Starting phenix.real_space_refine on Sun Jul 5 18:21:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.map" model { file = "/net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zce_14628/07_2026/7zce_14628.cif" } 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= 0.105 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 123 5.16 5 C 18753 2.51 5 N 4849 2.21 5 O 5777 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s 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: 29502 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 7897 Classifications: {'peptide': 1011} Link IDs: {'PTRANS': 55, 'TRANS': 955} Chain breaks: 7 Chain: "B" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7891 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 55, 'TRANS': 954} Chain breaks: 7 Chain: "C" Number of atoms: 7891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7891 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 55, 'TRANS': 954} Chain breaks: 7 Chain: "E" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "F" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "G" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1703 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 10, 'TRANS': 214} Chain breaks: 1 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "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: "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: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 7.36, per 1000 atoms: 0.25 Number of scatterers: 29502 At special positions: 0 Unit cell: (138.684, 142.24, 224.028, 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 123 16.00 O 5777 8.00 N 4849 7.00 C 18753 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYS A 132 " - 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=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 132 " - pdb=" SG CYS B 166 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - 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=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.02 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 95 " distance=2.04 Simple disulfide: pdb=" SG CYS E 156 " - pdb=" SG CYS E 222 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 95 " distance=2.03 Simple disulfide: pdb=" SG CYS F 156 " - pdb=" SG CYS F 222 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 95 " distance=2.03 Simple disulfide: pdb=" SG CYS G 156 " - pdb=" SG CYS G 222 " 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 D 1 " - " NAG D 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 709 " " NAG A1302 " - " ASN A1074 " " NAG A1303 " - " ASN A 657 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 61 " " NAG A1307 " - " ASN A 282 " " NAG A1308 " - " ASN A 123 " " NAG A1309 " - " ASN A 343 " " NAG B1301 " - " ASN B 709 " " NAG B1302 " - " ASN B1074 " " NAG B1303 " - " ASN B 657 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 61 " " NAG B1307 " - " ASN B 282 " " NAG B1308 " - " ASN B 123 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 709 " " NAG C1302 " - " ASN C1074 " " NAG C1303 " - " ASN C 657 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 282 " " NAG C1307 " - " ASN C 123 " " NAG C1308 " - " ASN C 61 " " NAG C1309 " - " ASN C 343 " " NAG D 1 " - " ASN A 717 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN A 801 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN B 801 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C1134 " " NAG R 1 " - " ASN C 801 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 1.4 seconds 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6890 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 58 sheets defined 20.2% alpha, 21.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.771A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 4.238A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.521A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 removed outlier: 3.778A pdb=" N SER A 443 " --> pdb=" O ASN A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 747 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 760 through 783 removed outlier: 4.095A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.980A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.679A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.763A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.908A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP A 994 " --> pdb=" O GLU A 990 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.618A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.667A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 4.029A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.599A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.773A pdb=" N SER B 443 " --> pdb=" O ASN B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.795A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.542A 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 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.440A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.175A 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: 5.305A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 removed outlier: 3.544A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP B1146 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.648A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.150A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.632A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.713A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.771A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.741A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 890 " --> pdb=" O THR C 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 886 through 890' Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.881A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.750A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 988 Processing helix chain 'C' and resid 989 through 1033 Processing helix chain 'C' and resid 1142 through 1146 removed outlier: 3.991A pdb=" N ASP C1146 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 