Starting phenix.real_space_refine on Sun Jul 5 21:07:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwi_32866/07_2026/7wwi_32866.map" } resolution = 3.5 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= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19271 2.51 5 N 4986 2.21 5 O 5848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 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: 30237 Number of models: 1 Model: "" Number of chains: 26 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: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, '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: "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: 6.02, per 1000 atoms: 0.20 Number of scatterers: 30237 At special positions: 0 Unit cell: (145.14, 156.62, 222.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5848 8.00 N 4986 7.00 C 19271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, 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=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 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 A1098 " " NAG W 1 " - " ASN A1134 " Time building additional restraints: 2.41 Conformation dependent library (CDL) restraints added in 1.3 seconds 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7084 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 59 sheets defined 21.1% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.514A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.259A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.583A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.045A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.117A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.423A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.833A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.056A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.154A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.779A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.387A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.548A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.705A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.550A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.575A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.188A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.691A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) 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: 4.472A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.862A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.887A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.657A 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 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.146A 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: 3.714A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.779A 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: 4.046A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.795A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.090A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.949A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.465A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.374A 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: 3.801A 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: 3.588A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A 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: 8.302A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.871A 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: 7.328A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.247A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.896A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (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 654 through 655 removed outlier: 6.082A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.946A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.710A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.223A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.055A 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: 5.987A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.485A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.956A 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 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.709A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.001A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.892A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.508A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.390A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.501A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.187A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 13 removed outlier: 4.115A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 12 removed outlier: 8.600A pdb=" N TYR E 32 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE E 52 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG