Starting phenix.real_space_refine on Sun Jul 5 20:48:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.cif Found real_map, /net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.cif" model { file = "/net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8h00_34407/07_2026/8h00_34407.cif" } resolution = 3.41 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= 0.044 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 141 5.16 5 C 19242 2.51 5 N 4940 2.21 5 O 5858 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30181 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8121 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "H" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.48, per 1000 atoms: 0.21 Number of scatterers: 30181 At special positions: 0 Unit cell: (146.432, 153.92, 196.352, 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 141 16.00 O 5858 8.00 N 4940 7.00 C 19242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, 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=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " 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=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " 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=2.04 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 21 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 35 " - pdb=" SG CYS I 50 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG 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 X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " 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 A1074 " " NAG W 1 " - " ASN A1098 " " NAG X 1 " - " ASN A1134 " Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 1.3 seconds 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7078 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 62 sheets defined 20.8% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.718A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' 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: 4.142A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.595A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.228A 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: 4.426A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 1032 removed outlier: 4.237A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.266A 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 337 through 343 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.904A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.549A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 406 through 410 removed outlier: 3.534A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 616 through 620 removed outlier: 4.233A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.683A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.645A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) 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 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: 4.036A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (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: 4.431A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.931A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.867A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 388 removed outlier: 3.572A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 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: 3.732A 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 747 through 755 removed outlier: 3.671A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 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 removed outlier: 3.561A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 918 removed outlier: 4.110A 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: 3.580A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.235A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.613A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 removed outlier: 3.608A pdb=" N LYS E 66 " --> pdb=" O SER E 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.914A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 removed outlier: 3.630A pdb=" N LYS G 66 " --> pdb=" O SER G 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 63 through 66' Processing helix chain 'G' and resid 87 through 91 removed outlier: 4.024A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 66 removed outlier: 3.602A pdb=" N LYS I 66 " --> pdb=" O SER I 63 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 63 through 66' Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.878A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.533A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.591A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.169A 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: 3.578A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.833A 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: 4.078A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.626A 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: 8.199A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.292A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.444A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.878A 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: 6.972A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.593A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N TYR A 380 " --> pdb=" O GLY A 431 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 7.087A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 539 through 543 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 