final: 0.7846 (tppt) REVERT: A 517 THR cc_start: 0.8540 (m) cc_final: 0.8288 (t) REVERT: A 522 ARG cc_start: 0.7094 (ttt-90) cc_final: 0.6541 (ttp80) REVERT: A 548 ILE cc_start: 0.2808 (OUTLIER) cc_final: 0.2607 (mm) REVERT: A 549 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7299 (mm) REVERT: A 550 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8459 (m-30) REVERT: A 715 GLN cc_start: 0.8178 (mt0) cc_final: 0.7953 (mp10) REVERT: A 804 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7794 (mm) REVERT: B 45 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7523 (mtt180) REVERT: B 497 LEU cc_start: 0.5623 (OUTLIER) cc_final: 0.5129 (pp) REVERT: B 893 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8356 (pp30) REVERT: C 90 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7191 (pp20) REVERT: C 153 PHE cc_start: 0.7855 (m-10) cc_final: 0.7303 (m-10) REVERT: C 522 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.6437 (tpt90) REVERT: C 948 GLU cc_start: 0.8758 (tp30) cc_final: 0.8244 (tp30) outliers start: 76 outliers final: 45 residues processed: 149 average time/residue: 1.2057 time to fit residues: 216.8467 Evaluate side-chains 130 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 76 time to evaluate : 2.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 548 ILE Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 862 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 241 ILE Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 478 SER Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 770 SER Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 253 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 81 optimal weight: 5.9990 chunk 125 optimal weight: 10.0000 chunk 132 optimal weight: 3.9990 chunk 189 optimal weight: 4.9990 chunk 284 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN B 861 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 861 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.071878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.050338 restraints weight = 59436.306| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.29 r_work: 0.2550 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.108 26859 Z= 0.285 Angle : 0.659 10.676 36704 Z= 0.337 Chirality : 0.048 0.244 4347 Planarity : 0.004 0.062 4616 Dihedral : 7.122 89.840 5056 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.33 % Allowed : 19.61 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3201 helix: 0.42 (0.20), residues: 720 sheet: 0.10 (0.17), residues: 897 loop : -1.42 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 846 HIS 0.005 0.001 HIS C1024 PHE 0.030 0.002 PHE C 526 TYR 0.026 0.002 TYR A 459 ARG 0.004 0.000 ARG B 999 Details of bonding type rmsd link_NAG-ASN : bond 0.00296 ( 57) link_NAG-ASN : angle 2.21801 ( 171) link_BETA1-4 : bond 0.00204 ( 15) link_BETA1-4 : angle 1.27880 ( 45) hydrogen bonds : bond 0.05564 ( 932) hydrogen bonds : angle 5.29523 ( 2526) SS BOND : bond 0.00459 ( 42) SS BOND : angle 1.93386 ( 84) covalent geometry : bond 0.00693 (26745) covalent geometry : angle 0.63556 (36404) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 78 time to evaluate : 2.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8611 (m-80) cc_final: 0.8163 (m-80) REVERT: A 153 PHE cc_start: 0.8233 (m-10) cc_final: 0.7682 (m-10) REVERT: A 547 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.6753 (tt0) REVERT: A 549 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7376 (mm) REVERT: A 550 ASP cc_start: 0.8863 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: A 804 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7989 (mm) REVERT: A 1003 CYS cc_start: 0.9386 (OUTLIER) cc_final: 0.9082 (m) REVERT: B 497 LEU cc_start: 0.5924 (OUTLIER) cc_final: 0.5447 (pp) REVERT: B 547 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.6946 (tp30) REVERT: C 153 PHE cc_start: 0.7917 (m-10) cc_final: 0.7362 (m-10) REVERT: C 522 ARG cc_start: 0.7154 (OUTLIER) cc_final: 0.6527 (tpt90) REVERT: C 948 GLU cc_start: 0.8774 (tp30) cc_final: 0.8324 (tp30) outliers start: 93 outliers final: 57 residues processed: 162 average time/residue: 1.1124 time to fit residues: 218.6560 Evaluate side-chains 144 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 79 time to evaluate : 2.