Starting phenix.real_space_refine on Sun Jul 5 21:12:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.cif" model { file = "/net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws5_32744/07_2026/7ws5_32744.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.040 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 132 5.16 5 C 19267 2.51 5 N 4986 2.21 5 O 5843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30228 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8112 Classifications: {'peptide': 1035} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8135 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 57, 'TRANS': 978} Chain breaks: 8 Chain: "C" Number of atoms: 8130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8130 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 57, 'TRANS': 978} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 956 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.88, per 1000 atoms: 0.19 Number of scatterers: 30228 At special positions: 0 Unit cell: (143.936, 173.888, 210.496, 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 132 16.00 O 5843 8.00 N 4986 7.00 C 19267 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.05 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 282 " " NAG A1303 " - " ASN A 709 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 709 " " NAG C1301 " - " ASN C 234 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.3 seconds 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7102 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 65 sheets defined 20.9% alpha, 31.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.719A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.650A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.025A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.591A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.910A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.065A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.971A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.257A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.539A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.285A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 4.055A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.628A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.508A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.586A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.524A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.070A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.357A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.393A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.044A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.607A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.802A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.507A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.105A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.657A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.022A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.631A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'G' and resid 62 through 65 Processing helix chain 'I' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.829A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 264 " --> pdb=" O ILE A 95 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.355A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.882A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.086A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.219A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.397A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.738A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.967A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 327 through 328 removed outlier: 3.650A pdb=" N ARG A 328 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.638A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.870A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.526A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.975A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.557A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.564A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.964A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.552A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.868A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB9, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.376A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.029A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.176A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.016A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.723A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.590A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.426A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.426A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 787 through 789 removed outlier: 5.440A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.079A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.824A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.540A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER C 116 " --> pdb=" O CYS C 131 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS C 131 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N GLU C 132 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N CYS C 166 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 10.208A pdb=" N GLN C 134 " --> pdb=" O ASN C 164 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N ASN C 164 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS C 136 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 10.532A pdb=" N SER C 162 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 10.750A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.340A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.324A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.588A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.893A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.203A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.711A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.648A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.648A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'D' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AF3, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.534A pdb=" N SER D 53 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 4 through 6 removed outlier: 3.570A