5.966A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.545A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.606A 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 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.798A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.520A 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 789 removed outlier: 5.499A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 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: 8.323A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.514A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.000A 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: 3.703A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.506A 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: 5.282A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.807A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TYR B 380 " --> pdb=" O GLY B 431 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.976A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.972A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.626A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.812A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.626A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD4, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD6, first strand: chain 'C' and resid 27 through 30 removed outlier: 7.958A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.810A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.776A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER C 172 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 133 through 141 removed outlier: 6.616A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.808A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 10.770A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.062A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.395A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.617A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N TYR C 380 " --> pdb=" O GLY C 431 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.183A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 656 removed outlier: 5.910A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 8.351A pdb=" N VAL C 656 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.621A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.621A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF3, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF4, first strand: chain 'D' and resid 10 through 13 removed outlier: 6.350A pdb=" N VAL D 11 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR D 105 " --> pdb=" O TYR D 86 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.627A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 10 through 11 removed outlier: 7.340A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE E 48 " --> pdb=" O TRP E 36 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 10 through 11 removed outlier: 3.570A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF9, first strand: chain 'F' and resid 10 through 14 removed outlier: 6.471A pdb=" N VAL F 11 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LYS F 110 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLU F 13 " --> pdb=" O LYS F 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.438A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR F 85 " --> pdb=" O GLN F 38 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.781A pdb=" N MET G 83 " --> pdb=" O LEU G 17 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR G 78 " --> pdb=" O THR G 74 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 45 through 47 removed outlier: 3.886A pdb=" N LEU G 111 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 60 through 61 removed outlier: 4.249A pdb=" N ALA G 49 " --> pdb=" O TRP G 36 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N TRP G 36 " --> pdb=" O ALA G 49 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE G 51 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N MET G 34 " --> pdb=" O ILE G 51 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.511A pdb=" N VAL H 19 " --> pdb=" O ILE H 75 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.378A pdb=" N VAL H 11 " --> pdb=" O VAL H 108 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR H 105 " --> pdb=" O TYR H 86 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR H 85 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 5 through 6 removed outlier: 3.525A pdb=" N THR I 20 " --> pdb=" O SER I 6 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'I' and resid 10 through 11 removed outlier: 7.372A pdb=" N MET I 34 " --> pdb=" O CYS I 50 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N CYS I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE I 48 " --> pdb=" O TRP I 36 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3237 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: 7.96 Time building geometry restraints manager: 3.00 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: 9551 1.34 - 1.46: 7701 1.46 - 1.59: 13448 1.59 - 1.71: 0 1.71 - 1.83: 177 Bond restraints: 30877 Sorted by residual: bond pdb=" N VAL A1033 " pdb=" CA VAL A1033 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.21e+00 bond pdb=" N GLN F 70 " pdb=" CA GLN F 70 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.19e-02 7.06e+03 8.10e+00 bond pdb=" N GLY A1035 " pdb=" CA GLY A1035 " ideal model delta sigma weight residual 1.444 1.477 -0.033 1.19e-02 7.06e+03 7.62e+00 bond pdb=" N GLN F 38 " pdb=" CA GLN F 38 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.23e-02 