E 50 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.651A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 12 removed outlier: 8.695A pdb=" N TYR G 32 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE G 52 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.503A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.730A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3285 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: 7.27 Time building geometry restraints manager: 3.15 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: 9580 1.34 - 1.46: 7726 1.46 - 1.59: 13453 1.59 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 30927 Sorted by residual: bond pdb=" N THR C 19 " pdb=" CA THR C 19 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 1.01e+01 bond pdb=" N VAL B 736 " pdb=" CA VAL B 736 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.52e+00 bond pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.79e+00 bond pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.13e+00 bond pdb=" N VAL C 16 " pdb=" CA VAL C 16 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 7.00e+00 ... (remaining 30922 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 41042 1.76 - 3.53: 900 3.53 - 5.29: 83 5.29 - 7.05: 9 7.05 - 8.82: 4 Bond angle restraints: 42038 Sorted by residual: angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N VAL A 90 " ideal model delta sigma weight residual 114.86 118.38 -3.52 1.01e+00 9.80e-01 1.21e+01 angle pdb=" N MET B 740 " pdb=" CA MET B 740 " pdb=" C MET B 740 " ideal model delta sigma weight residual 113.23 109.07 4.16 1.24e+00 6.50e-01 1.12e+01 angle pdb=" N LYS A 528 " pdb=" CA LYS A 528 " pdb=" C LYS A 528 " ideal model delta sigma weight residual 113.89 108.64 5.25 1.58e+00 4.01e-01 1.10e+01 angle pdb=" N THR C 20 " pdb=" CA THR C 20 " pdb=" C THR C 20 " ideal model delta sigma weight residual 112.87 109.00 3.87 1.20e+00 6.94e-01 1.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.53 -3.83 1.22e+00 6.72e-01 9.85e+00 ... (remaining 42033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 16530 17.56 - 35.11: 1280 35.11 - 52.67: 215 52.67 - 70.23: 47 70.23 - 87.78: 37 Dihedral angle restraints: 18109 sinusoidal: 7090 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 -6.19 -79.81 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.58 -69.58 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 156.62 -63.62 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 18106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4412 0.087 - 0.174: 440 0.174 - 0.260: 8 0.260 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 4861 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+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 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+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 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4858 not shown) Planarity restraints: 5383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 987 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 7 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.74e+00 pdb=" N PRO F 8 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 52 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO G 53 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.030 5.00e-02 4.00e+02 ... (remaining 5380 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 494 2.67 - 3.22: 27802 3.22 - 3.78: 44920 3.78 - 4.34: 60548 4.34 - 4.90: 101865 Nonbonded interactions: 235629 Sorted by model distance: nonbonded pdb=" OG SER F 26 " pdb=" OE1 GLN F 27 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU B 156 " pdb=" NH1 ARG B 158 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR H 94 " pdb=" OD1 ASN I 59 " model vdw 2.251 3.040 ... (remaining 235624 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' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) selection = chain 'F' selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.670 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: 0.630 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 26.030 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31018 Z= 0.174 Angle : 0.619 10.494 42263 Z= 0.334 Chirality : 0.046 0.434 4861 Planarity : 0.004 0.057 5354 Dihedral : 13.128 87.783 10881 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 3725 helix: 2.20 (0.21), residues: 660 sheet: 0.65 (0.16), residues: 1032 loop : -0.96 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 466 TYR 0.025 0.001 TYR C 904 PHE 0.021 0.001 PHE A 515 TRP 0.018 0.001 TRP E 111 HIS 0.003 0.000 HIS C 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.17 (30927) covalent geometry : angle 0.60303 / 0.33 (42038) SS BOND : bond 0.00303 / 0.20 ( 48) SS BOND : angle 0.95726 / 0.71 ( 96) hydrogen bonds : bond 0.12987 / 8.47 ( 1215) hydrogen bonds : angle 6.30111 / 4.32 ( 3285) link_BETA1-4 : bond 0.00454 / 0.25 ( 14) link_BETA1-4 : angle 0.94352 / 0.64 ( 42) link_NAG-ASN : bond 0.00600 / 0.43 ( 29) link_NAG-ASN : angle 3.04029 / 2.13 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 289 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8721 (m-80) cc_final: 0.8391 (m-80) REVERT: B 740 MET cc_start: 0.8636 (tmm) cc_final: 0.8358 (tmm) REVERT: C 197 ILE cc_start: 0.9053 (mm) cc_final: 0.8707 (mm) REVERT: E 110 ASP cc_start: 0.7369 (t70) cc_final: 0.7146 (t0) REVERT: F 55 GLU cc_start: 0.8508 (tp30) cc_final: 0.8058 (tp30) REVERT: F 103 LYS cc_start: 0.9151 (tptt) cc_final: 0.8884 (tptp) REVERT: G 100 THR cc_start: 0.8939 (m) cc_final: 0.8729 (p) REVERT: G 101 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8297 (tm-30) REVERT: I 74 LYS cc_start: 0.8416 (tppt) cc_final: 0.8021 (tptt) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.1713 time to fit residues: 79.6793 Evaluate side-chains 200 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 0.0770 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.7344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 115 GLN A 188 ASN A 487 ASN A 762 GLN A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C1010 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.080328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.052369 restraints weight = 106644.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054480 restraints weight = 49903.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.055831 restraints weight = 31749.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056662 restraints weight = 24045.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 62)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.057210 restraints weight = 20267.250| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 31018 Z= 0.157 Angle : 0.575 10.715 42263 Z= 0.294 Chirality : 0.045 0.405 4861 Planarity : 0.004 0.070 5354 Dihedral : 4.018 22.647 4072 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.70 % Allowed : 6.63 % Favored : 92.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 3725 helix: 2.11 (0.21), residues: 667 sheet: 0.61 (0.16), residues: 1031 loop : -0.90 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1107 TYR 0.022 0.001 TYR F 49 PHE 0.022 0.001 PHE C 559 TRP 0.015 0.001 TRP G 36 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 (30927) covalent geometry : angle 0.55966 / 0.29 (42038) SS BOND : bond 0.00349 / 0.24 ( 48) SS BOND : angle 0.93714 / 0.71 ( 96) hydrogen bonds : bond 0.04716 / 3.08 ( 1215) hydrogen bonds : angle 5.28945 / 3.64 ( 3285) link_BETA1-4 : bond 0.00255 / 0.13 ( 14) link_BETA1-4 : angle 0.98321 / 0.69 ( 42) link_NAG-ASN : bond 0.00431 / 0.31 ( 29) link_NAG-ASN : angle 2.75680 / 1.97 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 210 time to evaluate : 0.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8918 (tmm) cc_final: 0.8464 (tmm) REVERT: C 269 TYR cc_start: 0.7622 (m-80) cc_final: 0.7347 (m-80) REVERT: F 103 LYS cc_start: 0.9171 (tptt) cc_final: 0.8906 (tptp) REVERT: G 101 GLU cc_start: 0.8757 (tm-30) cc_final: 0.8456 (tm-30) REVERT: H 70 GLU cc_start: 0.8262 (tp30) cc_final: 0.7948 (tp30) REVERT: H 82 ASP cc_start: 0.7857 (m-30) cc_final: 0.7472 (m-30) REVERT: H 104 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7916 (mt) REVERT: I 48 MET cc_start: 0.8349 (mtt) cc_final: 0.8129 (mtt) REVERT: I 74 LYS cc_start: 0.8400 (tppt) cc_final: 0.8016 (tptt) REVERT: I 98 ARG cc_start: 0.8087 (ttp80) cc_final: 0.7176 (ttp80) outliers start: 23 outliers final: 14 residues processed: 225 average time/residue: 0.1727 time to fit residues: 63.7502 Evaluate side-chains 202 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 187 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 163 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 144 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 chunk 140 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 310 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 211 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 613 GLN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 907 ASN B 314 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN B 613 GLN B 901 GLN B 907 ASN C 804 GLN C 935 GLN D 90 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN G 39 GLN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.076183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.048451 restraints weight = 107758.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.050982 restraints weight = 57839.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051643 restraints weight = 33660.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.051961 restraints weight = 26704.