Starting phenix.real_space_refine on Fri Mar 6 11:01:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ws5_32744/03_2026/7ws5_32744.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ws5_32744/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7ws5_32744/03_2026/7ws5_32744.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ws5_32744/03_2026/7ws5_32744.map" model { file = "/net/cci-nas-00/data/ceres_data/7ws5_32744/03_2026/7ws5_32744.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ws5_32744/03_2026/7ws5_32744.cif" } 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-5986/lib/python3.9/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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.51, per 1000 atoms: 0.22 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: 2.42 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: 1.14 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: 7.47 Time building geometry restraints manager: 3.28 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: 17340 17.76 - 35.53: 1233 35.53 - 53.29: 261 53.29 - 71.06: 65 71.06 - 88.82: 34 Dihedral angle restraints: 18933 sinusoidal: 7888 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 18930 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: 10.540 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: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 28.210 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 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 : 13.301 88.824 11693 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 covalent geometry : bond 0.00330 (30927) covalent geometry : angle 0.61330 (42051) SS BOND : bond 0.00319 ( 46) SS BOND : angle 1.05872 ( 92) hydrogen bonds : bond 0.14352 ( 1179) hydrogen bonds : angle 7.18717 ( 3324) link_BETA1-4 : bond 0.00507 ( 14) link_BETA1-4 : angle 1.58442 ( 42) link_NAG-ASN : bond 0.01107 ( 24) link_NAG-ASN : angle 4.79280 ( 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 : 0.932 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: 0.1936 time to fit residues: 90.2524 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 : 1.073 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN ** 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 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** ** E 115 GLN ** 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 = 0.3906 r_free = 0.3906 target = 0.098394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061736 restraints weight = 101891.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.063958 restraints weight = 47148.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065372 restraints weight = 29822.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066217 restraints weight = 22677.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.066669 restraints weight = 19214.815| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 31011 Z= 0.195 Angle : 0.630 20.259 42257 Z= 0.317 Chirality : 0.047 0.566 4833 Planarity : 0.004 0.057 5382 Dihedral : 6.288 56.909 4881 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.79 % Allowed : 5.47 % Favored : 93.74 % 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: 1.77 (0.20), residues: 687 sheet: 0.10 (0.15), residues: 1032 loop : -0.79 (0.13), residues: 2015 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 16 TYR 0.031 0.002 TYR H 49 PHE 0.018 0.002 PHE B 906 TRP 0.032 0.002 TRP B 436 HIS 0.007 0.001 HIS I 35 Details of bonding type rmsd covalent geometry : bond 0.00451 (30927) covalent geometry : angle 0.60084 (42051) SS BOND : bond 0.00634 ( 46) SS BOND : angle 1.39403 ( 92) hydrogen bonds : bond 0.04881 ( 1179) hydrogen bonds : angle 5.71082 ( 3324) link_BETA1-4 : bond 0.00277 ( 14) link_BETA1-4 : angle 1.15674 ( 42) link_NAG-ASN : bond 0.00723 ( 24) link_NAG-ASN : angle 4.31385 ( 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 247 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 392 PHE cc_start: 0.8382 (m-80) cc_final: 0.7971 (m-80) REVERT: A 574 ASP cc_start: 0.7573 (p0) cc_final: 0.7096 (t0) REVERT: B 1029 MET cc_start: 0.9149 (tpp) cc_final: 0.8589 (ttm) REVERT: C 390 LEU cc_start: 0.9420 (mt) cc_final: 0.8986 (mp) REVERT: D 4 MET cc_start: 0.7036 (ptt) cc_final: 0.5777 (tmm) REVERT: D 11 LEU cc_start: 0.4877 (mm) cc_final: 0.4194 (tt) REVERT: D 23 CYS cc_start: 0.6000 (p) cc_final: 0.4799 (p) REVERT: D 42 LYS cc_start: 0.8921 (ptpp) cc_final: 0.8434 (mmmt) REVERT: D 45 LYS cc_start: 0.8440 (ptmm) cc_final: 0.8234 (ptmm) REVERT: D 71 PHE cc_start: 0.7070 (m-80) cc_final: 0.6852 (m-10) REVERT: E 38 ARG cc_start: 0.8288 (ttp-170) cc_final: 0.8055 (ttt90) REVERT: E 83 MET cc_start: 0.4736 (mmm) cc_final: 0.4403 (mmm) REVERT: E 94 TYR cc_start: 0.8310 (m-80) cc_final: 0.7829 (m-80) REVERT: E 119 VAL cc_start: 0.2149 (m) cc_final: 0.1463 (t) REVERT: F 33 LEU cc_start: 0.4215 (tt) cc_final: 0.2992 (tp) REVERT: F 34 ASN cc_start: 0.2860 (m110) cc_final: 0.2207 (t0) REVERT: I 59 ASP cc_start: 0.8526 (t0) cc_final: 0.8067 (t0) REVERT: I 95 TYR cc_start: 0.7290 (m-80) cc_final: 0.7080 (m-80) REVERT: I 103 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7712 (tp30) REVERT: I 111 ASP cc_start: 