6.61e+03 6.78e+00 bond pdb=" N LEU A1034 " pdb=" CA LEU A1034 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.30e-02 5.92e+03 5.66e+00 ... (remaining 30872 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 40642 1.50 - 3.01: 1178 3.01 - 4.51: 166 4.51 - 6.01: 21 6.01 - 7.51: 7 Bond angle restraints: 42014 Sorted by residual: angle pdb=" N GLU B 516 " pdb=" CA GLU B 516 " pdb=" C GLU B 516 " ideal model delta sigma weight residual 114.75 110.04 4.71 1.26e+00 6.30e-01 1.40e+01 angle pdb=" CA GLY A1035 " pdb=" C GLY A1035 " pdb=" O GLY A1035 " ideal model delta sigma weight residual 121.38 118.23 3.15 9.40e-01 1.13e+00 1.12e+01 angle pdb=" N ARG C 102 " pdb=" CA ARG C 102 " pdb=" C ARG C 102 " ideal model delta sigma weight residual 113.88 110.10 3.78 1.23e+00 6.61e-01 9.43e+00 angle pdb=" N SER I 6 " pdb=" CA SER I 6 " pdb=" C SER I 6 " ideal model delta sigma weight residual 108.34 112.26 -3.92 1.31e+00 5.83e-01 8.94e+00 angle pdb=" CG ARG A 983 " pdb=" CD ARG A 983 " pdb=" NE ARG A 983 " ideal model delta sigma weight residual 112.00 118.51 -6.51 2.20e+00 2.07e-01 8.77e+00 ... (remaining 42009 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 16440 17.92 - 35.84: 1277 35.84 - 53.76: 201 53.76 - 71.68: 47 71.68 - 89.60: 35 Dihedral angle restraints: 18000 sinusoidal: 6981 harmonic: 11019 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 -11.80 -74.20 1 1.00e+01 1.00e-02 6.99e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 33.41 59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 33.61 59.39 1 1.00e+01 1.00e-02 4.71e+01 ... (remaining 17997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 4016 0.057 - 0.113: 782 0.113 - 0.170: 80 0.170 - 0.227: 1 0.227 - 0.283: 4 Chirality restraints: 4883 Sorted by residual: chirality pdb=" C1 NAG A1303 " pdb=" ND2 ASN A 282 " pdb=" C2 NAG A1303 " pdb=" O5 NAG A1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.12 -0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 4880 not shown) Planarity restraints: 5384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 112 " -0.017 2.00e-02 2.50e+03 1.80e-02 8.10e+00 pdb=" CG TRP G 112 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TRP G 112 " -0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP G 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP G 112 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 112 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 112 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP G 112 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO C 987 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO C 986 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " 0.029 5.00e-02 4.00e+02 ... (remaining 5381 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 1738 2.73 - 3.27: 29664 3.27 - 3.81: 47931 3.81 - 4.36: 56474 4.36 - 4.90: 100762 Nonbonded interactions: 236569 Sorted by model distance: nonbonded pdb=" OD1 ASP B 53 " pdb=" N LEU B 54 " model vdw 2.184 3.120 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.197 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" OD2 ASP A 53 " model vdw 2.207 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.211 3.040 nonbonded pdb=" OE1 GLN C 992 " pdb=" NH2 ARG C 995 " model vdw 2.222 3.120 ... (remaining 236564 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 15 through 827 or resid 853 through 1305)) selection = (chain 'C' and (resid 15 through 827 or resid 853 through 1305)) } 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' selection = chain 'X' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 28.600 Find NCS groups from input model: 0.970 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.005 0.052 30973 Z= 0.209 Angle : 0.628 11.874 42251 Z= 0.331 Chirality : 0.046 0.283 4883 Planarity : 0.004 0.058 5354 Dihedral : 13.231 89.605 10769 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.56 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.21 (0.13), residues: 3737 helix: 1.87 (0.21), residues: 651 sheet: 0.08 (0.17), residues: 915 loop : -0.88 (0.13), residues: 2171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 983 TYR 0.033 0.001 TYR C 904 PHE 0.032 0.002 PHE C 823 TRP 0.045 0.002 TRP G 112 HIS 0.004 0.001 HIS B1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (30877) covalent geometry : angle 0.60583 / 0.33 (42014) SS BOND : bond 0.00297 / 0.20 ( 51) SS BOND : angle 1.29396 / 0.90 ( 102) hydrogen bonds : bond 0.19103 / 12.25 ( 1157) hydrogen bonds : angle 8.06085 / 5.59 ( 3237) link_BETA1-4 : bond 0.00340 / 0.24 ( 15) link_BETA1-4 : angle 1.04814 / 0.69 ( 45) link_NAG-ASN : bond 0.00490 / 0.30 ( 30) link_NAG-ASN : angle 3.36100 / 2.26 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1050 MET cc_start: 0.8304 (ptm) cc_final: 0.8026 (ptm) REVERT: B 368 LEU cc_start: 0.8858 (mt) cc_final: 0.8099 (tp) REVERT: E 11 VAL cc_start: 0.7489 (t) cc_final: 0.7121 (m) REVERT: E 34 MET cc_start: 0.7986 (tpp) cc_final: 0.7599 (tpp) REVERT: E 71 ILE cc_start: 0.8027 (tt) cc_final: 0.7800 (tt) REVERT: F 76 ASN cc_start: 0.8387 (m-40) cc_final: 0.7892 (p0) REVERT: F 106 GLU cc_start: 0.8611 (pm20) cc_final: 0.8305 (pm20) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1780 time to fit residues: 76.1902 Evaluate side-chains 182 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 0.0470 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 3.9990 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN B 779 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN D 31 ASN D 90 GLN E 82 GLN F 31 ASN F 37 GLN F 70 GLN H 31 ASN ** H 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.091226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.063731 restraints weight = 76209.376| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.51 r_work: 0.2873 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30973 Z= 0.131 Angle : 0.569 10.574 42251 Z= 0.293 Chirality : 0.044 0.299 4883 Planarity : 0.004 0.071 5354 Dihedral : 4.137 20.697 4067 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.00 % Favored : 96.92 % Rotamer: Outliers : 0.43 % Allowed : 5.21 % Favored : 94.