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.052150 restraints weight = 28132.495| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 31018 Z= 0.438 Angle : 0.804 13.429 42263 Z= 0.412 Chirality : 0.051 0.527 4861 Planarity : 0.005 0.073 5354 Dihedral : 4.800 24.363 4072 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 1.57 % Allowed : 10.44 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.42 (0.13), residues: 3725 helix: 1.37 (0.20), residues: 672 sheet: 0.35 (0.16), residues: 977 loop : -1.19 (0.13), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 995 TYR 0.026 0.002 TYR H 94 PHE 0.044 0.003 PHE C 559 TRP 0.020 0.002 TRP G 36 HIS 0.009 0.002 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.01013 / 0.44 (30927) covalent geometry : angle 0.78761 / 0.41 (42038) SS BOND : bond 0.00510 / 0.35 ( 48) SS BOND : angle 1.45673 / 1.10 ( 96) hydrogen bonds : bond 0.06702 / 4.36 ( 1215) hydrogen bonds : angle 5.72500 / 3.94 ( 3285) link_BETA1-4 : bond 0.00554 / 0.33 ( 14) link_BETA1-4 : angle 1.49403 / 1.05 ( 42) link_NAG-ASN : bond 0.00776 / 0.51 ( 29) link_NAG-ASN : angle 3.33059 / 2.46 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 196 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8724 (m-80) cc_final: 0.8202 (m-80) REVERT: B 752 LEU cc_start: 0.9543 (mp) cc_final: 0.9314 (tt) REVERT: C 170 TYR cc_start: 0.8664 (t80) cc_final: 0.8377 (t80) REVERT: C 375 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8114 (p90) REVERT: E 110 ASP cc_start: 0.7449 (t70) cc_final: 0.7105 (t0) REVERT: F 42 LYS cc_start: 0.9516 (mtpp) cc_final: 0.9186 (mmmt) REVERT: G 101 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8428 (tm-30) REVERT: H 42 LYS cc_start: 0.8943 (mmmm) cc_final: 0.8740 (mppt) REVERT: H 70 GLU cc_start: 0.8485 (tp30) cc_final: 0.8203 (tp30) REVERT: I 98 ARG cc_start: 0.8247 (ttp80) cc_final: 0.7240 (ttp80) outliers start: 52 outliers final: 37 residues processed: 231 average time/residue: 0.2076 time to fit residues: 78.0097 Evaluate side-chains 211 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 315 THR Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 375 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 100 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 225 optimal weight: 6.9990 chunk 212 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 30 optimal weight: 9.9990 chunk 25 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 chunk 226 optimal weight: 20.0000 chunk 127 optimal weight: 5.9990 chunk 241 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 957 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 901 GLN B 907 ASN C 450 ASN D 37 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.078377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.050477 restraints weight = 105878.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.052559 restraints weight = 49100.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053892 restraints weight = 31087.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054717 restraints weight = 23472.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.055211 restraints weight = 19767.765| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 31018 Z= 0.150 Angle : 0.578 11.650 42263 Z= 0.297 Chirality : 0.045 0.450 4861 Planarity : 0.004 0.065 5354 Dihedral : 4.342 21.569 4072 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.48 % Allowed : 11.95 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.16 (0.14), residues: 3725 helix: 1.90 (0.21), residues: 674 sheet: 0.40 (0.16), residues: 999 loop : -1.09 (0.13), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 815 TYR 0.022 0.001 TYR H 94 PHE 0.024 0.001 PHE C 559 TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (30927) covalent geometry : angle 0.56388 / 0.29 (42038) SS BOND : bond 0.00365 / 0.24 ( 48) SS BOND : angle 1.00481 / 0.77 ( 96) hydrogen bonds : bond 0.05082 / 3.32 ( 1215) hydrogen bonds : angle 5.20028 / 3.57 ( 3285) link_BETA1-4 : bond 0.00306 / 0.18 ( 14) link_BETA1-4 : angle 0.80678 / 0.59 ( 42) link_NAG-ASN : bond 0.00412 / 0.29 ( 29) link_NAG-ASN : angle 2.71779 / 2.02 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8674 (m-80) cc_final: 0.8216 (m-80) REVERT: B 752 LEU cc_start: 0.9532 (mp) cc_final: 0.9319 (tt) REVERT: C 170 TYR cc_start: 0.8553 (t80) cc_final: 0.8293 (t80) REVERT: E 48 MET cc_start: 0.6396 (ptp) cc_final: 0.6035 (mpp) REVERT: E 110 ASP cc_start: 0.7577 (t70) cc_final: 0.7284 (t0) REVERT: F 103 LYS cc_start: 0.9252 (tptt) cc_final: 0.8957 (tppt) REVERT: G 101 GLU cc_start: 0.8761 (tm-30) cc_final: 0.8384 (tm-30) REVERT: H 70 GLU cc_start: 0.8349 (tp30) cc_final: 0.7943 (tp30) REVERT: I 98 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7166 (ttp80) outliers start: 49 outliers final: 28 residues processed: 242 average time/residue: 0.1976 time to fit residues: 78.1048 Evaluate side-chains 210 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 182 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 270 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 chunk 235 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 290 optimal weight: 4.9990 chunk 143 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.076505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.048796 restraints weight = 107829.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.051268 restraints weight = 57618.