0.8675 (t70) cc_final: 0.7643 (t70) REVERT: I 112 TYR cc_start: 0.8156 (m-80) cc_final: 0.7489 (m-10) outliers start: 26 outliers final: 20 residues processed: 231 average time/residue: 0.1880 time to fit residues: 70.9297 Evaluate side-chains 206 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.116 ------------------------------------------------------------------------------- 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: 1.9990 chunk 333 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 263 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 chunk 365 optimal weight: 4.9990 chunk 123 optimal weight: 20.0000 chunk 298 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3890 r_free = 0.3890 target = 0.100925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.064081 restraints weight = 101952.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.066136 restraints weight = 47487.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.067530 restraints weight = 29923.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.068401 restraints weight = 22557.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.068832 restraints weight = 19030.055| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 31011 Z= 0.227 Angle : 0.625 20.574 42257 Z= 0.315 Chirality : 0.046 0.521 4833 Planarity : 0.004 0.067 5382 Dihedral : 6.110 58.518 4881 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.18 % Allowed : 8.65 % Favored : 90.18 % 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: 1.66 (0.20), residues: 697 sheet: -0.01 (0.15), residues: 1050 loop : -0.89 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 87 TYR 0.028 0.001 TYR H 49 PHE 0.022 0.002 PHE A 238 TRP 0.025 0.001 TRP G 47 HIS 0.005 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00526 (30927) covalent geometry : angle 0.59647 (42051) SS BOND : bond 0.00408 ( 46) SS BOND : angle 1.39516 ( 92) hydrogen bonds : bond 0.04901 ( 1179) hydrogen bonds : angle 5.54928 ( 3324) link_BETA1-4 : bond 0.00181 ( 14) link_BETA1-4 : angle 1.14193 ( 42) link_NAG-ASN : bond 0.00708 ( 24) link_NAG-ASN : angle 4.25914 ( 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 247 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8363 (t70) cc_final: 0.8154 (t70) REVERT: A 392 PHE cc_start: 0.8470 (m-80) cc_final: 0.8132 (m-80) REVERT: A 515 PHE cc_start: 0.8182 (m-10) cc_final: 0.7965 (m-10) REVERT: A 574 ASP cc_start: 0.7703 (p0) cc_final: 0.7191 (t0) REVERT: B 1029 MET cc_start: 0.9137 (tpp) cc_final: 0.8542 (ttm) REVERT: C 390 LEU cc_start: 0.9502 (mt) cc_final: 0.9106 (mp) REVERT: D 4 MET cc_start: 0.7077 (ptt) cc_final: 0.5878 (tmm) REVERT: D 11 LEU cc_start: 0.5296 (mm) cc_final: 0.4593 (tp) REVERT: D 23 CYS cc_start: 0.5194 (p) cc_final: 0.4877 (p) REVERT: D 32 TYR cc_start: 0.7418 (m-10) cc_final: 0.6982 (m-10) REVERT: D 42 LYS cc_start: 0.8952 (ptpp) cc_final: 0.8228 (mmmt) REVERT: E 3 GLN cc_start: 0.7793 (tp-100) cc_final: 0.7348 (tp40) REVERT: E 38 ARG cc_start: 0.8264 (ttp-170) cc_final: 0.8050 (ttt90) REVERT: E 83 MET cc_start: 0.4818 (mmm) cc_final: 0.4518 (mmm) REVERT: E 94 TYR cc_start: 0.8298 (m-80) cc_final: 0.7889 (m-80) REVERT: E 119 VAL cc_start: 0.1881 (m) cc_final: 0.1104 (t) REVERT: F 33 LEU cc_start: 0.4155 (tt) cc_final: 0.2957 (tp) REVERT: F 34 ASN cc_start: 0.3156 (m110) cc_final: 0.2267 (t0) REVERT: H 69 THR cc_start: 0.8747 (p) cc_final: 0.8288 (t) REVERT: I 59 ASP cc_start: 0.8577 (t0) cc_final: 0.8102 (t0) REVERT: I 103 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7735 (tp30) outliers start: 39 outliers final: 24 residues processed: 231 average time/residue: 0.1890 time to fit residues: 71.1798 Evaluate side-chains 211 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 TRP Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 931 ILE 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 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 C residue 934 ILE 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 20 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 132 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 150 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 264 optimal weight: 1.9990 chunk 181 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 chunk 115 optimal weight: 7.9990 chunk 357 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** E 13 GLN ** 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 = 0.3897 r_free = 0.3897 target = 0.098126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.061470 restraints weight = 100378.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063675 restraints weight = 46551.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.065072 restraints weight = 29432.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.065908 restraints weight = 22369.