removed outlier: 4.155A pdb=" N GLY E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 217 removed outlier: 3.814A pdb=" N PHE E 217 " --> pdb=" O PRO E 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 217 removed outlier: 4.042A pdb=" N PHE F 217 " --> pdb=" O PRO F 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 217 removed outlier: 3.910A pdb=" N PHE G 217 " --> pdb=" O PRO G 214 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.692A pdb=" N THR A 29 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.889A 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 Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 51 removed outlier: 4.026A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'A' and resid 85 through 86 removed outlier: 3.717A pdb=" N LEU A 85 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ILE A 106 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 127 through 128 removed outlier: 4.054A pdb=" N VAL A 127 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER A 172 " --> pdb=" O VAL A 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 131 through 132 removed outlier: 3.692A pdb=" N PHE A 168 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.999A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 648 " --> pdb=" O THR A 645 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AB1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.636A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.502A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 583 through 586 removed outlier: 4.569A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.978A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 removed outlier: 7.103A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.785A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.737A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU B 224 " --> pdb=" O SER B 205 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.712A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.953A pdb=" N LEU B 85 " --> pdb=" O PHE B 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.770A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 325 through 327 removed outlier: 6.775A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU B 546 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.625A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.235A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.777A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 721 " --> pdb=" O THR B1066 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.631A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 788 through 789 removed outlier: 5.589A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.790A pdb=" N VAL B1133 " --> pdb=" O ALA B1080 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.912A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.278A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.844A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLN C 271 " --> pdb=" O PHE C 55 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 85 through 86 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.747A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.675A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 325 through 328 removed outlier: 4.041A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.584A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.514A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.264A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 712 through 728 removed outlier: 7.091A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.654A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AF1, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF2, first strand: chain 'E' and resid 18 through 19 removed outlier: 3.576A pdb=" N THR E 68 " --> pdb=" O GLN E 81 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 57 through 59 removed outlier: 5.387A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR E 33 " --> pdb=" O ASP E 98 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 137 through 139 removed outlier: 3.506A pdb=" N ALA E 152 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP E 204 " --> pdb=" O SER E 201 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 187 through 188 removed outlier: 3.808A pdb=" N SER E 187 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP E 169 " --> pdb=" O LEU E 181 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N TYR E 183 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N LEU E 167 " --> pdb=" O TYR E 183 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL E 219 " --> pdb=" O GLN E 172 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR E 231 " --> pdb=" O GLN E 224 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 18 through 20 removed outlier: 3.757A pdb=" N LEU F 80 " --> pdb=" O LEU F 20 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR F 68 " --> pdb=" O GLN F 81 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 57 through 59 removed outlier: 3.646A pdb=" N SER F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR F 33 " --> pdb=" O ASP F 98 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'F' and resid 137 through 139 removed outlier: 3.505A pdb=" N ALA F 152 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE F 209 " --> pdb=" O ALA F 152 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 187 through 188 removed outlier: 3.995A pdb=" N SER F 187 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP F 169 " --> pdb=" O LEU F 181 " (cutoff:3.500A) removed outlier: 5.604A pdb=" N TYR F 183 " --> pdb=" O LEU F 167 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU F 167 " --> pdb=" O TYR F 183 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR F 231 " --> pdb=" O GLN F 224 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'G' and resid 18 through 20 removed outlier: 3.562A pdb=" N LEU G 80 " --> pdb=" O LEU G 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'G' and resid 57 through 59 removed outlier: 5.305A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TYR G 33 " --> pdb=" O ASP G 98 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'G' and resid 137 through 139 removed outlier: 3.634A pdb=" N ALA G 152 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE G 209 " --> pdb=" O ALA G 152 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'G' and resid 187 through 188 removed outlier: 3.876A pdb=" N SER G 187 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TRP G 169 " --> pdb=" O LEU G 181 " (cutoff:3.500A) removed outlier: 5.765A pdb=" N TYR G 183 " --> pdb=" O LEU G 167 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU G 167 " --> pdb=" O TYR G 183 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR G 231 " --> pdb=" O GLN G 224 " (cutoff:3.500A) 941 hydrogen bonds defined for protein. 