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.052369 restraints weight = 33667.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052413 restraints weight = 26783.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.052660 restraints weight = 26331.103| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 31018 Z= 0.326 Angle : 0.689 12.707 42263 Z= 0.352 Chirality : 0.048 0.491 4861 Planarity : 0.004 0.066 5354 Dihedral : 4.579 23.306 4072 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.91 % Allowed : 12.86 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.37 (0.13), residues: 3725 helix: 1.68 (0.20), residues: 671 sheet: 0.31 (0.16), residues: 997 loop : -1.24 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 995 TYR 0.022 0.002 TYR A1067 PHE 0.035 0.002 PHE C 559 TRP 0.018 0.002 TRP G 36 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00758 / 0.33 (30927) covalent geometry : angle 0.67355 / 0.35 (42038) SS BOND : bond 0.00421 / 0.28 ( 48) SS BOND : angle 1.24406 / 0.95 ( 96) hydrogen bonds : bond 0.05925 / 3.86 ( 1215) hydrogen bonds : angle 5.39756 / 3.71 ( 3285) link_BETA1-4 : bond 0.00365 / 0.21 ( 14) link_BETA1-4 : angle 1.24043 / 0.89 ( 42) link_NAG-ASN : bond 0.00610 / 0.40 ( 29) link_NAG-ASN : angle 3.02203 / 2.25 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 180 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.8477 (t0) cc_final: 0.7710 (p0) REVERT: A 981 PHE cc_start: 0.8592 (m-10) cc_final: 0.8386 (m-10) REVERT: B 456 PHE cc_start: 0.8754 (m-80) cc_final: 0.8208 (m-80) REVERT: C 170 TYR cc_start: 0.8729 (t80) cc_final: 0.8520 (t80) REVERT: C 1002 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8027 (tm-30) REVERT: D 62 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7815 (m-10) REVERT: E 48 MET cc_start: 0.6201 (ptp) cc_final: 0.5828 (mpp) REVERT: E 110 ASP cc_start: 0.7468 (t70) cc_final: 0.7109 (t0) REVERT: F 103 LYS cc_start: 0.9248 (tptt) cc_final: 0.8976 (tppt) REVERT: G 101 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8432 (tm-30) REVERT: I 98 ARG cc_start: 0.8226 (ttp80) cc_final: 0.7171 (ttp80) outliers start: 63 outliers final: 47 residues processed: 227 average time/residue: 0.1892 time to fit residues: 71.3970 Evaluate side-chains 221 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 172 time to evaluate : 1.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 15 VAL Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 81 MET Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 217 optimal weight: 20.0000 chunk 149 optimal weight: 6.9990 chunk 345 optimal weight: 9.9990 chunk 138 optimal weight: 0.9980 chunk 213 optimal weight: 10.0000 chunk 268 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 12 optimal weight: 0.0030 chunk 81 optimal weight: 0.8980 chunk 200 optimal weight: 7.9990 chunk 334 optimal weight: 10.0000 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 907 ASN C 992 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.078862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051155 restraints weight = 105887.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.053264 restraints weight = 48870.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.054613 restraints weight = 30811.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055469 restraints weight = 23166.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.055973 restraints weight = 19396.684| |-----------------------------------------------------------------------------| r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 31018 Z= 0.110 Angle : 0.554 11.157 42263 Z= 0.283 Chirality : 0.045 0.426 4861 Planarity : 0.004 0.064 5354 Dihedral : 4.187 21.107 4072 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.63 % Allowed : 13.74 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.14), residues: 3725 helix: 2.10 (0.21), residues: 670 sheet: 0.57 (0.16), residues: 977 loop : -1.10 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 466 TYR 0.020 0.001 TYR F 49 PHE 0.019 0.001 PHE C 559 TRP 0.013 0.001 TRP C 436 HIS 0.002 0.001 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (30927) covalent geometry : angle 0.54151 / 0.28 (42038) SS BOND : bond 0.00339 / 0.22 ( 48) SS BOND : angle 0.92638 / 0.71 ( 96) hydrogen bonds : bond 0.04557 / 2.98 ( 1215) hydrogen bonds : angle 4.98221 / 3.42 ( 3285) link_BETA1-4 : bond 0.00408 / 0.23 ( 14) link_BETA1-4 : angle 0.77758 / 0.57 ( 42) link_NAG-ASN : bond 0.00421 / 0.29 ( 29) link_NAG-ASN : angle 2.49891 / 1.86 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 206 time to evaluate : 1.