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 3737 helix: 1.90 (0.21), residues: 666 sheet: 0.33 (0.17), residues: 936 loop : -0.88 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B1107 TYR 0.024 0.001 TYR B 756 PHE 0.027 0.001 PHE A 374 TRP 0.021 0.001 TRP G 112 HIS 0.004 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (30877) covalent geometry : angle 0.54987 / 0.29 (42014) SS BOND : bond 0.00339 / 0.22 ( 51) SS BOND : angle 1.03008 / 0.69 ( 102) hydrogen bonds : bond 0.04689 / 3.09 ( 1157) hydrogen bonds : angle 6.06142 / 4.21 ( 3237) link_BETA1-4 : bond 0.00435 / 0.28 ( 15) link_BETA1-4 : angle 1.01322 / 0.68 ( 45) link_NAG-ASN : bond 0.00433 / 0.23 ( 30) link_NAG-ASN : angle 3.01479 / 2.02 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8615 (m-10) cc_final: 0.8368 (m-10) REVERT: A 981 PHE cc_start: 0.7629 (m-80) cc_final: 0.7235 (m-10) REVERT: B 200 TYR cc_start: 0.8402 (m-80) cc_final: 0.8046 (m-80) REVERT: B 318 PHE cc_start: 0.8000 (t80) cc_final: 0.7729 (t80) REVERT: B 368 LEU cc_start: 0.8875 (mt) cc_final: 0.8192 (tp) REVERT: B 1092 GLU cc_start: 0.8398 (pm20) cc_final: 0.8077 (pt0) REVERT: E 71 ILE cc_start: 0.7937 (tt) cc_final: 0.7712 (tt) REVERT: F 76 ASN cc_start: 0.8370 (m-40) cc_final: 0.7983 (p0) REVERT: F 106 GLU cc_start: 0.8736 (pm20) cc_final: 0.8281 (pm20) REVERT: G 34 MET cc_start: 0.7708 (tpp) cc_final: 0.6744 (tpp) outliers start: 14 outliers final: 7 residues processed: 217 average time/residue: 0.1835 time to fit residues: 67.0669 Evaluate side-chains 185 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 178 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain I residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 150 optimal weight: 2.9990 chunk 140 optimal weight: 7.9990 chunk 230 optimal weight: 1.9990 chunk 228 optimal weight: 4.9990 chunk 359 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 chunk 7 optimal weight: 0.9990 chunk 145 optimal weight: 0.0670 chunk 309 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 245 HIS B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 505 HIS C1142 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.062727 restraints weight = 75543.845| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.39 r_work: 0.2859 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30973 Z= 0.157 Angle : 0.550 10.809 42251 Z= 0.281 Chirality : 0.044 0.299 4883 Planarity : 0.004 0.062 5354 Dihedral : 4.090 20.209 4067 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.18 % Favored : 96.74 % Rotamer: Outliers : 0.82 % Allowed : 7.43 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.11 (0.13), residues: 3737 helix: 1.91 (0.21), residues: 673 sheet: 0.25 (0.17), residues: 959 loop : -0.90 (0.13), residues: 2105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.019 0.001 TYR C1067 PHE 0.036 0.001 PHE B 374 TRP 0.017 0.001 TRP G 112 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (30877) covalent geometry : angle 0.53262 / 0.28 (42014) SS BOND : bond 0.00283 / 0.18 ( 51) SS BOND : angle 0.96786 / 0.67 ( 102) hydrogen bonds : bond 0.04410 / 2.92 ( 1157) hydrogen bonds : angle 5.56342 / 3.87 ( 3237) link_BETA1-4 : bond 0.00332 / 0.23 ( 15) link_BETA1-4 : angle 1.03586 / 0.69 ( 45) link_NAG-ASN : bond 0.00392 / 0.22 ( 30) link_NAG-ASN : angle 2.84967 / 1.92 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8592 (m-10) cc_final: 0.8303 (m-10) REVERT: A 981 PHE cc_start: 0.7795 (m-80) cc_final: 0.7436 (m-10) REVERT: B 200 TYR cc_start: 0.8446 (m-80) cc_final: 0.8024 (m-80) REVERT: B 368 LEU cc_start: 0.8914 (mt) cc_final: 0.8257 (tp) REVERT: B 1029 MET cc_start: 0.9246 (tpp) cc_final: 0.8959 (ttm) REVERT: B 1092 GLU cc_start: 0.8462 (pm20) cc_final: 0.8185 (pt0) REVERT: C 314 GLN cc_start: 0.8813 (tt0) cc_final: 0.8517 (tm-30) REVERT: C 950 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8082 (m-30) REVERT: D 4 MET cc_start: 0.7776 (mtp) cc_final: 0.7573 (mtp) REVERT: E 28 PHE cc_start: 0.7300 (m-10) cc_final: 0.7097 (m-10) REVERT: E 71 ILE cc_start: 0.7967 (tt) cc_final: 0.7679 (tt) REVERT: F 106 GLU cc_start: 0.8712 (pm20) cc_final: 0.8248 (pm20) outliers start: 27 outliers final: 18 residues processed: 207 average time/residue: 0.1733 time to fit residues: 61.4237 Evaluate side-chains 194 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 201 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 373 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 225 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.061917 restraints weight = 75620.308| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 3.37 r_work: 0.2838 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30973 Z= 0.188 Angle : 0.571 10.562 42251 Z= 0.291 Chirality : 0.045 0.288 4883 Planarity : 0.004 0.059 5354 Dihedral : 4.183 20.222 4067 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 1.40 % Allowed : 9.07 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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 (0.14), residues: 3737 helix: 1.89 (0.21), residues: 671 sheet: 0.27 (0.17), residues: 959 loop : -0.93 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.019 