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 455 THR Chi-restraints excluded: chain A residue 459 TYR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 549 LEU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 67 PHE Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 547 GLU Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 917 GLN Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 117 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 200 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 206 optimal weight: 4.9990 chunk 258 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.072992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051528 restraints weight = 59209.726| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.27 r_work: 0.2580 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 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 : 0.004 0.074 26859 Z= 0.176 Angle : 0.600 12.506 36704 Z= 0.305 Chirality : 0.046 0.236 4347 Planarity : 0.004 0.059 4616 Dihedral : 6.999 89.960 5054 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.83 % Allowed : 20.11 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.15), residues: 3201 helix: 0.47 (0.21), residues: 702 sheet: 0.12 (0.17), residues: 894 loop : -1.44 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 846 HIS 0.004 0.001 HIS B1024 PHE 0.018 0.001 PHE C 526 TYR 0.026 0.001 TYR C 459 ARG 0.003 0.000 ARG C 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00221 ( 57) link_NAG-ASN : angle 2.14275 ( 171) link_BETA1-4 : bond 0.00283 ( 15) link_BETA1-4 : angle 1.20530 ( 45) hydrogen bonds : bond 0.04841 ( 932) hydrogen bonds : angle 5.20079 ( 2526) SS BOND : bond 0.00362 ( 42) SS BOND : angle 1.76289 ( 84) covalent geometry : bond 0.00423 (26745) covalent geometry : angle 0.57702 (36404) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 78 time to evaluate : 3.051 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8591 (m-80) cc_final: 0.8145 (m-80) REVERT: A 153 PHE cc_start: 0.8247 (m-10) cc_final: 0.7727 (m-10) REVERT: A 522 ARG cc_start: 0.7121 (ttt-90) cc_final: 0.6550 (ttp80) REVERT: A 547 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6574 (tp30) REVERT: A 550 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: A 804 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7841 (mm) REVERT: A 1003 CYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9086 (m) REVERT: B 497 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5343 (pp) REVERT: B 893 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8304 (pp30) REVERT: B 1010 MET cc_start: 0.9466 (ptm) cc_final: 0.9225 (ptm) REVERT: C 153 PHE cc_start: 0.7916 (m-10) cc_final: 0.7352 (m-10) REVERT: C 522 ARG cc_start: 0.7143 (OUTLIER) cc_final: 0.6492 (tpt90) REVERT: C 948 GLU cc_start: 0.8768 (tp30) cc_final: 0.8309 (tp30) outliers start: 79 outliers final: 62 residues processed: 149 average time/residue: 1.1531 time to fit residues: 208.9509 Evaluate side-chains 143 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 74 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 547 GLU Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 67 PHE Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 962 GLN Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 147 optimal weight: 5.9990 chunk 255 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 263 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 260 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.072952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.051496 restraints weight = 59336.522| |-----------------------------------------------------------------------------| r_work (start): 0.2729 rms_B_bonded: 3.28 r_work: 0.2579 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 26859 Z= 0.175 Angle : 0.597 12.210 36704 Z= 0.304 Chirality : 0.045 0.269 4347 Planarity : 0.004 0.059 4616 Dihedral : 6.972 89.529 5054 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.98 % Allowed : 20.04 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.15), residues: 3201 helix: 0.51 (0.21), residues: 702 sheet: 0.14 (0.17), residues: 894 loop : -1.42 (0.15), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 846 HIS 0.004 0.001 HIS B1024 PHE 0.019 0.001 PHE C 526 TYR 0.026 0.001 TYR C 459 ARG 0.003 0.000 ARG C 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 57) link_NAG-ASN : angle 2.12413 ( 171) link_BETA1-4 : bond 0.00235 ( 15) link_BETA1-4 : angle 1.19860 ( 45) hydrogen bonds : bond 0.04817 ( 932) hydrogen bonds : angle 5.17644 ( 2526) SS BOND : bond 0.00356 ( 42) SS BOND : angle 1.67839 ( 84) covalent geometry : bond 0.00420 (26745) covalent geometry : angle 0.57481 (36404) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 76 time to evaluate : 3.