pdb=" N THR E 69 " --> pdb=" O GLN E 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.848A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY E 50 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ASP E 59 " --> pdb=" O GLY E 50 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.827A pdb=" N LYS E 98 " --> pdb=" O ASP E 111 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 4 through 6 Processing sheet with id=AF8, first strand: chain 'F' and resid 10 through 11 Processing sheet with id=AF9, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.590A pdb=" N SER F 53 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN F 90 " --> pdb=" O THR F 98 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR F 98 " --> pdb=" O GLN F 90 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 4 through 7 removed outlier: 3.605A pdb=" N THR G 69 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AG3, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.683A pdb=" N ASP G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 50 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LYS G 98 " --> pdb=" O ASP G 111 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 58 through 60 removed outlier: 3.683A pdb=" N ASP G 59 " --> pdb=" O GLY G 50 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY G 50 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP G 36 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLY G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N MET G 34 " --> pdb=" O GLY G 50 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.589A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.604A pdb=" N SER H 53 " --> pdb=" O TYR H 49 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 4 through 7 Processing sheet with id=AG9, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AH1, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS I 98 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'I' and resid 58 through 60 removed outlier: 6.652A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) 1228 hydrogen bonds defined for protein. 3324 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: 7.76 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9587 1.34 - 1.46: 7167 1.46 - 1.58: 14005 1.58 - 1.70: 0 1.70 - 1.82: 168 Bond restraints: 30927 Sorted by residual: bond pdb=" N CYS B 738 " pdb=" CA CYS B 738 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.19e-02 7.06e+03 8.59e+00 bond pdb=" N ASN A 487 " pdb=" CA ASN A 487 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.67e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.55e+00 bond pdb=" N LEU A 858 " pdb=" CA LEU A 858 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.22e-02 6.72e+03 6.60e+00 bond pdb=" N THR A 859 " pdb=" CA THR A 859 " ideal model delta sigma weight residual 1.455 1.487 -0.033 1.29e-02 6.01e+03 6.44e+00 ... (remaining 30922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 40331 1.39 - 2.78: 1411 2.78 - 4.18: 248 4.18 - 5.57: 54 5.57 - 6.96: 7 Bond angle restraints: 42051 Sorted by residual: angle pdb=" N PHE B 855 " pdb=" CA PHE B 855 " pdb=" C PHE B 855 " ideal model delta sigma weight residual 113.18 107.87 5.31 1.21e+00 6.83e-01 1.93e+01 angle pdb=" N LYS A 856 " pdb=" CA LYS A 856 " pdb=" C LYS A 856 " ideal model delta sigma weight residual 113.15 108.01 5.14 1.19e+00 7.06e-01 1.86e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 115.23 -4.53 1.22e+00 6.72e-01 1.38e+01 angle pdb=" N ASP A 571 " pdb=" CA ASP A 571 " pdb=" C ASP A 571 " ideal model delta sigma weight residual 113.23 108.75 4.48 1.22e+00 6.72e-01 1.35e+01 angle pdb=" C ASN A 641 " pdb=" N VAL A 642 " pdb=" CA VAL A 642 " ideal model delta sigma weight residual 123.14 118.35 4.79 1.31e+00 5.83e-01 1.34e+01 ... (remaining 42046 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 16633 17.76 - 35.53: 1196 35.53 - 53.29: 221 53.29 - 71.06: 51 71.06 - 88.82: 34 Dihedral angle restraints: 18135 sinusoidal: 7090 harmonic: 11045 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -17.25 -68.75 1 1.00e+01 1.00e-02 6.12e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 160.52 -67.52 1 1.00e+01 1.00e-02 5.93e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -29.49 -56.51 1 1.00e+01 1.00e-02 4.30e+01 ... (remaining 18132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.167: 4819 0.167 - 0.333: 10 0.333 - 0.500: 2 0.500 - 0.667: 0 0.667 - 0.833: 2 Chirality restraints: 4833 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.57 -0.83 2.00e-01 2.50e+01 1.74e+01 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -1.65 -0.75 2.00e-01 2.50e+01 1.42e+01 chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.90 -0.50 2.00e-01 2.50e+01 6.25e+00 ... (remaining 4830 not shown) Planarity restraints: 5406 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 61 " 0.034 2.00e-02 2.50e+03 3.13e-02 1.23e+01 pdb=" CG ASN A 61 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASN A 61 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN A 61 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG A1301 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 737 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.90e+00 pdb=" C ASP C 737 " 0.049 2.00e-02 2.50e+03 pdb=" O ASP C 737 " -0.019 2.00e-02 2.50e+03 pdb=" N CYS C 738 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 717 " -0.026 2.00e-02 2.50e+03 2.48e-02 7.67e+00 pdb=" CG ASN C 717 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 717 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 717 " 0.013 2.00e-02 2.50e+03 pdb=" C1 NAG O 1 " -0.020 2.00e-02 2.50e+03 ... (remaining 5403 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 1123 2.71 - 3.26: 29632 3.26 - 3.81: 48669 3.81 - 4.35: 58966 4.35 - 4.90: 101753 Nonbonded interactions: 240143 Sorted by model distance: nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.168 3.040 nonbonded pdb=" OH TYR B 756 " pdb=" OD1 ASP B 994 " model vdw 2.200 3.040 nonbonded pdb=" OD1 ASN F 34 " pdb=" OG SER G 109 " model vdw 2.202 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.210 3.040 nonbonded pdb=" OD1 ASN H 34 " pdb=" OG SER I 109 " model vdw 2.211 3.040 ... (remaining 240138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 14 through 497 or (resid 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 through 500 or (resid 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 through 518 or (resid 5 \ 19 through 520 and (name N or name CA or name C or name O or name CB )) or resid \ 521 through 827 or resid 853 through 1303)) selection = (chain 'C' and (resid 14 through 497 or (resid 498 and (name N or name CA or nam \ e C or name O or name CB )) or resid 499 through 500 or (resid 501 and (name N o \ r name CA or name C or name O or name CB )) or resid 502 through 827 or resid 85 \ 3 through 1303)) } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 26.830 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 31011 Z= 0.178 Angle : 0.647 21.305 42257 Z= 0.349 Chirality : 0.049 0.833 4833 Planarity : 0.004 0.068 5382 Dihedral : 13.208 88.824 10895 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.49 % Favored : 97.46 % Rotamer: Outliers : 0.09 % Allowed : 0.27 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3734 helix: 1.62 (0.21), residues: 682 sheet: 0.16 (0.15), residues: 1028 loop : -0.73 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 19 TYR 0.024 0.001 TYR C 904 PHE 0.023 0.001 PHE C 559 TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.18 (30927) covalent geometry : angle 0.61330 / 0.34 (42051) SS BOND : bond 0.00319 / 0.23 ( 46) SS BOND : angle 1.05872 / 0.63 ( 92) hydrogen bonds : bond 0.14352 / 9.04 ( 1179) hydrogen bonds : angle 7.18717 / 5.03 ( 3324) link_BETA1-4 : bond 0.00507 / 0.36 ( 14) link_BETA1-4 : angle 1.58442 / 1.01 ( 42) link_NAG-ASN : bond 0.01107 / 0.73 ( 24) link_NAG-ASN : angle 4.79280 / 3.43 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 289 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8333 (m-80) cc_final: 0.7991 (m-80) REVERT: A 418 ILE cc_start: 0.9270 (pt) cc_final: 0.8582 (pt) REVERT: A 574 ASP cc_start: 0.7467 (p0) cc_final: 0.7099 (t0) REVERT: D 4 MET cc_start: 0.6329 (ptt) cc_final: 0.5871 (tmm) REVERT: D 29 ILE cc_start: 0.7604 (pt) cc_final: 0.7199 (pt) REVERT: D 59 PRO cc_start: 0.8162 (Cg_exo) cc_final: 0.7921 (Cg_endo) REVERT: D 71 PHE cc_start: 0.7089 (m-80) cc_final: 0.6286 (m-10) REVERT: D 72 THR cc_start: 0.7896 (m) cc_final: 0.7558 (m) REVERT: E 94 TYR cc_start: 0.8088 (m-80) cc_final: 0.7880 (m-80) REVERT: E 119 VAL cc_start: 0.2334 (m) cc_final: 0.0969 (t) REVERT: F 33 LEU cc_start: 0.4159 (tt) cc_final: 0.3020 (tp) REVERT: F 34 ASN cc_start: 0.3334 (m110) cc_final: 0.2640 (t0) REVERT: H 45 LYS cc_start: 0.9043 (ttpp) cc_final: 0.8392 (ttpp) REVERT: H 69 THR cc_start: 0.8528 (p) cc_final: 0.8205 (t) REVERT: H 83 PHE cc_start: 0.8247 (t80) cc_final: 0.7770 (t80) REVERT: H 99 PHE cc_start: 0.8683 (m-80) cc_final: 0.8480 (m-80) REVERT: H 105 LEU cc_start: 0.8203 (tp) cc_final: 0.7999 (tp) REVERT: I 59 ASP cc_start: 0.8366 (t0) cc_final: 0.8010 (t0) REVERT: I 95 TYR cc_start: 0.7422 (m-80) cc_final: 0.7020 (m-80) REVERT: I 103 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7654 (tp30) REVERT: I 111 ASP cc_start: 0.8708 (t70) cc_final: 0.8213 (t70) outliers start: 3 outliers final: 0 residues processed: 292 average time/residue: 0.1814 time to fit residues: 84.3978 Evaluate side-chains 200 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.5980 chunk 298 optimal weight: 4.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN B 81 ASN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 474 GLN C 853 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.096841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059176 restraints weight = 100340.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061392 restraints weight = 46726.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062627 restraints weight = 29627.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.063583 restraints weight = 22981.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.064044 restraints weight = 19316.234| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 31011 Z= 0.196 Angle : 0.629 20.142 42257 Z= 0.318 Chirality : 0.047 0.516 4833 Planarity : 0.004 0.057 5382 Dihedral : 4.181 23.802 4083 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 0.76 % Allowed : 5.62 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.13), residues: 3734 helix: 1.76 (0.20), residues: 687 sheet: 0.10 (0.15), residues: 1033 loop : -0.79 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 983 TYR 0.031 0.002 TYR H 49 PHE 0.018 0.002 PHE B 906 TRP 0.031 0.002 TRP B 436 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (30927) covalent geometry : angle 0.60110 / 0.31 (42051) SS BOND : bond 0.00480 / 0.33 ( 46) SS BOND : angle 1.36244 / 0.94 ( 92) hydrogen bonds : bond 0.04865 / 3.15 ( 1179) hydrogen bonds : angle 5.69879 / 3.95 ( 3324) link_BETA1-4 : bond 0.00192 / 0.11 ( 14) link_BETA1-4 : angle 1.10736 / 0.78 ( 42) link_NAG-ASN : bond 0.00712 / 0.47 ( 24) link_NAG-ASN : angle 4.25670 / 3.05 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 221 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8388 (m-80) cc_final: 0.8018 (m-80) REVERT: A 574 ASP cc_start: 0.7583 (p0) cc_final: 0.7109 (t0) REVERT: B 1029 MET cc_start: 0.9149 (tpp) cc_final: 0.8584 (ttm) REVERT: C 390 LEU cc_start: 0.9421 (mt) cc_final: 0.8996 (mp) REVERT: D 4 MET cc_start: 0.7075 (ptt) cc_final: 0.5773 (tmm) REVERT: D 11 LEU cc_start: 0.4924 (mm) cc_final: 0.4247 (tt) REVERT: D 23 CYS cc_start: 0.6231 (p) cc_final: 0.4518 (p) REVERT: D 24 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7649 (mmm160) REVERT: D 42 LYS cc_start: 0.8953 (ptpp) cc_final: 0.8489 (mmmt) REVERT: D 45 LYS cc_start: 0.8395 (ptmm) cc_final: 0.8148 (ptmm) REVERT: D 71 PHE cc_start: 0.7022 (m-80) cc_final: 0.6571 (m-10) REVERT: E 38 ARG cc_start: 0.8303 (ttp-170) cc_final: 0.8065 (ttt90) REVERT: E 83 MET cc_start: 0.4859 (mmm) cc_final: 0.4484 (mmm) REVERT: E 94 TYR cc_start: 0.8268 (m-80) cc_final: 0.7776 (m-80) REVERT: E 119 VAL cc_start: 0.2147 (m) cc_final: 0.1387 (t) REVERT: F 33 LEU cc_start: 0.4249 (tt) cc_final: 0.3029 (tp) REVERT: F 34 ASN cc_start: 0.3172 (m110) cc_final: 0.2276 (t0) REVERT: I 59 ASP cc_start: 0.8541 (t0) cc_final: 0.8083 (t0) REVERT: I 95 TYR cc_start: 0.7293 (m-80) cc_final: 0.7076 (m-80) REVERT: I 103 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7716 (tp30) REVERT: I 111 ASP cc_start: 0.8694 (t70) cc_final: 0.8312 (t70) outliers start: 25 outliers final: 19 residues processed: 232 average time/residue: 0.1785 time to fit residues: 67.8910 Evaluate side-chains 205 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 21 ILE Chi-restraints excluded: chain D residue 24 ARG Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 150 optimal weight: 9.9990 chunk 333 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 365 optimal weight: 5.9990 chunk 123 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 GLN B 81 ASN B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.101276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063920 restraints weight = 102160.