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066467 restraints weight = 18923.137| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31011 Z= 0.149 Angle : 0.569 20.489 42257 Z= 0.285 Chirality : 0.045 0.509 4833 Planarity : 0.004 0.066 5382 Dihedral : 5.765 58.248 4881 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.27 % Allowed : 10.22 % Favored : 88.51 % 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: -0.13 (0.13), residues: 3734 helix: 1.88 (0.20), residues: 685 sheet: 0.05 (0.15), residues: 1029 loop : -0.85 (0.13), residues: 2020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 16 TYR 0.028 0.001 TYR H 49 PHE 0.017 0.001 PHE D 36 TRP 0.024 0.001 TRP G 47 HIS 0.004 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00343 (30927) covalent geometry : angle 0.54074 (42051) SS BOND : bond 0.00319 ( 46) SS BOND : angle 1.35000 ( 92) hydrogen bonds : bond 0.04434 ( 1179) hydrogen bonds : angle 5.32955 ( 3324) link_BETA1-4 : bond 0.00257 ( 14) link_BETA1-4 : angle 1.04612 ( 42) link_NAG-ASN : bond 0.00654 ( 24) link_NAG-ASN : angle 4.04968 ( 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 244 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 202 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ASP cc_start: 0.8374 (t70) cc_final: 0.8136 (t70) REVERT: A 392 PHE cc_start: 0.8495 (m-80) cc_final: 0.8257 (m-80) REVERT: A 571 ASP cc_start: 0.8560 (t0) cc_final: 0.8253 (t0) REVERT: A 574 ASP cc_start: 0.7706 (p0) cc_final: 0.7108 (t0) REVERT: B 81 ASN cc_start: 0.6956 (OUTLIER) cc_final: 0.6707 (t0) REVERT: B 1029 MET cc_start: 0.9105 (tpp) cc_final: 0.8535 (ttm) REVERT: C 390 LEU cc_start: 0.9497 (mt) cc_final: 0.9095 (mp) REVERT: C 985 ASP cc_start: 0.7814 (t0) cc_final: 0.7559 (m-30) REVERT: D 11 LEU cc_start: 0.5589 (mm) cc_final: 0.4937 (tp) REVERT: D 24 ARG cc_start: 0.8042 (tpp-160) cc_final: 0.7755 (mmm160) REVERT: D 39 LYS cc_start: 0.7836 (mppt) cc_final: 0.7392 (mppt) REVERT: D 42 LYS cc_start: 0.9004 (ptpp) cc_final: 0.8790 (pttm) REVERT: E 3 GLN cc_start: 0.8027 (tp-100) cc_final: 0.7551 (tp40) REVERT: E 38 ARG cc_start: 0.8178 (ttp-170) cc_final: 0.7926 (ttt90) REVERT: E 119 VAL cc_start: 0.1656 (m) cc_final: 0.1418 (t) REVERT: F 33 LEU cc_start: 0.3964 (tt) cc_final: 0.2794 (tp) REVERT: F 34 ASN cc_start: 0.3272 (m110) cc_final: 0.2605 (t0) REVERT: G 47 TRP cc_start: 0.4127 (p90) cc_final: 0.3451 (p-90) REVERT: H 69 THR cc_start: 0.8777 (p) cc_final: 0.8290 (t) REVERT: H 104 LYS cc_start: 0.8398 (tptp) cc_final: 0.8059 (tptt) REVERT: I 35 HIS cc_start: 0.8647 (m170) cc_final: 0.8312 (m-70) REVERT: I 39 GLN cc_start: 0.7226 (tp40) cc_final: 0.6520 (tp-100) REVERT: I 59 ASP cc_start: 0.8590 (t0) cc_final: 0.8136 (t0) REVERT: I 95 TYR cc_start: 0.7243 (m-80) cc_final: 0.6865 (m-80) REVERT: I 103 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7698 (tp30) outliers start: 42 outliers final: 25 residues processed: 230 average time/residue: 0.1866 time to fit residues: 70.3699 Evaluate side-chains 213 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 187 time to evaluate : 0.980 ------------------------------------------------------------------------------- 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 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 582 LEU Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 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 C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU 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 H residue 33 LEU Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 89 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 24 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 180 optimal weight: 0.3980 chunk 218 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 216 optimal weight: 10.0000 chunk 263 optimal weight: 4.9990 chunk 337 optimal weight: 40.0000 chunk 322 optimal weight: 9.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 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** E 13 GLN ** G 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 34 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.096420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058451 restraints weight = 98349.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.060638 restraints weight = 46843.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.061799 restraints weight = 30181.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062689 restraints weight = 23897.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062689 restraints weight = 19775.580| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 31011 Z= 0.190 Angle : 0.593 20.529 42257 Z= 0.296 Chirality : 0.045 0.495 4833 Planarity : 0.004 0.062 5382 Dihedral : 5.620 58.054 4881 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.60 % Allowed : 10.64 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.50 % 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: -0.19 (0.13), residues: 3734 helix: 1.82 (0.20), residues: 691 sheet: -0.01 (0.15), residues: 1007 loop : -0.88 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 16 TYR 0.029 0.001 TYR H 49 PHE 0.024 0.001 PHE C 759 TRP 0.021 0.001 TRP E 113 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.00444 (30927) covalent geometry : angle 0.56520 (42051) SS BOND : bond 0.00280 ( 46) SS BOND : angle 1.47072 ( 92) hydrogen bonds : bond 0.04543 ( 1179) hydrogen bonds : angle 5.29515 ( 3324) link_BETA1-4 : bond 0.00207 ( 14) link_BETA1-4 : angle 1.10966 ( 42) link_NAG-ASN : bond 0.00646 ( 24) link_NAG-ASN : angle 4.00999 ( 