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.5748 (t80) cc_final: 0.5240 (t80) REVERT: A 448 ASN cc_start: 0.8610 (t0) cc_final: 0.7795 (p0) REVERT: B 1106 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: C 170 TYR cc_start: 0.8597 (t80) cc_final: 0.8394 (t80) REVERT: E 48 MET cc_start: 0.6649 (ptp) cc_final: 0.6161 (mpp) REVERT: F 42 LYS cc_start: 0.9435 (mtpp) cc_final: 0.9035 (ptpp) REVERT: F 103 LYS cc_start: 0.9264 (tptt) cc_final: 0.8962 (tppt) REVERT: G 101 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8365 (tm-30) REVERT: I 46 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7619 (pt0) REVERT: I 50 ARG cc_start: 0.9296 (ttp-110) cc_final: 0.9026 (ttp80) REVERT: I 87 ARG cc_start: 0.9188 (ttm-80) cc_final: 0.8910 (ttm-80) outliers start: 54 outliers final: 30 residues processed: 248 average time/residue: 0.2042 time to fit residues: 82.0196 Evaluate side-chains 214 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 183 time to evaluate : 1.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 99 optimal weight: 0.6980 chunk 79 optimal weight: 0.6980 chunk 153 optimal weight: 3.9990 chunk 372 optimal weight: 7.9990 chunk 302 optimal weight: 3.9990 chunk 271 optimal weight: 6.9990 chunk 73 optimal weight: 0.4980 chunk 316 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 144 optimal weight: 0.0770 chunk 48 optimal weight: 2.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.079032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.051367 restraints weight = 106165.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.053475 restraints weight = 49010.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.054816 restraints weight = 30972.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 66)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055680 restraints weight = 23315.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.056200 restraints weight = 19502.100| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31018 Z= 0.116 Angle : 0.550 10.998 42263 Z= 0.280 Chirality : 0.044 0.421 4861 Planarity : 0.004 0.062 5354 Dihedral : 4.013 20.352 4072 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.75 % Allowed : 14.37 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.03 (0.14), residues: 3725 helix: 2.17 (0.21), residues: 671 sheet: 0.57 (0.16), residues: 972 loop : -1.02 (0.13), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 67 TYR 0.020 0.001 TYR F 49 PHE 0.019 0.001 PHE C 559 TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (30927) covalent geometry : angle 0.53848 / 0.28 (42038) SS BOND : bond 0.00316 / 0.19 ( 48) SS BOND : angle 0.94277 / 0.71 ( 96) hydrogen bonds : bond 0.04311 / 2.82 ( 1215) hydrogen bonds : angle 4.86376 / 3.35 ( 3285) link_BETA1-4 : bond 0.00297 / 0.17 ( 14) link_BETA1-4 : angle 0.83136 / 0.61 ( 42) link_NAG-ASN : bond 0.00379 / 0.26 ( 29) link_NAG-ASN : angle 2.38871 / 1.79 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 202 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8359 (t80) cc_final: 0.8146 (t80) REVERT: A 448 ASN cc_start: 0.8633 (t0) cc_final: 0.7854 (p0) REVERT: A 902 MET cc_start: 0.8904 (tpp) cc_final: 0.8497 (tpt) REVERT: B 456 PHE cc_start: 0.8708 (m-80) cc_final: 0.8304 (m-80) REVERT: B 1106 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8560 (pt0) REVERT: C 933 LYS cc_start: 0.8775 (mmtm) cc_final: 0.8573 (mmtm) REVERT: E 110 ASP cc_start: 0.7607 (t70) cc_final: 0.7371 (t0) REVERT: F 42 LYS cc_start: 0.9449 (mtpp) cc_final: 0.9161 (ptpp) REVERT: F 103 LYS cc_start: 0.9279 (tptt) cc_final: 0.8961 (tppt) REVERT: G 101 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8377 (tm-30) REVERT: I 46 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7642 (pt0) REVERT: I 87 ARG cc_start: 0.9177 (ttm-80) cc_final: 0.8950 (ttm-80) outliers start: 58 outliers final: 39 residues processed: 248 average time/residue: 0.1752 time to fit residues: 71.7201 Evaluate side-chains 227 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 14 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 363 optimal weight: 8.9990 chunk 301 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 291 optimal weight: 0.0050 chunk 292 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 263 optimal weight: 6.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 239 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.077397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049592 restraints weight = 107096.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.051638 restraints weight = 50028.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.052927 restraints weight = 31752.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.053754 restraints weight = 24073.