0.001 TYR C1067 PHE 0.024 0.001 PHE C 559 TRP 0.013 0.001 TRP G 112 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (30877) covalent geometry : angle 0.55247 / 0.29 (42014) SS BOND : bond 0.00340 / 0.22 ( 51) SS BOND : angle 1.39861 / 0.91 ( 102) hydrogen bonds : bond 0.04419 / 2.93 ( 1157) hydrogen bonds : angle 5.38100 / 3.74 ( 3237) link_BETA1-4 : bond 0.00270 / 0.19 ( 15) link_BETA1-4 : angle 1.03719 / 0.68 ( 45) link_NAG-ASN : bond 0.00401 / 0.24 ( 30) link_NAG-ASN : angle 2.82086 / 1.92 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8587 (m-10) cc_final: 0.8258 (m-10) REVERT: A 981 PHE cc_start: 0.8004 (m-80) cc_final: 0.7658 (m-10) REVERT: A 1029 MET cc_start: 0.9436 (tpp) cc_final: 0.9202 (ttm) REVERT: B 200 TYR cc_start: 0.8493 (m-80) cc_final: 0.8062 (m-80) REVERT: B 368 LEU cc_start: 0.8917 (mt) cc_final: 0.8254 (tp) REVERT: B 1029 MET cc_start: 0.9274 (tpp) cc_final: 0.9044 (ttm) REVERT: B 1092 GLU cc_start: 0.8512 (pm20) cc_final: 0.8205 (pt0) REVERT: C 314 GLN cc_start: 0.8836 (tt0) cc_final: 0.8506 (tm-30) REVERT: C 950 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.8076 (m-30) REVERT: C 1002 GLN cc_start: 0.8707 (mm110) cc_final: 0.8369 (tm-30) REVERT: D 24 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: F 106 GLU cc_start: 0.8673 (pm20) cc_final: 0.8418 (pm20) outliers start: 46 outliers final: 28 residues processed: 223 average time/residue: 0.1694 time to fit residues: 64.6100 Evaluate side-chains 201 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 111 LEU Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 140 optimal weight: 3.9990 chunk 350 optimal weight: 9.9990 chunk 146 optimal weight: 4.9990 chunk 347 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN H 38 GLN I 39 GLN I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.085814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.059054 restraints weight = 76906.163| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.36 r_work: 0.2770 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8878 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 30973 Z= 0.389 Angle : 0.728 10.831 42251 Z= 0.370 Chirality : 0.050 0.337 4883 Planarity : 0.005 0.059 5354 Dihedral : 4.742 22.997 4067 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 2.34 % Allowed : 10.44 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.56 (0.13), residues: 3737 helix: 1.51 (0.20), residues: 663 sheet: -0.15 (0.16), residues: 984 loop : -1.12 (0.13), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 983 TYR 0.021 0.002 TYR G 103 PHE 0.038 0.002 PHE C 559 TRP 0.012 0.002 TRP G 112 HIS 0.008 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00927 / 0.39 (30877) covalent geometry : angle 0.70705 / 0.37 (42014) SS BOND : bond 0.00487 / 0.32 ( 51) SS BOND : angle 1.57318 / 1.07 ( 102) hydrogen bonds : bond 0.05649 / 3.78 ( 1157) hydrogen bonds : angle 5.64771 / 3.94 ( 3237) link_BETA1-4 : bond 0.00287 / 0.16 ( 15) link_BETA1-4 : angle 1.30357 / 0.85 ( 45) link_NAG-ASN : bond 0.00753 / 0.50 ( 30) link_NAG-ASN : angle 3.39400 / 2.32 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 174 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8845 (OUTLIER) cc_final: 0.8583 (m-30) REVERT: A 377 PHE cc_start: 0.8748 (p90) cc_final: 0.8546 (p90) REVERT: B 137 ASN cc_start: 0.8597 (t0) cc_final: 0.8289 (t0) REVERT: B 200 TYR cc_start: 0.8532 (m-80) cc_final: 0.8127 (m-80) REVERT: B 368 LEU cc_start: 0.8917 (mt) cc_final: 0.8214 (tp) REVERT: B 1092 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.8258 (pt0) REVERT: C 314 GLN cc_start: 0.8829 (tt0) cc_final: 0.8463 (tm-30) REVERT: C 1002 GLN cc_start: 0.8749 (mm110) cc_final: 0.8453 (tm-30) REVERT: E 71 ILE cc_start: 0.7943 (tt) cc_final: 0.7709 (tt) REVERT: F 106 GLU cc_start: 0.8530 (pm20) cc_final: 0.8271 (pm20) REVERT: G 34 MET cc_start: 0.7520 (tpp) cc_final: 0.7285 (tpp) outliers start: 77 outliers final: 48 residues processed: 233 average time/residue: 0.1490 time to fit residues: 60.4480 Evaluate side-chains 214 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1105 THR Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain D residue 73 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 73 LEU Chi-restraints excluded: chain F residue 76 ASN Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 71 ILE Chi-restraints excluded: chain H residue 24 GLN Chi-restraints excluded: chain H residue 98 ASP Chi-restraints excluded: chain I residue 71 ILE Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 95 optimal weight: 0.7980 chunk 181 optimal weight: 0.6980 chunk 334 optimal weight: 2.9990 chunk 256 optimal weight: 1.9990 chunk 348 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 354 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 317 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 271 GLN ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN E 82 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN I 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.062142 restraints weight = 75471.046| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.35 r_work: 0.2843 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 30973 Z= 0.123 Angle : 0.553 12.419 42251 Z= 0.280 Chirality : 0.044 0.278 4883 Planarity : 0.004 0.073 5354 Dihedral : 4.260 23.935 4067 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 1.37 % Allowed : 11.90 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.28 (0.14), residues: 3737 helix: 1.88 (0.21), residues: 674 sheet: -0.03 (0.17), residues: 982 loop : -0.98 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.043 0.001 PHE B 374 TRP 0.015 