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 256 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 203 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7762 (p0) cc_final: 0.7122 (t0) REVERT: A 855 PHE cc_start: 0.7881 (p90) cc_final: 0.7617 (p90) REVERT: B 1029 MET cc_start: 0.9125 (tpp) cc_final: 0.8555 (ttm) REVERT: C 387 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9458 (mm) REVERT: D 4 MET cc_start: 0.6912 (ptt) cc_final: 0.6210 (ppp) REVERT: D 11 LEU cc_start: 0.5427 (mm) cc_final: 0.4765 (tp) REVERT: D 24 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.7439 (mmm160) REVERT: E 3 GLN cc_start: 0.8237 (tp-100) cc_final: 0.7726 (tp40) REVERT: E 16 ARG cc_start: 0.7681 (ptt-90) cc_final: 0.7375 (ptt-90) REVERT: E 18 LEU cc_start: 0.5956 (OUTLIER) cc_final: 0.5192 (mp) REVERT: E 68 PHE cc_start: 0.7184 (m-10) cc_final: 0.6776 (m-80) REVERT: F 32 TYR cc_start: 0.4606 (m-80) cc_final: 0.4401 (m-80) REVERT: F 33 LEU cc_start: 0.3890 (tt) cc_final: 0.2680 (tp) REVERT: F 34 ASN cc_start: 0.3607 (m110) cc_final: 0.2681 (t0) REVERT: H 69 THR cc_start: 0.8742 (p) cc_final: 0.8308 (t) REVERT: H 83 PHE cc_start: 0.7664 (t80) cc_final: 0.7277 (t80) REVERT: H 104 LYS cc_start: 0.8510 (tptp) cc_final: 0.8282 (tptp) REVERT: I 35 HIS cc_start: 0.8634 (m170) cc_final: 0.8277 (m-70) REVERT: I 39 GLN cc_start: 0.7186 (tp40) cc_final: 0.6544 (tp-100) REVERT: I 59 ASP cc_start: 0.8630 (t0) cc_final: 0.8164 (t0) REVERT: I 95 TYR cc_start: 0.7281 (m-80) cc_final: 0.7035 (m-80) REVERT: I 103 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7726 (tp30) outliers start: 53 outliers final: 32 residues processed: 236 average time/residue: 0.1901 time to fit residues: 73.9711 Evaluate side-chains 222 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 188 time to evaluate : 1.133 ------------------------------------------------------------------------------- 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 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 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 362 VAL 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 1145 LEU Chi-restraints excluded: chain D residue 47 LEU 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 99 ASP 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 20 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 110 PHE 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: 2.9990 chunk 211 optimal weight: 2.9990 chunk 72 optimal weight: 0.2980 chunk 69 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 112 optimal weight: 3.9990 chunk 325 optimal weight: 0.7980 chunk 295 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN B 334 ASN ** B 955 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** ** E 115 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.098188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.061622 restraints weight = 100483.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.063821 restraints weight = 46411.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.065139 restraints weight = 29380.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.066029 restraints weight = 22415.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.066486 restraints weight = 18996.635| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 31011 Z= 0.131 Angle : 0.558 20.488 42257 Z= 0.280 Chirality : 0.044 0.492 4833 Planarity : 0.004 0.066 5382 Dihedral : 5.325 57.731 4881 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.27 % Allowed : 11.61 % Favored : 87.12 % 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: -0.10 (0.14), residues: 3734 helix: 2.18 (0.21), residues: 672 sheet: 0.00 (0.16), residues: 987 loop : -0.86 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 16 TYR 0.028 0.001 TYR H 49 PHE 0.015 0.001 PHE E 27 TRP 0.020 0.001 TRP G 47 HIS 0.003 0.001 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00301 (30927) covalent geometry : angle 0.53202 (42051) SS BOND : bond 0.00261 ( 46) SS BOND : angle 1.29432 ( 92) hydrogen bonds : bond 0.04186 ( 1179) hydrogen bonds : angle 5.14786 ( 3324) link_BETA1-4 : bond 0.00270 ( 14) link_BETA1-4 : angle 1.02667 ( 42) link_NAG-ASN : bond 0.00629 ( 24) link_NAG-ASN : angle 3.85824 ( 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 250 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 1.065 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7708 (p0) cc_final: 0.7058 (t0) REVERT: A 855 PHE cc_start: 0.7925 (p90) cc_final: 0.7595 (p90) REVERT: B 1029 MET cc_start: 0.9076 (tpp) cc_final: 0.8546 (ttm) REVERT: C 387 LEU cc_start: 0.9731 (OUTLIER) cc_final: 0.9452 (mm) REVERT: D 11 LEU cc_start: 0.5460 (mm) cc_final: 0.4807 (tp) REVERT: D 24 ARG cc_start: 0.8219 (tpp-160) cc_final: 0.7338 (mmm160) REVERT: E 3 GLN cc_start: 0.8096 (tp-100) cc_final: 0.7608 (tp40) REVERT: E 16 ARG cc_start: 0.7492 (ptt-90) cc_final: 0.7151 (ptt-90) REVERT: E 18 LEU cc_start: 0.5944 (OUTLIER) cc_final: 0.5192 (mp) REVERT: E 68 PHE cc_start: 0.7470 (m-10) cc_final: 0.7015 (m-80) REVERT: E 94 TYR cc_start: 0.8351 (m-80) cc_final: 0.7932 (m-10) REVERT: F 33 LEU cc_start: 0.3839 (tt) cc_final: 0.2712 (tp) REVERT: F 34 ASN cc_start: 0.3362 (m110) cc_final: 0.2690 (t0) REVERT: G 47 TRP cc_start: 0.4304 (p-90) cc_final: 0.3611 (p-90) REVERT: H 69 THR cc_start: 0.8753 (p) cc_final: 0.7782 (t) REVERT: H 70 ASP cc_start: 0.8923 (p0) cc_final: 0.7772 (t0) REVERT: H 83 PHE cc_start: 0.7626 (t80) cc_final: 0.7221 (t80) REVERT: H 104 LYS cc_start: 0.8542 (tptp) cc_final: 0.8303 (tptp) REVERT: I 35 HIS cc_start: 0.8494 (m170) cc_final: 0.8138 (m-70) REVERT: I 39 GLN cc_start: 0.7161 (tp40) cc_final: 0.6555 (tp-100) REVERT: I 59 ASP cc_start: 0.8590 (t0) cc_final: 0.8070 (t0) REVERT: I 103 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7712 (tp30) outliers start: 42 outliers final: 29 residues processed: 238 average time/residue: 0.1857 time to fit residues: 73.0206 Evaluate side-chains 224 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.175 ------------------------------------------------------------------------------- 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 739 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 334 ASN 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 1145 LEU Chi-restraints excluded: chain D residue 47 LEU 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 H residue 33 LEU Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 110 PHE 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: 0.0670 chunk 55 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 351 optimal weight: 2.9990 chunk 265 optimal weight: 0.0770 chunk 167 optimal weight: 0.9990 chunk 331 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 chunk 206 optimal weight: 20.0000 overall best weight: 1.4282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** 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** E 35 HIS F 38 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.098321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.061783 restraints weight = 101500.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.063870 restraints weight = 48670.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.065215 restraints weight = 31379.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.066064 restraints weight = 23904.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066513 restraints weight = 20373.378| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31011 Z= 0.146 Angle : 0.567 20.410 42257 Z= 0.283 Chirality : 0.045 0.488 4833 Planarity : 0.004 0.053 5382 Dihedral : 5.166 57.538 4881 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.33 % Allowed : 12.27 % Favored : 86.40 % 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: -0.04 (0.14), residues: 3734 helix: 2.18 (0.20), residues: 672 sheet: 0.11 (0.15), residues: 1012 loop : -0.85 (0.13), residues: 2050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 16 TYR 0.027 0.001 TYR H 49 PHE 0.050 0.001 PHE A 186 TRP 0.012 0.001 TRP E 113 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00339 (30927) covalent geometry : angle 0.53895 (42051) SS BOND : bond 0.00317 ( 46) SS BOND : angle 1.76892 ( 92) hydrogen bonds : bond 0.04181 ( 1179) hydrogen bonds : angle 5.11555 ( 3324) link_BETA1-4 : bond 0.00228 ( 14) link_BETA1-4 : angle 1.05563 ( 42) link_NAG-ASN : bond 0.00617 ( 24) link_NAG-ASN : angle 3.83241 ( 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 246 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 202 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7711 (p0) cc_final: 0.6986 (t0) REVERT: A 855 PHE cc_start: 0.7980 (p90) cc_final: 0.7681 (p90) REVERT: B 1029 MET cc_start: 0.9070 (tpp) cc_final: 0.8509 (ttm) REVERT: C 387 LEU cc_start: 0.9740 (OUTLIER) cc_final: 0.9460 (mm) REVERT: D 11 LEU cc_start: 0.5521 (mm) cc_final: 0.4855 (tp) REVERT: D 24 ARG cc_start: 0.8203 (tpp-160) cc_final: 0.7298 (mmm160) REVERT: D 71 PHE cc_start: 0.7731 (m-10) cc_final: 0.7224 (m-10) REVERT: E 3 GLN cc_start: 0.8087 (tp-100) cc_final: 0.7579 (tp40) REVERT: E 16 ARG cc_start: 0.7463 (ptt-90) cc_final: 0.7245 (ptt-90) REVERT: E 68 PHE cc_start: 0.7450 (m-10) cc_final: 0.7067 (m-80) REVERT: E 94 TYR cc_start: 0.8350 (m-80) cc_final: 0.7877 (m-10) REVERT: F 32 TYR cc_start: 0.4218 (m-80) cc_final: 0.4000 (m-80) REVERT: F 33 LEU cc_start: 0.3754 (tt) cc_final: 0.2625 (tp) REVERT: F 34 ASN cc_start: 0.3506 (m110) cc_final: 0.2821 (t0) REVERT: G 47 TRP cc_start: 0.4310 (p-90) cc_final: 0.3635 (p-90) REVERT: H 69 THR cc_start: 0.8746 (p) cc_final: 0.7777 (t) REVERT: H 70 ASP cc_start: 0.8920 (p0) cc_final: 0.7791 (t0) REVERT: H 83 PHE cc_start: 0.7547 (t80) cc_final: 0.7125 (t80) REVERT: H 101 GLN cc_start: 0.7797 (pm20) cc_final: 0.7105 (pm20) REVERT: H 104 LYS cc_start: 0.8542 (tptp) cc_final: 0.8297 (tptp) REVERT: I 35 HIS cc_start: 0.8470 (m170) cc_final: 0.8099 (m-70) REVERT: I 39 GLN cc_start: 0.7093 (tp40) cc_final: 0.6656 (tp-100) REVERT: I 59 ASP cc_start: 0.8539 (t0) cc_final: 0.8090 (t0) REVERT: I 73 ASP cc_start: 0.7134 (p0) cc_final: 0.6881 (p0) REVERT: I 103 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7695 (tp30) outliers start: 44 outliers final: 34 residues processed: 234 average time/residue: 0.1729 time to fit residues: 66.9141 Evaluate side-chains 228 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 1.335 ------------------------------------------------------------------------------- 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 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU 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 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 392 PHE Chi-restraints excluded: chain B residue 867 ASP 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 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 47 LEU 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 28 THR Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 45 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 253 optimal weight: 6.9990 chunk 343 optimal weight: 30.0000 chunk 263 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 119 optimal weight: 5.9990 chunk 200 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 299 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 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 E 13 GLN G 35 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.095941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059860 restraints weight = 101028.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.062521 restraints weight = 49864.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.063191 restraints weight = 29557.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.063399 restraints weight = 22817.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.063700 restraints weight = 23694.659| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 31011 Z= 0.109 Angle : 0.546 20.312 42257 Z= 0.272 Chirality : 0.044 0.485 4833 Planarity : 0.004 0.049 5382 Dihedral : 4.876 56.913 4881 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.42 % Allowed : 12.61 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.14), residues: 3734 helix: 2.30 (0.21), residues: 666 sheet: 0.18 (0.16), residues: 1013 loop : -0.80 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 87 TYR 0.027 0.001 TYR H 49 PHE 0.022 0.001 PHE A 186 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00247 (30927) covalent geometry : angle 0.52017 (42051) SS BOND : bond 0.00243 ( 46) SS BOND : angle 1.40206 ( 92) hydrogen bonds : bond 0.03851 ( 1179) hydrogen bonds : angle 4.99016 ( 3324) link_BETA1-4 : bond 0.00311 ( 14) link_BETA1-4 : angle 1.00485 ( 42) link_NAG-ASN : bond 0.00637 ( 24) link_NAG-ASN : angle 3.70814 ( 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 248 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 201 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7692 (p0) cc_final: 0.6991 (t0) REVERT: B 1029 MET cc_start: 0.9048 (tpp) cc_final: 0.8440 (ttm) REVERT: C 387 LEU cc_start: 0.9725 (OUTLIER) cc_final: 0.9477 (mm) REVERT: D 11 LEU cc_start: 0.5529 (mm) cc_final: 0.4884 (tp) REVERT: D 24 ARG cc_start: 0.8402 (tpp-160) cc_final: 0.7507 (mmm160) REVERT: D 71 PHE cc_start: 0.7810 (m-10) cc_final: 0.7245 (m-10) REVERT: E 3 GLN cc_start: 0.8195 (tp-100) cc_final: 0.7711 (tp40) REVERT: E 13 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7884 (pp30) REVERT: E 16 ARG cc_start: 0.7580 (ptt-90) cc_final: 0.7300 (ptt-90) REVERT: E 18 LEU cc_start: 0.5909 (OUTLIER) cc_final: 0.5225 (mp) REVERT: E 94 TYR cc_start: 0.8297 (m-80) cc_final: 0.7781 (m-10) REVERT: F 4 MET cc_start: 0.4734 (mpp) cc_final: 0.4489 (mpp) REVERT: F 33 LEU cc_start: 0.3562 (tt) cc_final: 0.2477 (tp) REVERT: F 34 ASN cc_start: 0.3403 (m110) cc_final: 0.2772 (t0) REVERT: G 47 TRP cc_start: 0.4331 (p-90) cc_final: 0.3689 (p-90) REVERT: G 106 THR cc_start: 0.2636 (OUTLIER) cc_final: 0.1761 (t) REVERT: H 69 THR cc_start: 0.8711 (p) cc_final: 0.8221 (t) REVERT: H 104 LYS cc_start: 0.8497 (tptp) cc_final: 0.8224 (tptt) REVERT: I 35 HIS cc_start: 0.8497 (m170) cc_final: 0.8066 (m-70) REVERT: I 39 GLN cc_start: 0.7022 (tp40) cc_final: 0.6673 (tp40) REVERT: I 59 ASP cc_start: 0.8546 (t0) cc_final: 0.8084 (t0) REVERT: I 103 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7679 (tp30) outliers start: 47 outliers final: 33 residues processed: 236 average time/residue: 0.1785 time to fit residues: 69.5516 Evaluate side-chains 225 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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 324 GLU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 368 LEU 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 41 LYS 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 392 PHE 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 1145 LEU Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 94 THR Chi-restraints excluded: chain E residue 13 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 99 ASP 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 G residue 106 THR Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 20 THR Chi-restraints excluded: chain H residue 22 THR 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: 0.7980 chunk 346 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 20 optimal weight: 7.9990 chunk 359 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 200 optimal weight: 0.0670 chunk 124 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 256 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** 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 ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.096791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.060436 restraints weight = 100318.