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.066101 restraints weight = 48376.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.067452 restraints weight = 30827.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.068279 restraints weight = 23491.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.068716 restraints weight = 19892.388| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 31011 Z= 0.304 Angle : 0.695 20.581 42257 Z= 0.350 Chirality : 0.048 0.478 4833 Planarity : 0.005 0.068 5382 Dihedral : 4.504 25.040 4083 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.21 % Allowed : 9.16 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3734 helix: 1.42 (0.20), residues: 702 sheet: -0.09 (0.15), residues: 998 loop : -1.02 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 87 TYR 0.028 0.002 TYR H 49 PHE 0.023 0.002 PHE C 559 TRP 0.030 0.002 TRP G 47 HIS 0.007 0.001 HIS A1064 Details of bonding type rmsd/Z covalent geometry : bond 0.00709 / 0.30 (30927) covalent geometry : angle 0.66879 / 0.34 (42051) SS BOND : bond 0.00431 / 0.27 ( 46) SS BOND : angle 1.54011 / 1.01 ( 92) hydrogen bonds : bond 0.05386 / 3.50 ( 1179) hydrogen bonds : angle 5.68295 / 3.94 ( 3324) link_BETA1-4 : bond 0.00241 / 0.12 ( 14) link_BETA1-4 : angle 1.18198 / 0.84 ( 42) link_NAG-ASN : bond 0.00785 / 0.51 ( 24) link_NAG-ASN : angle 4.31165 / 3.09 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 205 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8391 (t70) cc_final: 0.8188 (t0) REVERT: A 392 PHE cc_start: 0.8539 (m-80) cc_final: 0.8323 (m-80) REVERT: A 574 ASP cc_start: 0.7757 (p0) cc_final: 0.7290 (t0) REVERT: A 740 MET cc_start: 0.8787 (ttt) cc_final: 0.8587 (ttt) REVERT: C 762 GLN cc_start: 0.8049 (mt0) cc_final: 0.7838 (mt0) REVERT: D 11 LEU cc_start: 0.5310 (mm) cc_final: 0.4623 (tp) REVERT: D 32 TYR cc_start: 0.7571 (m-10) cc_final: 0.7153 (m-10) REVERT: D 42 LYS cc_start: 0.8945 (ptpp) cc_final: 0.8198 (mmmt) REVERT: E 38 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7989 (ttt90) REVERT: E 67 ARG cc_start: 0.5021 (ttm170) cc_final: 0.4377 (ttm170) REVERT: E 94 TYR cc_start: 0.8339 (m-80) cc_final: 0.7876 (m-10) REVERT: F 33 LEU cc_start: 0.4057 (tt) cc_final: 0.2905 (tp) REVERT: F 34 ASN cc_start: 0.3216 (m110) cc_final: 0.2239 (t0) REVERT: G 47 TRP cc_start: 0.4229 (p90) cc_final: 0.3663 (p-90) REVERT: H 69 THR cc_start: 0.8781 (p) cc_final: 0.8356 (t) REVERT: I 59 ASP cc_start: 0.8583 (t0) cc_final: 0.8138 (t0) REVERT: I 103 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7763 (tp30) REVERT: I 111 ASP cc_start: 0.8676 (t70) cc_final: 0.7643 (t0) REVERT: I 112 TYR cc_start: 0.8128 (m-80) cc_final: 0.7466 (m-80) outliers start: 40 outliers final: 20 residues processed: 228 average time/residue: 0.1958 time to fit residues: 73.1030 Evaluate side-chains 201 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 181 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 132 optimal weight: 10.0000 chunk 161 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 42 optimal weight: 0.0070 chunk 252 optimal weight: 0.6980 chunk 171 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 357 optimal weight: 7.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 901 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 HIS ** G 35 HIS ** 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 = 0.3882 r_free = 0.3882 target = 0.095810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.058208 restraints weight = 99391.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060380 restraints weight = 45987.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061720 restraints weight = 29173.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.062629 restraints weight = 22160.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.063021 restraints weight = 18663.712| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 31011 Z= 0.141 Angle : 0.575 20.510 42257 Z= 0.288 Chirality : 0.045 0.469 4833 Planarity : 0.004 0.068 5382 Dihedral : 4.222 24.490 4083 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.36 % Allowed : 10.73 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 3734 helix: 1.82 (0.20), residues: 685 sheet: -0.01 (0.16), residues: 970 loop : -0.90 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 16 TYR 0.028 0.001 TYR H 49 PHE 0.017 0.001 PHE A 238 TRP 0.027 0.001 TRP E 113 HIS 0.004 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (30927) covalent geometry : angle 0.54795 / 0.28 (42051) SS BOND : bond 0.00418 / 0.22 ( 46) SS BOND : angle 1.31202 / 0.78 ( 92) hydrogen bonds : bond 0.04510 / 2.97 ( 1179) hydrogen bonds : angle 5.34299 / 3.70 ( 3324) link_BETA1-4 : bond 0.00282 / 0.19 ( 14) link_BETA1-4 : angle 0.95574 / 0.68 ( 42) link_NAG-ASN : bond 0.00655 / 0.47 ( 24) link_NAG-ASN : angle 3.98058 / 2.87 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 204 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7714 (p0) cc_final: 0.7142 (t0) REVERT: A 740 MET cc_start: 0.8835 (OUTLIER) cc_final: 0.8619 (ttt) REVERT: B 1029 MET cc_start: 0.9105 (tpp) cc_final: 0.8550 (ttm) REVERT: C 387 LEU cc_start: 0.9748 (OUTLIER) cc_final: 0.9488 (mm) REVERT: C 762 GLN cc_start: 0.7940 (mt0) cc_final: 0.7715 (mt0) REVERT: C 900 MET cc_start: 0.8688 (mtm) cc_final: 0.8480 (mtm) REVERT: D 4 MET cc_start: 0.6996 (ptt) cc_final: 0.6257 (ppp) REVERT: D 11 LEU cc_start: 0.5358 (mm) cc_final: 0.4689 (tp) REVERT: D 39 LYS cc_start: 0.7814 (mppt) cc_final: 0.7224 (mppt) REVERT: D 42 LYS cc_start: 0.8954 (ptpp) cc_final: 0.8747 (pttp) REVERT: E 3 GLN cc_start: 0.8153 (tp-100) cc_final: 0.7752 (tp40) REVERT: E 16 ARG cc_start: 0.8172 (ptt-90) cc_final: 0.7851 (ptt90) REVERT: E 99 ASP cc_start: 0.7697 (t0) cc_final: 0.7491 (t70) REVERT: E 119 VAL cc_start: 0.1641 (m) cc_final: 0.1430 (t) REVERT: F 32 TYR cc_start: 0.4538 (m-80) cc_final: 0.4328 (m-80) REVERT: F 33 LEU cc_start: 0.3965 (tt) cc_final: 0.2755 (tp) REVERT: F 34 ASN cc_start: 0.3463 (m110) cc_final: 0.2538 (t0) REVERT: H 69 THR cc_start: 0.8784 (p) cc_final: 0.7862 (t) REVERT: H 70 ASP cc_start: 0.8716 (p0) cc_final: 0.7958 (t0) REVERT: H 83 PHE cc_start: 0.7746 (t80) cc_final: 0.7481 (t80) REVERT: I 35 HIS cc_start: 0.8713 (m170) cc_final: 0.8422 (m-70) REVERT: I 39 GLN cc_start: 0.7256 (tp40) cc_final: 0.6539 (tp-100) REVERT: I 59 ASP cc_start: 0.8629 (t0) cc_final: 0.8165 (t0) REVERT: I 87 ARG cc_start: 0.9059 (mtm-85) cc_final: 0.8352 (mtm-85) REVERT: I 95 TYR cc_start: 0.7282 (m-80) cc_final: 0.6837 (m-80) REVERT: I 103 GLU cc_start: 0.8272 (mm-30) cc_final: 0.7711 (tp30) outliers start: 45 outliers final: 27 residues processed: 235 average time/residue: 0.1677 time to fit residues: 65.2526 Evaluate side-chains 216 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 187 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 110 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 24 optimal weight: 0.0870 chunk 92 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 218 optimal weight: 4.9990 chunk 217 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 216 optimal weight: 10.0000 chunk 263 optimal weight: 0.9990 chunk 337 optimal weight: 40.0000 chunk 322 optimal weight: 10.0000 overall best weight: 1.3962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.095454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.057907 restraints weight = 100324.