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8589 (m-80) cc_final: 0.8142 (m-80) REVERT: A 153 PHE cc_start: 0.8234 (m-10) cc_final: 0.7716 (m-10) REVERT: A 522 ARG cc_start: 0.7114 (ttt-90) cc_final: 0.6548 (ttp80) REVERT: A 550 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8641 (m-30) REVERT: A 804 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7835 (mm) REVERT: A 1003 CYS cc_start: 0.9372 (OUTLIER) cc_final: 0.9086 (m) REVERT: B 497 LEU cc_start: 0.5872 (OUTLIER) cc_final: 0.5336 (pp) REVERT: B 893 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8361 (pp30) REVERT: C 153 PHE cc_start: 0.7883 (m-10) cc_final: 0.7311 (m-10) REVERT: C 522 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6493 (tpt90) REVERT: C 948 GLU cc_start: 0.8776 (tp30) cc_final: 0.8319 (tp30) outliers start: 83 outliers final: 66 residues processed: 153 average time/residue: 1.1411 time to fit residues: 211.9895 Evaluate side-chains 148 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 76 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 67 PHE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 599 VAL Chi-restraints excluded: chain A residue 609 THR Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 718 SER Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 917 GLN Chi-restraints excluded: chain A residue 962 GLN Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 120 LEU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 377 SER Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 508 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 609 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 954 ASP Chi-restraints excluded: chain B residue 965 GLN Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 459 TYR Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 542 ASP Chi-restraints excluded: chain C residue 552 THR Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 954 ASP Chi-restraints excluded: chain C residue 962 GLN Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Chi-restraints excluded: chain C residue 1096 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 126 optimal weight: 5.9990 chunk 189 optimal weight: 0.9980 chunk 196 optimal weight: 0.0980 chunk 231 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 318 optimal weight: 3.9990 chunk 86 optimal weight: 4.9990 chunk 256 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 208 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 893 GLN B 592 GLN B 861 GLN B 893 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 915 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.074956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.053471 restraints weight = 58805.276| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.31 r_work: 0.2628 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 26859 Z= 0.102 Angle : 0.545 10.807 36704 Z= 0.276 Chirality : 0.044 0.244 4347 Planarity : 0.004 0.055 4616 Dihedral : 6.704 88.893 5054 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.26 % Allowed : 20.87 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.15), residues: 3201 helix: 0.64 (0.21), residues: 702 sheet: 0.18 (0.17), residues: 897 loop : -1.31 (0.15), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 846 HIS 0.002 0.000 HIS B 147 PHE 0.013 0.001 PHE B 153 TYR 0.020 0.001 TYR C 459 ARG 0.002 0.000 ARG C 307 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 57) link_NAG-ASN : angle 1.97776 ( 171) link_BETA1-4 : bond 0.00336 ( 15) link_BETA1-4 : angle 1.10328 ( 45) hydrogen bonds : bond 0.03916 ( 932) hydrogen bonds : angle 5.00774 ( 2526) SS BOND : bond 0.00273 ( 42) SS BOND : angle 1.31620 ( 84) covalent geometry : bond 0.00228 (26745) covalent geometry : angle 0.52459 (36404) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 78 time to evaluate : 3.