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.063184 restraints weight = 50213.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.063880 restraints weight = 28328.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.064059 restraints weight = 22692.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.064349 restraints weight = 23187.708| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 31011 Z= 0.105 Angle : 0.553 20.163 42257 Z= 0.274 Chirality : 0.044 0.483 4833 Planarity : 0.004 0.050 5382 Dihedral : 4.738 56.763 4881 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.21 % Allowed : 12.94 % Favored : 85.85 % 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: 0.10 (0.14), residues: 3734 helix: 2.29 (0.21), residues: 666 sheet: 0.23 (0.16), residues: 1013 loop : -0.77 (0.14), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 16 TYR 0.027 0.001 TYR H 49 PHE 0.052 0.001 PHE A 855 TRP 0.010 0.001 TRP B 436 HIS 0.003 0.000 HIS C 954 Details of bonding type rmsd covalent geometry : bond 0.00240 (30927) covalent geometry : angle 0.52806 (42051) SS BOND : bond 0.00215 ( 46) SS BOND : angle 1.31895 ( 92) hydrogen bonds : bond 0.03740 ( 1179) hydrogen bonds : angle 4.92812 ( 3324) link_BETA1-4 : bond 0.00342 ( 14) link_BETA1-4 : angle 1.03796 ( 42) link_NAG-ASN : bond 0.00636 ( 24) link_NAG-ASN : angle 3.67073 ( 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 237 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7690 (p0) cc_final: 0.6993 (t0) REVERT: B 1029 MET cc_start: 0.9023 (tpp) cc_final: 0.8423 (ttm) REVERT: C 387 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9470 (mm) REVERT: D 11 LEU cc_start: 0.5417 (mm) cc_final: 0.4782 (tp) REVERT: E 3 GLN cc_start: 0.8233 (tp-100) cc_final: 0.7770 (tp40) REVERT: E 16 ARG cc_start: 0.7939 (ptt-90) cc_final: 0.7632 (ptt-90) REVERT: E 18 LEU cc_start: 0.5880 (OUTLIER) cc_final: 0.5202 (mp) REVERT: E 68 PHE cc_start: 0.7346 (m-10) cc_final: 0.7133 (m-10) REVERT: E 94 TYR cc_start: 0.8272 (m-80) cc_final: 0.7784 (m-10) REVERT: F 4 MET cc_start: 0.4652 (mpp) cc_final: 0.4417 (mpp) REVERT: F 32 TYR cc_start: 0.4158 (m-80) cc_final: 0.3928 (m-80) REVERT: F 33 LEU cc_start: 0.3589 (tt) cc_final: 0.2457 (tp) REVERT: F 34 ASN cc_start: 0.3471 (m110) cc_final: 0.2782 (t0) REVERT: F 36 PHE cc_start: 0.4736 (OUTLIER) cc_final: 0.4333 (t80) REVERT: G 47 TRP cc_start: 0.4333 (p-90) cc_final: 0.3363 (t60) REVERT: G 106 THR cc_start: 0.2763 (OUTLIER) cc_final: 0.1863 (t) REVERT: H 69 THR cc_start: 0.8678 (p) cc_final: 0.8172 (t) REVERT: I 35 HIS cc_start: 0.8510 (m170) cc_final: 0.8051 (m-70) REVERT: I 39 GLN cc_start: 0.7011 (tp40) cc_final: 0.6608 (tp40) REVERT: I 59 ASP cc_start: 0.8551 (t0) cc_final: 0.8088 (t0) REVERT: I 103 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7655 (tp30) outliers start: 40 outliers final: 33 residues processed: 226 average time/residue: 0.1891 time to fit residues: 70.6260 Evaluate side-chains 226 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 1.155 ------------------------------------------------------------------------------- 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 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 739 THR Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 41 LYS 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 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 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 36 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 G residue 106 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 89 GLU 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: 1.9990 chunk 88 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 271 optimal weight: 0.5980 chunk 206 optimal weight: 20.0000 chunk 196 optimal weight: 0.7980 chunk 210 optimal weight: 0.6980 chunk 124 optimal weight: 6.9990 chunk 305 optimal weight: 0.9990 chunk 205 optimal weight: 5.9990 chunk 133 optimal weight: 20.0000 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.098558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062713 restraints weight = 100129.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.065418 restraints weight = 49905.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065959 restraints weight = 30242.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.066256 restraints weight = 23255.