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 76)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060109 restraints weight = 46462.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.061480 restraints weight = 29412.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.062193 restraints weight = 22334.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.062739 restraints weight = 19098.982| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31011 Z= 0.144 Angle : 0.566 20.279 42257 Z= 0.284 Chirality : 0.045 0.459 4833 Planarity : 0.004 0.049 5382 Dihedral : 4.174 30.455 4083 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.39 % Allowed : 11.37 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.13), residues: 3734 helix: 2.08 (0.20), residues: 667 sheet: 0.03 (0.15), residues: 1011 loop : -0.90 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 38 TYR 0.028 0.001 TYR H 49 PHE 0.025 0.001 PHE E 68 TRP 0.026 0.001 TRP G 47 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (30927) covalent geometry : angle 0.53969 / 0.28 (42051) SS BOND : bond 0.00282 / 0.20 ( 46) SS BOND : angle 1.46913 / 0.84 ( 92) hydrogen bonds : bond 0.04341 / 2.86 ( 1179) hydrogen bonds : angle 5.24050 / 3.63 ( 3324) link_BETA1-4 : bond 0.00220 / 0.14 ( 14) link_BETA1-4 : angle 0.96054 / 0.67 ( 42) link_NAG-ASN : bond 0.00619 / 0.45 ( 24) link_NAG-ASN : angle 3.85414 / 2.79 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 209 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7762 (p0) cc_final: 0.7132 (t0) REVERT: A 740 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.8598 (ttt) REVERT: A 773 GLU cc_start: 0.8659 (tp30) cc_final: 0.8420 (tp30) REVERT: B 1029 MET cc_start: 0.9105 (tpp) cc_final: 0.8568 (ttm) REVERT: C 387 LEU cc_start: 0.9742 (OUTLIER) cc_final: 0.9477 (mm) REVERT: C 762 GLN cc_start: 0.7937 (mt0) cc_final: 0.7710 (mt0) REVERT: C 900 MET cc_start: 0.8694 (mtm) cc_final: 0.8374 (mtm) REVERT: D 4 MET cc_start: 0.7112 (ptt) cc_final: 0.6302 (ppp) REVERT: D 11 LEU cc_start: 0.5435 (mm) cc_final: 0.4751 (tp) REVERT: D 35 TRP cc_start: 0.7079 (m-90) cc_final: 0.6759 (m-90) REVERT: D 39 LYS cc_start: 0.7813 (mppt) cc_final: 0.7497 (mppt) REVERT: E 3 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7681 (tp40) REVERT: E 18 LEU cc_start: 0.5864 (OUTLIER) cc_final: 0.5065 (mp) REVERT: E 87 ARG cc_start: 0.9196 (ptp90) cc_final: 0.8868 (ptt-90) REVERT: E 94 TYR cc_start: 0.8195 (m-80) cc_final: 0.7806 (m-10) REVERT: E 119 VAL cc_start: 0.1383 (m) cc_final: 0.0646 (t) REVERT: F 33 LEU cc_start: 0.3903 (tt) cc_final: 0.2735 (tp) REVERT: F 34 ASN cc_start: 0.3677 (m110) cc_final: 0.2712 (t0) REVERT: H 69 THR cc_start: 0.8750 (p) cc_final: 0.8335 (t) REVERT: H 83 PHE cc_start: 0.7528 (t80) cc_final: 0.7287 (t80) REVERT: H 101 GLN cc_start: 0.7590 (pm20) cc_final: 0.6985 (pm20) REVERT: H 104 LYS cc_start: 0.8248 (tptt) cc_final: 0.8037 (tptt) REVERT: I 35 HIS cc_start: 0.8687 (m170) cc_final: 0.8373 (m-70) REVERT: I 39 GLN cc_start: 0.7205 (tp40) cc_final: 0.6501 (tp-100) REVERT: I 59 ASP cc_start: 0.8625 (t0) cc_final: 0.8143 (t0) REVERT: I 95 TYR cc_start: 0.7315 (m-80) cc_final: 0.6943 (m-80) REVERT: I 103 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7704 (tp30) outliers start: 46 outliers final: 31 residues processed: 237 average time/residue: 0.1795 time to fit residues: 70.0089 Evaluate side-chains 226 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 192 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 90 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 211 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 325 optimal weight: 20.0000 chunk 295 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN B 334 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.094812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.058187 restraints weight = 101121.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.060981 restraints weight = 50699.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.061305 restraints weight = 31008.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061790 restraints weight = 23646.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.062027 restraints weight = 23567.714| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 31011 Z= 0.174 Angle : 0.585 20.271 42257 Z= 0.293 Chirality : 0.045 0.460 4833 Planarity : 0.004 0.043 5382 Dihedral : 4.181 27.117 4083 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.72 % Allowed : 12.36 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.13), residues: 3734 helix: 2.08 (0.20), residues: 672 sheet: -0.04 (0.15), residues: 1009 loop : -0.91 (0.13), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 87 TYR 0.029 0.001 TYR H 49 PHE 0.030 0.001 PHE E 68 TRP 0.024 0.001 TRP G 47 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.17 (30927) covalent geometry : angle 0.56035 / 0.29 (42051) SS BOND : bond 0.00280 / 0.19 ( 46) SS BOND : angle 1.38690 / 0.83 ( 92) hydrogen bonds : bond 0.04421 / 2.91 ( 1179) hydrogen bonds : angle 5.23364 / 3.63 ( 3324) link_BETA1-4 : bond 0.00190 / 0.12 ( 14) link_BETA1-4 : angle 0.99690 / 0.70 ( 42) link_NAG-ASN : bond 0.00622 / 0.45 ( 24) link_NAG-ASN : angle 3.82100 / 2.77 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 205 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7722 (p0) cc_final: 0.7067 (t0) REVERT: A 740 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8647 (ttt) REVERT: A 855 PHE cc_start: 0.8108 (p90) cc_final: 0.7806 (p90) REVERT: B 1029 MET cc_start: 0.9127 (tpp) cc_final: 0.8500 (ttm) REVERT: C 387 LEU cc_start: 0.9755 (OUTLIER) cc_final: 0.9476 (mm) REVERT: C 762 GLN cc_start: 0.7933 (mt0) cc_final: 0.7700 (mt0) REVERT: C 900 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: D 11 LEU cc_start: 0.5494 (mm) cc_final: 0.4817 (tp) REVERT: D 39 LYS cc_start: 0.7816 (mppt) cc_final: 0.7256 (mppt) REVERT: E 3 GLN cc_start: 0.8159 (tp-100) cc_final: 0.7706 (tp40) REVERT: E 18 LEU cc_start: 0.5940 (OUTLIER) cc_final: 0.5065 (mp) REVERT: E 87 ARG cc_start: 0.9182 (ptp90) cc_final: 0.8885 (ptt-90) REVERT: E 94 TYR cc_start: 0.8247 (m-80) cc_final: 0.7822 (m-10) REVERT: E 119 VAL cc_start: 0.1408 (m) cc_final: 0.0638 (t) REVERT: F 33 LEU cc_start: 0.3648 (tt) cc_final: 0.2534 (tp) REVERT: F 34 ASN cc_start: 0.3243 (m110) cc_final: 0.2572 (t0) REVERT: G 47 TRP cc_start: 0.4146 (p-90) cc_final: 0.3481 (p-90) REVERT: H 69 THR cc_start: 0.8716 (p) cc_final: 0.8217 (t) REVERT: I 35 HIS cc_start: 0.8684 (m170) cc_final: 0.8337 (m-70) REVERT: I 39 GLN cc_start: 0.7167 (tp40) cc_final: 0.6465 (tp-100) REVERT: I 59 ASP cc_start: 0.8654 (t0) cc_final: 0.8114 (t0) REVERT: I 73 ASP cc_start: 0.8386 (t0) cc_final: 0.8113 (p0) REVERT: I 95 TYR cc_start: 0.7315 (m-80) cc_final: 0.6999 (m-80) REVERT: I 103 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7721 (tp30) outliers start: 57 outliers final: 37 residues processed: 243 average time/residue: 0.1734 time to fit residues: 69.7855 Evaluate side-chains 229 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 334 ASN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 985 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 152 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 293 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 237 optimal weight: 8.9990 chunk 351 optimal weight: 30.0000 chunk 265 optimal weight: 6.9990 chunk 167 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 chunk 272 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS B 81 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 HIS F 6 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.094584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057948 restraints weight = 101931.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.060643 restraints weight = 51324.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.060911 restraints weight = 32843.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.061455 restraints weight = 24492.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.061603 restraints weight = 24478.986| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 31011 Z= 0.179 Angle : 0.586 20.301 42257 Z= 0.292 Chirality : 0.045 0.461 4833 Planarity : 0.004 0.043 5382 Dihedral : 4.183 26.177 4083 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.84 % Allowed : 12.52 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.14), residues: 3734 helix: 2.10 (0.20), residues: 671 sheet: -0.02 (0.15), residues: 999 loop : -0.93 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 87 TYR 0.029 0.001 TYR H 49 PHE 0.039 0.001 PHE A 186 TRP 0.015 0.001 TRP E 113 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (30927) covalent geometry : angle 0.56172 / 0.29 (42051) SS BOND : bond 0.00316 / 0.22 ( 46) SS BOND : angle 1.35130 / 0.83 ( 92) hydrogen bonds : bond 0.04409 / 2.90 ( 1179) hydrogen bonds : angle 5.22578 / 3.62 ( 3324) link_BETA1-4 : bond 0.00193 / 0.12 ( 14) link_BETA1-4 : angle 0.98820 / 0.69 ( 42) link_NAG-ASN : bond 0.00628 / 0.45 ( 24) link_NAG-ASN : angle 3.79950 / 2.75 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 193 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.6159 (t80) cc_final: 0.5540 (t80) REVERT: A 574 ASP cc_start: 0.7741 (p0) cc_final: 0.7044 (t0) REVERT: A 740 MET cc_start: 0.8901 (OUTLIER) cc_final: 0.8675 (ttt) REVERT: A 855 PHE cc_start: 0.8255 (p90) cc_final: 0.7943 (p90) REVERT: B 1029 MET cc_start: 0.9115 (tpp) cc_final: 0.8513 (ttm) REVERT: C 387 LEU cc_start: 0.9747 (OUTLIER) cc_final: 0.9455 (mm) REVERT: C 900 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8351 (mtm) REVERT: D 11 LEU cc_start: 0.5515 (mm) cc_final: 0.4855 (tp) REVERT: D 39 LYS cc_start: 0.7860 (mppt) cc_final: 0.7646 (mppt) REVERT: E 3 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7764 (tp40) REVERT: E 18 LEU cc_start: 0.5918 (OUTLIER) cc_final: 0.5099 (mp) REVERT: E 94 TYR cc_start: 0.8294 (m-80) cc_final: 0.7871 (m-10) REVERT: E 119 VAL cc_start: 0.1405 (m) cc_final: 0.0590 (t) REVERT: F 32 TYR cc_start: 0.4321 (m-80) cc_final: 0.4099 (m-80) REVERT: F 33 LEU cc_start: 0.3691 (tt) cc_final: 0.2581 (tp) REVERT: F 34 ASN cc_start: 0.3366 (m110) cc_final: 0.2670 (t0) REVERT: G 47 TRP cc_start: 0.4418 (p-90) cc_final: 0.3744 (p-90) REVERT: G 106 THR cc_start: 0.2790 (OUTLIER) cc_final: 0.1903 (t) REVERT: H 69 THR cc_start: 0.8707 (p) cc_final: 0.7706 (t) REVERT: H 70 ASP cc_start: 0.8958 (p0) cc_final: 0.7852 (t0) REVERT: I 35 HIS cc_start: 0.8685 (m170) cc_final: 0.8314 (m-70) REVERT: I 39 GLN cc_start: 0.7092 (tp40) cc_final: 0.6400 (tp40) REVERT: I 59 ASP cc_start: 0.8610 (t0) cc_final: 0.8138 (t0) REVERT: I 83 MET cc_start: 0.8461 (mmm) cc_final: 0.8260 (mmm) REVERT: I 95 TYR cc_start: 0.7393 (m-80) cc_final: 0.7021 (m-80) REVERT: I 103 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7725 (tp30) outliers start: 61 outliers final: 45 residues processed: 234 average time/residue: 0.1739 time to fit residues: 67.8169 Evaluate side-chains 234 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 582 LEU Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 110 PHE Chi-restraints excluded: chain I residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 253 optimal weight: 5.9990 chunk 343 optimal weight: 6.9990 chunk 263 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 119 optimal weight: 5.9990 chunk 200 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 299 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 262 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 HIS ** H 34 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 = 0.3880 r_free = 0.3880 target = 0.095315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.057966 restraints weight = 100813.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060170 restraints weight = 46498.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061506 restraints weight = 29319.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.062227 restraints weight = 22234.