0.001 TRP C 436 HIS 0.005 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (30877) covalent geometry : angle 0.53569 / 0.28 (42014) SS BOND : bond 0.00406 / 0.25 ( 51) SS BOND : angle 1.11459 / 0.74 ( 102) hydrogen bonds : bond 0.04160 / 2.76 ( 1157) hydrogen bonds : angle 5.30048 / 3.69 ( 3237) link_BETA1-4 : bond 0.00351 / 0.23 ( 15) link_BETA1-4 : angle 0.98055 / 0.65 ( 45) link_NAG-ASN : bond 0.00345 / 0.19 ( 30) link_NAG-ASN : angle 2.74514 / 1.89 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 188 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8545 (m-10) cc_final: 0.8252 (m-10) REVERT: A 981 PHE cc_start: 0.8326 (m-80) cc_final: 0.8120 (m-10) REVERT: B 200 TYR cc_start: 0.8455 (m-80) cc_final: 0.8086 (m-80) REVERT: B 368 LEU cc_start: 0.8946 (mt) cc_final: 0.8293 (tp) REVERT: B 1029 MET cc_start: 0.9240 (tpp) cc_final: 0.8998 (ttm) REVERT: B 1092 GLU cc_start: 0.8510 (pm20) cc_final: 0.8120 (pt0) REVERT: C 164 ASN cc_start: 0.8250 (OUTLIER) cc_final: 0.7204 (p0) REVERT: C 314 GLN cc_start: 0.8791 (tt0) cc_final: 0.8527 (tm-30) REVERT: C 950 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8027 (m-30) REVERT: C 1002 GLN cc_start: 0.8678 (mm110) cc_final: 0.8369 (tm-30) REVERT: D 24 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: D 76 ASN cc_start: 0.8016 (p0) cc_final: 0.7240 (m-40) REVERT: E 71 ILE cc_start: 0.7953 (tt) cc_final: 0.7691 (tt) REVERT: F 36 TYR cc_start: 0.8375 (m-80) cc_final: 0.8042 (m-80) REVERT: F 106 GLU cc_start: 0.8537 (pm20) cc_final: 0.8267 (pm20) REVERT: G 5 GLU cc_start: 0.7002 (mm-30) cc_final: 0.6456 (mp0) REVERT: G 46 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7479 (mt-10) REVERT: I 98 ARG cc_start: 0.7289 (ttp-170) cc_final: 0.6814 (ttt90) outliers start: 45 outliers final: 27 residues processed: 223 average time/residue: 0.1703 time to fit residues: 66.0483 Evaluate side-chains 206 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 176 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 24 GLN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 353 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 293 optimal weight: 5.9990 chunk 270 optimal weight: 2.9990 chunk 323 optimal weight: 0.9990 chunk 96 optimal weight: 0.9980 chunk 202 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 336 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 358 optimal weight: 0.6980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN E 82 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.088848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.062185 restraints weight = 75450.135| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.35 r_work: 0.2847 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30973 Z= 0.125 Angle : 0.543 11.847 42251 Z= 0.275 Chirality : 0.044 0.275 4883 Planarity : 0.004 0.067 5354 Dihedral : 4.123 24.515 4067 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.29 % Favored : 96.63 % Rotamer: Outliers : 1.61 % Allowed : 12.02 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.17 (0.14), residues: 3737 helix: 2.07 (0.21), residues: 662 sheet: 0.12 (0.17), residues: 968 loop : -0.97 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.019 0.001 TYR C1067 PHE 0.018 0.001 PHE B 168 TRP 0.013 0.001 TRP G 36 HIS 0.005 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.12 (30877) covalent geometry : angle 0.52638 / 0.27 (42014) SS BOND : bond 0.00293 / 0.19 ( 51) SS BOND : angle 1.28292 / 0.90 ( 102) hydrogen bonds : bond 0.03991 / 2.65 ( 1157) hydrogen bonds : angle 5.13396 / 3.57 ( 3237) link_BETA1-4 : bond 0.00298 / 0.20 ( 15) link_BETA1-4 : angle 0.96403 / 0.64 ( 45) link_NAG-ASN : bond 0.00334 / 0.19 ( 30) link_NAG-ASN : angle 2.60986 / 1.80 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 191 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 904 TYR cc_start: 0.8553 (m-10) cc_final: 0.8288 (m-10) REVERT: B 200 TYR cc_start: 0.8439 (m-80) cc_final: 0.8073 (m-80) REVERT: B 368 LEU cc_start: 0.8951 (mt) cc_final: 0.8320 (tp) REVERT: C 164 ASN cc_start: 0.8234 (OUTLIER) cc_final: 0.7175 (p0) REVERT: C 314 GLN cc_start: 0.8777 (tt0) cc_final: 0.8555 (tm-30) REVERT: C 950 ASP cc_start: 0.8399 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: C 1002 GLN cc_start: 0.8696 (mm110) cc_final: 0.8378 (tm-30) REVERT: D 76 ASN cc_start: 0.7973 (p0) cc_final: 0.7190 (m-40) REVERT: E 71 ILE cc_start: 0.7972 (tt) cc_final: 0.7702 (tt) REVERT: F 36 TYR cc_start: 0.8388 (m-80) cc_final: 0.8092 (m-80) REVERT: G 5 GLU cc_start: 0.6966 (mm-30) cc_final: 0.6411 (mp0) REVERT: I 98 ARG cc_start: 0.7272 (ttp-170) cc_final: 0.6444 (ttp-110) outliers start: 53 outliers final: 37 residues processed: 230 average time/residue: 0.1742 time to fit residues: 69.2308 Evaluate side-chains 218 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 179 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 736 VAL Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 6.9990 chunk 247 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 304 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 258 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 218 GLN B 563 GLN B 957 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.087229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.060552 restraints weight = 76131.510| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.35 r_work: 0.2807 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 30973 Z= 0.224 Angle : 0.602 12.048 42251 Z= 0.305 Chirality : 0.046 0.291 4883 Planarity : 0.004 0.066 5354 Dihedral : 4.287 23.315 4067 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 1.67 % Allowed : 