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.054269 restraints weight = 20259.225| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 31018 Z= 0.222 Angle : 0.615 11.907 42263 Z= 0.313 Chirality : 0.046 0.459 4861 Planarity : 0.004 0.063 5354 Dihedral : 4.199 21.104 4072 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.85 % Allowed : 14.28 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.14), residues: 3725 helix: 2.00 (0.21), residues: 671 sheet: 0.53 (0.16), residues: 988 loop : -1.09 (0.13), residues: 2066 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 50 TYR 0.021 0.001 TYR A 904 PHE 0.028 0.001 PHE C 559 TRP 0.014 0.001 TRP G 36 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00514 / 0.22 (30927) covalent geometry : angle 0.60163 / 0.31 (42038) SS BOND : bond 0.00339 / 0.21 ( 48) SS BOND : angle 1.06204 / 0.80 ( 96) hydrogen bonds : bond 0.05110 / 3.34 ( 1215) hydrogen bonds : angle 5.04965 / 3.48 ( 3285) link_BETA1-4 : bond 0.00242 / 0.13 ( 14) link_BETA1-4 : angle 1.03624 / 0.76 ( 42) link_NAG-ASN : bond 0.00423 / 0.28 ( 29) link_NAG-ASN : angle 2.65209 / 1.98 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 190 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.8647 (t0) cc_final: 0.7850 (p0) REVERT: B 456 PHE cc_start: 0.8733 (m-80) cc_final: 0.8323 (m-80) REVERT: B 740 MET cc_start: 0.8838 (OUTLIER) cc_final: 0.8078 (tmm) REVERT: B 1106 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.8490 (pt0) REVERT: C 239 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8395 (tp40) REVERT: C 378 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8837 (ttmm) REVERT: C 1002 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8157 (tm-30) REVERT: E 110 ASP cc_start: 0.7556 (t70) cc_final: 0.7303 (t0) REVERT: F 42 LYS cc_start: 0.9478 (mtpp) cc_final: 0.9204 (ptpp) REVERT: F 103 LYS cc_start: 0.9288 (tptt) cc_final: 0.8965 (tppt) REVERT: G 101 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8432 (tm-30) REVERT: I 46 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7734 (pt0) REVERT: I 87 ARG cc_start: 0.9175 (ttm-80) cc_final: 0.8966 (ttm-80) outliers start: 61 outliers final: 42 residues processed: 239 average time/residue: 0.1847 time to fit residues: 73.4499 Evaluate side-chains 226 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 180 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 302 optimal weight: 1.9990 chunk 340 optimal weight: 10.0000 chunk 286 optimal weight: 0.8980 chunk 344 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 236 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 362 optimal weight: 6.9990 chunk 259 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.078373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.050560 restraints weight = 106424.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052649 restraints weight = 49458.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.053984 restraints weight = 31416.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054812 restraints weight = 23734.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 67)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055349 restraints weight = 19968.542| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 31018 Z= 0.142 Angle : 0.576 11.359 42263 Z= 0.293 Chirality : 0.045 0.433 4861 Planarity : 0.004 0.063 5354 Dihedral : 4.088 20.073 4072 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.72 % Allowed : 14.52 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.03 (0.14), residues: 3725 helix: 2.09 (0.21), residues: 671 sheet: 0.57 (0.16), residues: 982 loop : -1.07 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 67 TYR 0.028 0.001 TYR A 423 PHE 0.021 0.001 PHE C 559 TRP 0.012 0.001 TRP C 436 HIS 0.002 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (30927) covalent geometry : angle 0.56458 / 0.29 (42038) SS BOND : bond 0.00327 / 0.20 ( 48) SS BOND : angle 0.93146 / 0.70 ( 96) hydrogen bonds : bond 0.04609 / 3.01 ( 1215) hydrogen bonds : angle 4.91738 / 3.39 ( 3285) link_BETA1-4 : bond 0.00312 / 0.17 ( 14) link_BETA1-4 : angle 0.84876 / 0.63 ( 42) link_NAG-ASN : bond 0.00368 / 0.25 ( 29) link_NAG-ASN : angle 2.46976 / 1.85 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 195 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8409 (t80) cc_final: 0.8195 (t80) REVERT: A 448 ASN cc_start: 0.8631 (t0) cc_final: 0.7835 (p0) REVERT: B 238 PHE cc_start: 0.7977 (p90) cc_final: 0.7769 (p90) REVERT: B 740 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8070 (tmm) REVERT: B 1106 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8494 (pt0) REVERT: C 239 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8144 (mm-40) REVERT: C 378 LYS cc_start: 0.9029 (ttmm) cc_final: 0.8804 (ttmm) REVERT: E 110 ASP cc_start: 0.7624 (t70) cc_final: 0.7338 (t0) REVERT: F 42 LYS cc_start: 0.9465 (mtpp) cc_final: 0.9185 (ptpp) REVERT: G 101 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8398 (tm-30) REVERT: I 46 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7712 (pt0) REVERT: I 98 ARG cc_start: 0.8118 (ttp80) cc_final: 0.7183 (ttp80) outliers start: 57 outliers final: 47 residues processed: 241 average time/residue: 0.1869 time to fit residues: 74.8230 Evaluate side-chains 237 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 187 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 317 optimal weight: 9.9990 chunk 240 optimal weight: 0.9980 chunk 275 optimal weight: 3.9990 chunk 319 optimal weight: 8.9990 chunk 261 optimal weight: 3.9990 chunk 338 optimal weight: 8.9990 chunk 324 optimal weight: 5.9990 chunk 290 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 chunk 289 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.077817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050041 restraints weight = 106054.