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066528 restraints weight = 24117.760| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31011 Z= 0.120 Angle : 0.556 20.115 42257 Z= 0.276 Chirality : 0.044 0.491 4833 Planarity : 0.004 0.045 5382 Dihedral : 4.624 56.982 4881 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.21 % Allowed : 13.12 % Favored : 85.67 % 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 (0.14), residues: 3734 helix: 2.27 (0.21), residues: 666 sheet: 0.25 (0.16), residues: 961 loop : -0.76 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1107 TYR 0.027 0.001 TYR H 49 PHE 0.041 0.001 PHE A 855 TRP 0.011 0.001 TRP B 436 HIS 0.003 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00278 (30927) covalent geometry : angle 0.53188 (42051) SS BOND : bond 0.00227 ( 46) SS BOND : angle 1.27043 ( 92) hydrogen bonds : bond 0.03812 ( 1179) hydrogen bonds : angle 4.90624 ( 3324) link_BETA1-4 : bond 0.00249 ( 14) link_BETA1-4 : angle 1.03953 ( 42) link_NAG-ASN : bond 0.00614 ( 24) link_NAG-ASN : angle 3.66686 ( 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 237 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 197 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 574 ASP cc_start: 0.7712 (p0) cc_final: 0.7004 (t0) REVERT: B 153 MET cc_start: 0.4597 (ppp) cc_final: 0.4382 (ppp) REVERT: B 1029 MET cc_start: 0.9061 (tpp) cc_final: 0.8438 (ttm) REVERT: C 387 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9468 (mm) REVERT: D 11 LEU cc_start: 0.5450 (mm) cc_final: 0.4850 (tp) REVERT: D 23 CYS cc_start: 0.6795 (t) cc_final: 0.6149 (p) REVERT: D 24 ARG cc_start: 0.8532 (tpp-160) cc_final: 0.7548 (mmm160) REVERT: D 33 LEU cc_start: 0.8637 (tp) cc_final: 0.7634 (mt) REVERT: E 3 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7701 (tp40) REVERT: E 16 ARG cc_start: 0.7516 (ptt-90) cc_final: 0.7227 (ptt-90) REVERT: E 18 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5228 (mp) REVERT: E 94 TYR cc_start: 0.8298 (m-80) cc_final: 0.7784 (m-10) REVERT: F 32 TYR cc_start: 0.3941 (m-80) cc_final: 0.3731 (m-80) REVERT: F 33 LEU cc_start: 0.3550 (tt) cc_final: 0.2472 (tp) REVERT: F 34 ASN cc_start: 0.3227 (m110) cc_final: 0.2755 (t0) REVERT: F 36 PHE cc_start: 0.4869 (OUTLIER) cc_final: 0.4324 (t80) REVERT: G 47 TRP cc_start: 0.4422 (p-90) cc_final: 0.3482 (t60) REVERT: G 106 THR cc_start: 0.2998 (OUTLIER) cc_final: 0.2125 (t) REVERT: H 45 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8358 (ptmm) REVERT: H 69 THR cc_start: 0.8694 (p) cc_final: 0.8182 (t) REVERT: I 35 HIS cc_start: 0.8407 (m170) cc_final: 0.7976 (m-70) REVERT: I 39 GLN cc_start: 0.7060 (tp40) cc_final: 0.6651 (tp-100) REVERT: I 59 ASP cc_start: 0.8565 (t0) cc_final: 0.8129 (t0) REVERT: I 103 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7655 (tp30) outliers start: 40 outliers final: 33 residues processed: 227 average time/residue: 0.1848 time to fit residues: 68.9690 Evaluate side-chains 228 residues out of total 3315 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.947 ------------------------------------------------------------------------------- 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 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 739 THR Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain B residue 41 LYS 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 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 1145 LEU Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 72 THR 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 F residue 36 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 G residue 106 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 45 LYS Chi-restraints excluded: chain I residue 89 GLU 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: 3.9990 chunk 133 optimal weight: 20.0000 chunk 139 optimal weight: 30.0000 chunk 221 optimal weight: 6.9990 chunk 322 optimal weight: 7.9990 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: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN A1083 HIS B 314 GLN B 613 GLN B 762 GLN B 901 GLN B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN C 853 GLN D 79 GLN ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** F 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.099486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.062264 restraints weight = 103563.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.064339 restraints weight = 49467.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.065538 restraints weight = 31881.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.066418 restraints weight = 24517.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066833 restraints weight = 20823.170| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 31011 Z= 0.430 Angle : 0.802 20.886 42257 Z= 0.404 Chirality : 0.051 0.540 4833 Planarity : 0.005 0.069 5382 Dihedral : 5.570 58.189 4881 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.33 % Allowed : 13.27 % 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: -0.54 (0.13), residues: 3734 helix: 1.34 (0.19), residues: 689 sheet: -0.11 (0.15), residues: 1012 loop : -1.09 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.031 0.002 TYR H 49 PHE 0.048 0.003 PHE C 759 TRP 0.037 0.002 TRP B 436 HIS 0.009 0.002 HIS B1058 Details of bonding type rmsd covalent geometry : bond 0.01004 (30927) covalent geometry : angle 0.77798 (42051) SS BOND : bond 0.00473 ( 46) SS BOND : angle 1.88464 ( 92) hydrogen bonds : bond 0.05757 ( 1179) hydrogen bonds : angle 5.59642 ( 3324) link_BETA1-4 : bond 0.00323 ( 14) link_BETA1-4 : angle 1.45564 ( 42) link_NAG-ASN : bond 0.00960 ( 24) link_NAG-ASN : angle 4.28133 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5842.05 seconds wall clock time: 101 minutes 43.62 seconds (6103.62 seconds total)