12.51 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.28 (0.14), residues: 3737 helix: 2.00 (0.21), residues: 656 sheet: 0.02 (0.17), residues: 969 loop : -1.02 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 983 TYR 0.019 0.001 TYR C1067 PHE 0.047 0.002 PHE B 374 TRP 0.009 0.001 TRP C 436 HIS 0.011 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.22 (30877) covalent geometry : angle 0.58493 / 0.30 (42014) SS BOND : bond 0.00367 / 0.24 ( 51) SS BOND : angle 1.31911 / 0.94 ( 102) hydrogen bonds : bond 0.04577 / 3.05 ( 1157) hydrogen bonds : angle 5.22395 / 3.64 ( 3237) link_BETA1-4 : bond 0.00229 / 0.16 ( 15) link_BETA1-4 : angle 1.06161 / 0.70 ( 45) link_NAG-ASN : bond 0.00440 / 0.28 ( 30) link_NAG-ASN : angle 2.78794 / 1.92 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 175 time to evaluate : 1.021 Fit side-chains revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: A 904 TYR cc_start: 0.8614 (m-10) cc_final: 0.8263 (m-10) REVERT: A 1029 MET cc_start: 0.9477 (tpp) cc_final: 0.9206 (ttm) REVERT: B 137 ASN cc_start: 0.8582 (t0) cc_final: 0.8273 (t0) REVERT: B 200 TYR cc_start: 0.8498 (m-80) cc_final: 0.8102 (m-80) REVERT: B 368 LEU cc_start: 0.8947 (mt) cc_final: 0.8307 (tp) REVERT: B 957 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8393 (tm-30) REVERT: B 1029 MET cc_start: 0.9318 (tpp) cc_final: 0.9064 (ttm) REVERT: B 1092 GLU cc_start: 0.8487 (pm20) cc_final: 0.8193 (pt0) REVERT: C 164 ASN cc_start: 0.8282 (OUTLIER) cc_final: 0.7406 (p0) REVERT: C 314 GLN cc_start: 0.8764 (tt0) cc_final: 0.8507 (tm-30) REVERT: C 950 ASP cc_start: 0.8498 (m-30) cc_final: 0.8065 (m-30) REVERT: C 1002 GLN cc_start: 0.8728 (mm110) cc_final: 0.8395 (tm-30) REVERT: E 71 ILE cc_start: 0.7939 (tt) cc_final: 0.7665 (tt) REVERT: F 36 TYR cc_start: 0.8435 (m-80) cc_final: 0.8121 (m-80) REVERT: G 34 MET cc_start: 0.7863 (tpp) cc_final: 0.7408 (tpp) outliers start: 55 outliers final: 39 residues processed: 219 average time/residue: 0.1599 time to fit residues: 60.9725 Evaluate side-chains 209 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain H residue 7 THR Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 76 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 333 optimal weight: 0.0770 chunk 56 optimal weight: 2.9990 chunk 225 optimal weight: 4.9990 chunk 346 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 197 optimal weight: 0.7980 chunk 186 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 243 optimal weight: 2.9990 overall best weight: 1.0940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 563 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 354 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN I 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.088269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.061593 restraints weight = 75517.998| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.35 r_work: 0.2834 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30973 Z= 0.135 Angle : 0.558 12.854 42251 Z= 0.281 Chirality : 0.044 0.275 4883 Planarity : 0.004 0.065 5354 Dihedral : 4.163 21.761 4067 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.32 % Favored : 96.63 % Rotamer: Outliers : 1.58 % Allowed : 13.00 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.21 (0.14), residues: 3737 helix: 2.07 (0.21), residues: 662 sheet: 0.09 (0.17), residues: 968 loop : -0.99 (0.13), residues: 2107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 983 TYR 0.020 0.001 TYR C1067 PHE 0.040 0.001 PHE B 374 TRP 0.012 0.001 TRP C 436 HIS 0.009 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (30877) covalent geometry : angle 0.54250 / 0.28 (42014) SS BOND : bond 0.00325 / 0.21 ( 51) SS BOND : angle 1.09245 / 0.78 ( 102) hydrogen bonds : bond 0.04143 / 2.75 ( 1157) hydrogen bonds : angle 5.14149 / 3.58 ( 3237) link_BETA1-4 : bond 0.00284 / 0.19 ( 15) link_BETA1-4 : angle 0.98198 / 0.65 ( 45) link_NAG-ASN : bond 0.00335 / 0.19 ( 30) link_NAG-ASN : angle 2.60748 / 1.80 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 170 time to evaluate : 1.216 Fit side-chains revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8477 (m-30) REVERT: A 904 TYR cc_start: 0.8557 (m-10) cc_final: 0.8253 (m-10) REVERT: A 1029 MET cc_start: 0.9458 (tpp) cc_final: 0.9152 (ttm) REVERT: B 137 ASN cc_start: 0.8584 (t0) cc_final: 0.8284 (t0) REVERT: B 200 TYR cc_start: 0.8464 (m-80) cc_final: 0.8097 (m-80) REVERT: B 368 LEU cc_start: 0.8975 (mt) cc_final: 0.8358 (tp) REVERT: B 957 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: B 1092 GLU cc_start: 0.8507 (pm20) cc_final: 0.8206 (pt0) REVERT: C 164 ASN cc_start: 0.8254 (OUTLIER) cc_final: 0.7386 (p0) REVERT: C 314 GLN cc_start: 0.8744 (tt0) cc_final: 0.8537 (tm-30) REVERT: C 950 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7974 (m-30) REVERT: C 1002 GLN cc_start: 0.8691 (mm110) cc_final: 0.8383 (tm-30) REVERT: D 76 ASN cc_start: 0.7951 (p0) cc_final: 0.7135 (m-40) REVERT: E 71 ILE cc_start: 0.7940 (tt) cc_final: 0.7728 (tt) REVERT: F 36 TYR cc_start: 0.8419 (m-80) cc_final: 0.8043 (m-80) REVERT: F 106 GLU cc_start: 0.8681 (pm20) cc_final: 0.8375 (pm20) REVERT: G 34 MET cc_start: 0.7962 (tpp) cc_final: 0.7530 (tpp) outliers start: 52 outliers final: 39 residues processed: 209 average time/residue: 0.1701 time to fit residues: 61.8168 Evaluate side-chains 211 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 340 optimal weight: 2.9990 chunk 286 optimal weight: 1.9990 chunk 206 optimal weight: 20.0000 chunk 259 optimal weight: 0.9980 chunk 254 optimal weight: 0.0970 chunk 5 optimal weight: 7.9990 chunk 117 optimal weight: 0.9990 chunk 178 optimal