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 69)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.062866 restraints weight = 18945.074| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31011 Z= 0.127 Angle : 0.561 20.143 42257 Z= 0.279 Chirality : 0.044 0.455 4833 Planarity : 0.004 0.043 5382 Dihedral : 4.082 25.506 4083 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.81 % Allowed : 12.79 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3734 helix: 2.22 (0.21), residues: 666 sheet: 0.06 (0.15), residues: 1004 loop : -0.89 (0.13), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG I 87 TYR 0.028 0.001 TYR H 49 PHE 0.030 0.001 PHE A 186 TRP 0.017 0.001 TRP E 113 HIS 0.003 0.001 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (30927) covalent geometry : angle 0.53706 / 0.27 (42051) SS BOND : bond 0.00314 / 0.23 ( 46) SS BOND : angle 1.20602 / 0.74 ( 92) hydrogen bonds : bond 0.04113 / 2.72 ( 1179) hydrogen bonds : angle 5.10904 / 3.54 ( 3324) link_BETA1-4 : bond 0.00232 / 0.14 ( 14) link_BETA1-4 : angle 0.92866 / 0.64 ( 42) link_NAG-ASN : bond 0.00617 / 0.46 ( 24) link_NAG-ASN : angle 3.69045 / 2.68 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 192 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.5809 (OUTLIER) cc_final: 0.3931 (p90) REVERT: A 574 ASP cc_start: 0.7716 (p0) cc_final: 0.7002 (t0) REVERT: B 1029 MET cc_start: 0.9076 (tpp) cc_final: 0.8504 (ttm) REVERT: C 387 LEU cc_start: 0.9728 (OUTLIER) cc_final: 0.9466 (mm) REVERT: C 900 MET cc_start: 0.8691 (OUTLIER) cc_final: 0.8319 (mtm) REVERT: D 11 LEU cc_start: 0.5471 (mm) cc_final: 0.4812 (tp) REVERT: D 39 LYS cc_start: 0.8165 (mppt) cc_final: 0.7754 (mppt) REVERT: E 3 GLN cc_start: 0.8152 (tp-100) cc_final: 0.7701 (tp40) REVERT: E 18 LEU cc_start: 0.5782 (OUTLIER) cc_final: 0.5017 (mp) REVERT: E 94 TYR cc_start: 0.8339 (m-80) cc_final: 0.8032 (m-10) REVERT: E 119 VAL cc_start: 0.1468 (m) cc_final: 0.0670 (t) REVERT: F 4 MET cc_start: 0.3886 (mpp) cc_final: 0.3636 (mpp) REVERT: F 32 TYR cc_start: 0.4599 (m-80) cc_final: 0.4358 (m-80) REVERT: F 33 LEU cc_start: 0.3781 (tt) cc_final: 0.2637 (tp) REVERT: F 34 ASN cc_start: 0.3967 (m110) cc_final: 0.2943 (t0) REVERT: G 47 TRP cc_start: 0.4546 (p-90) cc_final: 0.3913 (p-90) REVERT: G 106 THR cc_start: 0.3803 (OUTLIER) cc_final: 0.2720 (t) REVERT: H 69 THR cc_start: 0.8743 (p) cc_final: 0.7773 (t) REVERT: H 70 ASP cc_start: 0.8925 (p0) cc_final: 0.7902 (t0) REVERT: I 35 HIS cc_start: 0.8557 (m170) cc_final: 0.8238 (m-70) REVERT: I 39 GLN cc_start: 0.7222 (tp40) cc_final: 0.6441 (tp40) REVERT: I 59 ASP cc_start: 0.8557 (t0) cc_final: 0.8100 (t0) REVERT: I 83 MET cc_start: 0.8461 (mmm) cc_final: 0.8244 (mmm) REVERT: I 95 TYR cc_start: 0.7433 (m-80) cc_final: 0.6988 (m-80) REVERT: I 103 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7672 (tp30) outliers start: 60 outliers final: 42 residues processed: 236 average time/residue: 0.1824 time to fit residues: 71.1727 Evaluate side-chains 233 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 186 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 67 ARG Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 172 optimal weight: 0.4980 chunk 299 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 359 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.095366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058906 restraints weight = 101127.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.061525 restraints weight = 50174.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.062131 restraints weight = 30098.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062348 restraints weight = 23467.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062649 restraints weight = 24263.629| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31011 Z= 0.130 Angle : 0.565 20.026 42257 Z= 0.280 Chirality : 0.044 0.454 4833 Planarity : 0.004 0.045 5382 Dihedral : 4.038 26.057 4083 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.48 % Allowed : 12.94 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3734 helix: 2.23 (0.21), residues: 666 sheet: 0.13 (0.15), residues: 1001 loop : -0.89 (0.13), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG I 87 TYR 0.028 0.001 TYR H 49 PHE 0.044 0.001 PHE A 855 TRP 0.016 0.001 TRP E 113 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (30927) covalent geometry : angle 0.54205 / 0.27 (42051) SS BOND : bond 0.00293 / 0.21 ( 46) SS BOND : angle 1.24073 / 0.73 ( 92) hydrogen bonds : bond 0.04039 / 2.67 ( 1179) hydrogen bonds : angle 5.06363 / 3.51 ( 3324) link_BETA1-4 : bond 0.00243 / 0.15 ( 14) link_BETA1-4 : angle 0.95259 / 0.65 ( 42) link_NAG-ASN : bond 0.00608 / 0.45 ( 24) link_NAG-ASN : angle 3.65152 / 2.66 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 198 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.6320 (OUTLIER) cc_final: 0.4163 (p90) REVERT: A 574 ASP cc_start: 0.7753 (p0) cc_final: 0.7037 (t0) REVERT: B 153 MET cc_start: 0.4529 (ppp) cc_final: 0.4317 (ppp) REVERT: B 1029 MET cc_start: 0.9079 (tpp) cc_final: 0.8492 (ttm) REVERT: C 387 LEU cc_start: 0.9723 (OUTLIER) cc_final: 0.9466 (mm) REVERT: C 900 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8309 (mtm) REVERT: C 963 VAL cc_start: 0.9391 (OUTLIER) cc_final: 0.9160 (p) REVERT: D 11 LEU cc_start: 0.5427 (mm) cc_final: 0.4784 (tp) REVERT: D 39 LYS cc_start: 0.8155 (mppt) cc_final: 0.7918 (mppt) REVERT: E 3 GLN cc_start: 0.8192 (tp-100) cc_final: 0.7723 (tp40) REVERT: E 18 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5073 (mp) REVERT: E 94 TYR cc_start: 0.8373 (m-80) cc_final: 0.7969 (m-10) REVERT: E 119 VAL cc_start: 0.1428 (m) cc_final: 0.0593 (t) REVERT: F 4 MET cc_start: 0.4636 (mpp) cc_final: 0.4418 (mpp) REVERT: F 32 TYR cc_start: 0.4135 (m-80) cc_final: 0.3919 (m-80) REVERT: F 33 LEU cc_start: 0.3595 (tt) cc_final: 0.2515 (tp) REVERT: F 34 ASN cc_start: 0.3503 (m110) cc_final: 0.2815 (t0) REVERT: G 47 TRP cc_start: 0.4323 (p-90) cc_final: 0.3297 (t60) REVERT: G 106 THR cc_start: 0.2788 (OUTLIER) cc_final: 0.1903 (t) REVERT: H 45 LYS cc_start: 0.8751 (OUTLIER) cc_final: 0.8331 (ptmm) REVERT: H 69 THR cc_start: 0.8724 (p) cc_final: 0.8236 (t) REVERT: I 35 HIS cc_start: 0.8629 (m170) cc_final: 0.8261 (m-70) REVERT: I 39 GLN cc_start: 0.7160 (tp40) cc_final: 0.6392 (tp40) REVERT: I 59 ASP cc_start: 0.8574 (t0) cc_final: 0.8117 (t0) REVERT: I 95 TYR cc_start: 0.7422 (m-80) cc_final: 0.6957 (m-80) REVERT: I 103 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7659 (tp30) outliers start: 49 outliers final: 37 residues processed: 234 average time/residue: 0.1791 time to fit residues: 69.7870 Evaluate side-chains 234 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 190 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 162 optimal weight: 0.0570 chunk 88 optimal weight: 7.9990 chunk 155 optimal weight: 9.9990 chunk 271 optimal weight: 0.9980 chunk 206 optimal weight: 20.0000 chunk 196 optimal weight: 0.5980 chunk 210 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 2.9990 chunk 205 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.095608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.059049 restraints weight = 100266.