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.052099 restraints weight = 49677.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053412 restraints weight = 31669.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054241 restraints weight = 23988.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 70)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.054761 restraints weight = 20178.559| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 31018 Z= 0.184 Angle : 0.598 11.551 42263 Z= 0.305 Chirality : 0.045 0.443 4861 Planarity : 0.004 0.063 5354 Dihedral : 4.135 20.305 4072 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 1.66 % Allowed : 14.64 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.14), residues: 3725 helix: 2.08 (0.21), residues: 665 sheet: 0.55 (0.16), residues: 991 loop : -1.11 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 67 TYR 0.023 0.001 TYR A 904 PHE 0.046 0.001 PHE G 29 TRP 0.010 0.001 TRP A 258 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.18 (30927) covalent geometry : angle 0.58525 / 0.30 (42038) SS BOND : bond 0.00359 / 0.22 ( 48) SS BOND : angle 1.19306 / 0.84 ( 96) hydrogen bonds : bond 0.04841 / 3.17 ( 1215) hydrogen bonds : angle 4.95199 / 3.41 ( 3285) link_BETA1-4 : bond 0.00269 / 0.14 ( 14) link_BETA1-4 : angle 0.93836 / 0.69 ( 42) link_NAG-ASN : bond 0.00377 / 0.26 ( 29) link_NAG-ASN : angle 2.53262 / 1.90 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 192 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8435 (t80) cc_final: 0.8230 (t80) REVERT: A 448 ASN cc_start: 0.8657 (t0) cc_final: 0.7870 (p0) REVERT: B 238 PHE cc_start: 0.7877 (p90) cc_final: 0.7633 (p90) REVERT: B 740 MET cc_start: 0.8805 (OUTLIER) cc_final: 0.8076 (tmm) REVERT: B 1106 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8466 (pt0) REVERT: C 239 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8349 (mm-40) REVERT: C 378 LYS cc_start: 0.9042 (ttmm) cc_final: 0.8821 (ttmm) REVERT: C 1002 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8127 (tm-30) REVERT: D 62 PHE cc_start: 0.8120 (OUTLIER) cc_final: 0.7854 (m-10) REVERT: E 81 MET cc_start: 0.4656 (tmm) cc_final: 0.4114 (tmm) REVERT: E 110 ASP cc_start: 0.7607 (t70) cc_final: 0.7353 (t0) REVERT: G 101 GLU cc_start: 0.8824 (tm-30) cc_final: 0.8430 (tm-30) REVERT: I 12 LYS cc_start: 0.8853 (mtpp) cc_final: 0.8508 (mtpp) REVERT: I 46 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7716 (pt0) REVERT: I 98 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7183 (ttp80) outliers start: 55 outliers final: 47 residues processed: 238 average time/residue: 0.1905 time to fit residues: 74.7618 Evaluate side-chains 239 residues out of total 3306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 819 GLU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 618 THR Chi-restraints excluded: chain C residue 742 ILE Chi-restraints excluded: chain C residue 991 VAL Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 75 ILE Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 46 optimal weight: 10.0000 chunk 195 optimal weight: 0.0970 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 269 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 chunk 355 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 277 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.078102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.050351 restraints weight = 106991.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052436 restraints weight = 49739.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.053750 restraints weight = 31560.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.054594 restraints weight = 23883.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.055102 restraints weight = 20067.850| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 31018 Z= 0.159 Angle : 0.588 11.386 42263 Z= 0.300 Chirality : 0.045 0.436 4861 Planarity : 0.004 0.063 5354 Dihedral : 4.105 19.976 4072 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.88 % Allowed : 14.49 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3725 helix: 2.10 (0.21), residues: 665 sheet: 0.58 (0.16), residues: 982 loop : -1.10 (0.13), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 67 TYR 0.022 0.001 TYR A 904 PHE 0.029 0.001 PHE C 168 TRP 0.011 0.001 TRP C 436 HIS 0.003 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (30927) covalent geometry : angle 0.57550 / 0.30 (42038) SS BOND : bond 0.00330 / 0.20 ( 48) SS BOND : angle 1.20417 / 0.83 ( 96) hydrogen bonds : bond 0.04700 / 3.08 ( 1215) hydrogen bonds : angle 4.91533 / 3.39 ( 3285) link_BETA1-4 : bond 0.00269 / 0.14 ( 14) link_BETA1-4 : angle 0.88499 / 0.65 ( 42) link_NAG-ASN : bond 0.00366 / 0.25 ( 29) link_NAG-ASN : angle 2.48205 / 1.86 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6476.22 seconds wall clock time: 112 minutes 20.58 seconds (6740.58 seconds total)