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8550 (m-80) cc_final: 0.8093 (m-80) REVERT: A 153 PHE cc_start: 0.8197 (m-10) cc_final: 0.7708 (m-10) REVERT: A 511 LYS cc_start: 0.8183 (tptt) cc_final: 0.7906 (tppt) REVERT: A 516 LEU cc_start: 0.7809 (tm) cc_final: 0.7444 (tm) REVERT: A 522 ARG cc_start: 0.7100 (ttt-90) cc_final: 0.6539 (ttp80) REVERT: A 550 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8596 (m-30) REVERT: A 804 ILE cc_start: 0.7904 (OUTLIER) cc_final: 0.7699 (mm) REVERT: A 1003 CYS cc_start: 0.9339 (OUTLIER) cc_final: 0.9053 (m) REVERT: B 45 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7576 (mtt180) REVERT: B 497 LEU cc_start: 0.5735 (OUTLIER) cc_final: 0.5233 (pp) REVERT: B 549 LEU cc_start: 0.7995 (mt) cc_final: 0.7770 (mm) REVERT: B 893 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7885 (pp30) REVERT: C 90 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7108 (pp20) REVERT: C 153 PHE cc_start: 0.7845 (m-10) cc_final: 0.7215 (m-10) REVERT: C 522 ARG cc_start: 0.7127 (OUTLIER) cc_final: 0.6441 (tpt90) REVERT: C 948 GLU cc_start: 0.8736 (tp30) cc_final: 0.8268 (tp30) outliers start: 63 outliers final: 42 residues processed: 136 average time/residue: 1.2472 time to fit residues: 205.8275 Evaluate side-chains 123 residues out of total 2790 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 73 time to evaluate : 3.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 141 ASN Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain A residue 465 VAL Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 550 ASP Chi-restraints excluded: chain A residue 698 CYS Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 805 SER Chi-restraints excluded: chain A residue 860 MET Chi-restraints excluded: chain A residue 1003 CYS Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 241 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 458 THR Chi-restraints excluded: chain B residue 459 TYR Chi-restraints excluded: chain B residue 465 VAL Chi-restraints excluded: chain B residue 497 LEU Chi-restraints excluded: chain B residue 552 THR Chi-restraints excluded: chain B residue 656 THR Chi-restraints excluded: chain B residue 698 CYS Chi-restraints excluded: chain B residue 893 GLN Chi-restraints excluded: chain B residue 923 VAL Chi-restraints excluded: chain B residue 1003 CYS Chi-restraints excluded: chain B residue 1089 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 90 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 124 VAL Chi-restraints excluded: chain C residue 229 THR Chi-restraints excluded: chain C residue 310 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain C residue 653 VAL Chi-restraints excluded: chain C residue 656 THR Chi-restraints excluded: chain C residue 700 MET Chi-restraints excluded: chain C residue 894 ILE Chi-restraints excluded: chain C residue 951 VAL Chi-restraints excluded: chain C residue 1003 CYS Chi-restraints excluded: chain C residue 1042 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 188 optimal weight: 4.9990 chunk 299 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 139 optimal weight: 4.9990 chunk 296 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 265 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 893 GLN B 861 GLN B 893 GLN B 895 GLN ** C 483 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.071494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.050107 restraints weight = 59423.457| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.27 r_work: 0.2545 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 26859 Z= 0.299 Angle : 0.676 12.227 36704 Z= 0.346 Chirality : 0.049 0.256 4347 Planarity : 0.004 0.063 4616 Dihedral : 7.083 89.409 5054 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.55 % Allowed : 20.54 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.15), residues: 3201 helix: 0.45 (0.20), residues: 720 sheet: 0.13 (0.17), residues: 897 loop : -1.40 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 846 HIS 0.006 0.001 HIS C1024 PHE 0.031 0.002 PHE C 526 TYR 0.036 0.002 TYR C 459 ARG 0.004 0.000 ARG B 541 Details of bonding type rmsd link_NAG-ASN : bond 0.00313 ( 57) link_NAG-ASN : angle 2.20489 ( 171) link_BETA1-4 : bond 0.00199 ( 15) link_BETA1-4 : angle 1.28268 ( 45) hydrogen bonds : bond 0.05707 ( 932) hydrogen bonds : angle 5.28452 ( 2526) SS BOND : bond 0.00471 ( 42) SS BOND : angle 1.97539 ( 84) covalent geometry : bond 0.00727 (26745) covalent geometry : angle 0.65286 (36404) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16855.90 seconds wall clock time: 297 minutes 3.10 seconds (17823.10 seconds total)