weight: 0.0370 chunk 10 optimal weight: 4.9990 chunk 303 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 39 GLN I 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.088915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.062163 restraints weight = 75008.357| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.35 r_work: 0.2847 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30973 Z= 0.119 Angle : 0.551 12.952 42251 Z= 0.278 Chirality : 0.044 0.270 4883 Planarity : 0.004 0.066 5354 Dihedral : 4.108 21.068 4067 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.21 % Favored : 96.74 % Rotamer: Outliers : 1.49 % Allowed : 13.03 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.14 (0.14), residues: 3737 helix: 2.14 (0.21), residues: 662 sheet: 0.14 (0.17), residues: 958 loop : -0.95 (0.13), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 983 TYR 0.019 0.001 TYR C1067 PHE 0.040 0.001 PHE B 374 TRP 0.013 0.001 TRP G 36 HIS 0.010 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (30877) covalent geometry : angle 0.53484 / 0.27 (42014) SS BOND : bond 0.00374 / 0.26 ( 51) SS BOND : angle 1.44612 / 0.82 ( 102) hydrogen bonds : bond 0.03933 / 2.60 ( 1157) hydrogen bonds : angle 5.08547 / 3.54 ( 3237) link_BETA1-4 : bond 0.00313 / 0.21 ( 15) link_BETA1-4 : angle 0.94625 / 0.63 ( 45) link_NAG-ASN : bond 0.00323 / 0.18 ( 30) link_NAG-ASN : angle 2.49033 / 1.73 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7474 Ramachandran restraints generated. 3737 Oldfield, 0 Emsley, 3737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 180 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 287 ASP cc_start: 0.8749 (OUTLIER) cc_final: 0.8475 (m-30) REVERT: A 904 TYR cc_start: 0.8544 (m-10) cc_final: 0.8248 (m-10) REVERT: B 137 ASN cc_start: 0.8605 (t0) cc_final: 0.8306 (t0) REVERT: B 200 TYR cc_start: 0.8463 (m-80) cc_final: 0.8102 (m-80) REVERT: B 368 LEU cc_start: 0.8986 (mt) cc_final: 0.8400 (tp) REVERT: B 957 GLN cc_start: 0.8563 (OUTLIER) cc_final: 0.8354 (tm-30) REVERT: B 1092 GLU cc_start: 0.8496 (pm20) cc_final: 0.8192 (pt0) REVERT: C 164 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7367 (p0) REVERT: C 314 GLN cc_start: 0.8709 (tt0) cc_final: 0.8509 (tm-30) REVERT: C 950 ASP cc_start: 0.8419 (OUTLIER) cc_final: 0.7972 (m-30) REVERT: C 1002 GLN cc_start: 0.8675 (mm110) cc_final: 0.8370 (tm-30) REVERT: C 1029 MET cc_start: 0.9299 (tpp) cc_final: 0.9082 (ttm) REVERT: D 76 ASN cc_start: 0.7931 (p0) cc_final: 0.7102 (m-40) REVERT: E 33 ASP cc_start: 0.7497 (m-30) cc_final: 0.6966 (m-30) REVERT: E 71 ILE cc_start: 0.8032 (tt) cc_final: 0.7756 (tt) REVERT: F 36 TYR cc_start: 0.8410 (m-80) cc_final: 0.7986 (m-80) REVERT: F 106 GLU cc_start: 0.8687 (pm20) cc_final: 0.8379 (pm20) REVERT: G 34 MET cc_start: 0.8031 (tpp) cc_final: 0.7603 (tpp) outliers start: 49 outliers final: 42 residues processed: 217 average time/residue: 0.1755 time to fit residues: 65.7559 Evaluate side-chains 218 residues out of total 3285 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 380 TYR Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 515 PHE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 779 GLN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 991 VAL Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 258 TRP Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 407 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 957 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 258 TRP Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 380 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 518 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain F residue 80 CYS Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 58 ASN Chi-restraints excluded: chain G residue 83 MET Chi-restraints excluded: chain I residue 46 GLU Chi-restraints excluded: chain I residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 282 optimal weight: 1.9990 chunk 322 optimal weight: 7.9990 chunk 317 optimal weight: 0.9990 chunk 269 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 344 optimal weight: 9.9990 chunk 347 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 115 GLN B 218 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.087628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.060592 restraints weight = 76226.902| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 3.40 r_work: 0.2816 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30973 Z= 0.198 Angle : 0.594 12.588 42251 Z= 0.300 Chirality : 0.045 0.281 4883 Planarity : 0.004 0.066 5354 Dihedral : 4.239 24.387 4067 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.91 % Favored : 96.04 % Rotamer: Outliers : 1.52 % Allowed : 13.15 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % 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: -0.21 (0.14), residues: 3737 helix: 2.07 (0.21), residues: 656 sheet: 0.11 (0.16), residues: 992 loop : -1.02 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 983 TYR 0.019 0.001 TYR B 904 PHE 0.037 0.001 PHE B 374 TRP 0.017 0.001 TRP I 36 HIS 0.010 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (30877) covalent geometry : angle 0.57597 / 0.30 (42014) SS BOND : bond 0.00335 / 0.22 ( 51) SS BOND : angle 1.69414 / 0.93 ( 102) hydrogen bonds : bond 0.04373 / 2.91 ( 1157) hydrogen bonds : angle 5.14278 / 3.58 ( 3237) link_BETA1-4 : bond 0.00233 / 0.17 ( 15) link_BETA1-4 : angle 1.02224 / 0.68 ( 45) link_NAG-ASN : bond 0.00391 / 0.24 ( 30) link_NAG-ASN : angle 2.63262 / 1.82 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5922.91 seconds wall clock time: 103 minutes 7.58 seconds (6187.58 seconds total)