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.061617 restraints weight = 50519.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.062210 restraints weight = 30919.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.062603 restraints weight = 23277.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.062925 restraints weight = 23429.283| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 31011 Z= 0.127 Angle : 0.566 19.990 42257 Z= 0.281 Chirality : 0.044 0.456 4833 Planarity : 0.004 0.043 5382 Dihedral : 4.006 26.095 4083 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.45 % Allowed : 13.48 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.14), residues: 3734 helix: 2.26 (0.21), residues: 666 sheet: 0.15 (0.15), residues: 1008 loop : -0.86 (0.13), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG I 87 TYR 0.028 0.001 TYR H 49 PHE 0.043 0.001 PHE A 855 TRP 0.014 0.001 TRP E 113 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (30927) covalent geometry : angle 0.54387 / 0.28 (42051) SS BOND : bond 0.00268 / 0.19 ( 46) SS BOND : angle 1.21642 / 0.72 ( 92) hydrogen bonds : bond 0.03985 / 2.64 ( 1179) hydrogen bonds : angle 5.01902 / 3.48 ( 3324) link_BETA1-4 : bond 0.00238 / 0.16 ( 14) link_BETA1-4 : angle 0.94274 / 0.65 ( 42) link_NAG-ASN : bond 0.00607 / 0.45 ( 24) link_NAG-ASN : angle 3.62318 / 2.64 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7468 Ramachandran restraints generated. 3734 Oldfield, 0 Emsley, 3734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 194 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 186 PHE cc_start: 0.6367 (OUTLIER) cc_final: 0.4343 (p90) REVERT: A 574 ASP cc_start: 0.7740 (p0) cc_final: 0.7019 (t0) REVERT: B 1029 MET cc_start: 0.9064 (tpp) cc_final: 0.8469 (ttm) REVERT: C 387 LEU cc_start: 0.9729 (OUTLIER) cc_final: 0.9477 (mm) REVERT: C 900 MET cc_start: 0.8655 (OUTLIER) cc_final: 0.8245 (mtm) REVERT: C 963 VAL cc_start: 0.9381 (OUTLIER) cc_final: 0.9150 (p) REVERT: D 11 LEU cc_start: 0.5441 (mm) cc_final: 0.4809 (tp) REVERT: D 85 THR cc_start: 0.8745 (t) cc_final: 0.8530 (m) REVERT: E 3 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7737 (tp40) REVERT: E 18 LEU cc_start: 0.5900 (OUTLIER) cc_final: 0.5153 (mp) REVERT: E 94 TYR cc_start: 0.8303 (m-80) cc_final: 0.7944 (m-10) REVERT: E 119 VAL cc_start: 0.1384 (m) cc_final: 0.0535 (t) REVERT: F 4 MET cc_start: 0.4576 (mpp) cc_final: 0.4364 (mpp) REVERT: F 32 TYR cc_start: 0.4177 (m-80) cc_final: 0.3955 (m-80) REVERT: F 33 LEU cc_start: 0.3637 (tt) cc_final: 0.2530 (tp) REVERT: F 34 ASN cc_start: 0.3530 (m110) cc_final: 0.2826 (t0) REVERT: G 47 TRP cc_start: 0.4399 (p-90) cc_final: 0.3383 (t60) REVERT: G 106 THR cc_start: 0.2939 (OUTLIER) cc_final: 0.2052 (t) REVERT: H 45 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8359 (ptmm) REVERT: H 69 THR cc_start: 0.8730 (p) cc_final: 0.8234 (t) REVERT: I 35 HIS cc_start: 0.8631 (m170) cc_final: 0.8261 (m-70) REVERT: I 39 GLN cc_start: 0.7168 (tp40) cc_final: 0.6406 (tp40) REVERT: I 59 ASP cc_start: 0.8567 (t0) cc_final: 0.8116 (t0) REVERT: I 95 TYR cc_start: 0.7420 (m-80) cc_final: 0.6944 (m-80) REVERT: I 103 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7641 (tp30) outliers start: 48 outliers final: 39 residues processed: 228 average time/residue: 0.1914 time to fit residues: 72.7000 Evaluate side-chains 235 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 186 PHE Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 739 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain C residue 240 THR Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 900 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 106 THR Chi-restraints excluded: chain E residue 110 PHE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 97 TYR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain H residue 83 PHE Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain I residue 80 TYR Chi-restraints excluded: chain I residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 350 optimal weight: 30.0000 chunk 107 optimal weight: 6.9990 chunk 133 optimal weight: 5.9990 chunk 139 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 322 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 315 optimal weight: 30.0000 chunk 60 optimal weight: 3.9990 chunk 248 optimal weight: 9.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 853 GLN ** D 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 34 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 = 0.3842 r_free = 0.3842 target = 0.097948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.060827 restraints weight = 103121.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.062865 restraints weight = 48934.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.064069 restraints weight = 31218.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.064970 restraints weight = 23893.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.065379 restraints weight = 20289.951| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 31011 Z= 0.348 Angle : 0.723 20.582 42257 Z= 0.363 Chirality : 0.048 0.502 4833 Planarity : 0.004 0.052 5382 Dihedral : 4.472 26.250 4083 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.57 % Allowed : 13.57 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.13), residues: 3734 helix: 1.72 (0.20), residues: 677 sheet: -0.16 (0.15), residues: 1005 loop : -1.07 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG I 87 TYR 0.034 0.002 TYR C 904 PHE 0.041 0.002 PHE E 68 TRP 0.011 0.002 TRP E 113 HIS 0.007 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00814 / 0.35 (30927) covalent geometry : angle 0.70003 / 0.36 (42051) SS BOND : bond 0.00418 / 0.27 ( 46) SS BOND : angle 1.66779 / 1.04 ( 92) hydrogen bonds : bond 0.05216 / 3.42 ( 1179) hydrogen bonds : angle 5.42737 / 3.77 ( 3324) link_BETA1-4 : bond 0.00313 / 0.16 ( 14) link_BETA1-4 : angle 1.19932 / 0.85 ( 42) link_NAG-ASN : bond 0.00818 / 0.54 ( 24) link_NAG-ASN : angle 4.03544 / 2.91 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5823.57 seconds wall clock time: 101 minutes 25.13 seconds (6085.13 seconds total)