2580 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: 7.94 Time building geometry restraints manager: 3.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4779 1.26 - 1.40: 7528 1.40 - 1.54: 17599 1.54 - 1.68: 97 1.68 - 1.82: 153 Bond restraints: 30156 Sorted by residual: bond pdb=" CG PRO E 53 " pdb=" CD PRO E 53 " ideal model delta sigma weight residual 1.503 1.123 0.380 3.40e-02 8.65e+02 1.25e+02 bond pdb=" CB PRO E 53 " pdb=" CG PRO E 53 " ideal model delta sigma weight residual 1.492 1.141 0.351 5.00e-02 4.00e+02 4.94e+01 bond pdb=" C PRO F 174 " pdb=" N GLY F 175 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.43e-02 4.89e+03 1.08e+01 bond pdb=" C PRO G 174 " pdb=" N GLY G 175 " ideal model delta sigma weight residual 1.333 1.380 -0.047 1.57e-02 4.06e+03 8.95e+00 bond pdb=" C PRO E 174 " pdb=" N GLY E 175 " ideal model delta sigma weight residual 1.331 1.373 -0.041 1.46e-02 4.69e+03 7.99e+00 ... (remaining 30151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.55: 41024 9.55 - 19.09: 3 19.09 - 28.64: 2 28.64 - 38.18: 0 38.18 - 47.73: 1 Bond angle restraints: 41030 Sorted by residual: angle pdb=" N PRO E 53 " pdb=" CD PRO E 53 " pdb=" CG PRO E 53 " ideal model delta sigma weight residual 103.20 76.11 27.09 1.50e+00 4.44e-01 3.26e+02 angle pdb=" CB PRO E 53 " pdb=" CG PRO E 53 " pdb=" CD PRO E 53 " ideal model delta sigma weight residual 106.10 153.83 -47.73 3.20e+00 9.77e-02 2.22e+02 angle pdb=" CA PRO E 53 " pdb=" CB PRO E 53 " pdb=" CG PRO E 53 " ideal model delta sigma weight residual 104.50 78.70 25.80 1.90e+00 2.77e-01 1.84e+02 angle pdb=" CA PRO E 53 " pdb=" N PRO E 53 " pdb=" CD PRO E 53 " ideal model delta sigma weight residual 112.00 102.21 9.79 1.40e+00 5.10e-01 4.89e+01 angle pdb=" CA PRO F 193 " pdb=" N PRO F 193 " pdb=" CD PRO F 193 " ideal model delta sigma weight residual 112.00 105.81 6.19 1.40e+00 5.10e-01 1.95e+01 ... (remaining 41025 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 15828 17.96 - 35.91: 1409 35.91 - 53.87: 244 53.87 - 71.82: 49 71.82 - 89.78: 30 Dihedral angle restraints: 17560 sinusoidal: 6823 harmonic: 10737 Sorted by residual: dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual -86.00 -167.53 81.53 1 1.00e+01 1.00e-02 8.19e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 169.09 -76.09 1 1.00e+01 1.00e-02 7.29e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual -86.00 -14.83 -71.17 1 1.00e+01 1.00e-02 6.50e+01 ... (remaining 17557 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4118 0.066 - 0.132: 641 0.132 - 0.198: 29 0.198 - 0.264: 2 0.264 - 0.330: 2 Chirality restraints: 4792 Sorted by residual: chirality pdb=" C1 NAG A1306 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1306 " pdb=" O5 NAG A1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 657 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.50e+00 ... (remaining 4789 not shown) Planarity restraints: 5287 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 82 " 0.072 5.00e-02 4.00e+02 1.07e-01 1.83e+01 pdb=" N PRO C 83 " -0.185 5.00e-02 4.00e+02 pdb=" CA PRO C 83 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO C 83 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE F 192 " -0.061 5.00e-02 4.00e+02 8.89e-02 1.26e+01 pdb=" N PRO F 193 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO F 193 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO F 193 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 52 " -0.050 5.00e-02 4.00e+02 6.94e-02 7.72e+00 pdb=" N PRO E 53 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO E 53 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 53 " -0.038 5.00e-02 4.00e+02 ... (remaining 5284 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 336 2.64 - 3.21: 26239 3.21 - 3.77: 42052 3.77 - 4.34: 56607 4.34 - 4.90: 95397 Nonbonded interactions: 220631 Sorted by model distance: nonbonded pdb=" OH TYR B 756 " pdb=" OD2 ASP B 994 " model vdw 2.080 3.040 nonbonded pdb=" O LEU A 455 " pdb=" OH TYR G 33 " model vdw 2.117 3.040 nonbonded pdb=" OH TYR C 421 " pdb=" O PRO E 53 " model vdw 2.174 3.040 nonbonded pdb=" O LEU B 455 " pdb=" OH TYR F 33 " model vdw 2.178 3.040 nonbonded pdb=" OD1 ASN C 280 " pdb=" OG1 THR C 286 " model vdw 2.202 3.040 ... (remaining 220626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 1146 or resid 1301 through 1309)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 6.570 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: 0.050 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.340 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.380 30251 Z= 0.190 Angle : 0.717 47.728 41271 Z= 0.364 Chirality : 0.046 0.330 4792 Planarity : 0.005 0.107 5248 Dihedral : 14.047 89.778 10538 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.03 % Allowed : 0.47 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.09 (0.14), residues: 3646 helix: 2.46 (0.22), residues: 583 sheet: 0.05 (0.18), residues: 886 loop : -2.11 (0.12), residues: 2177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 765 TYR 0.017 0.001 TYR E 52 PHE 0.029 0.001 PHE C 906 TRP 0.014 0.001 TRP B 886 HIS 0.009 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.19 (30156) covalent geometry : angle 0.70067 / 0.36 (41030) SS BOND : bond 0.00281 / 0.18 ( 44) SS BOND : angle 1.35667 / 0.89 ( 88) hydrogen bonds : bond 0.14261 / 8.89 ( 939) hydrogen bonds : angle 5.87151 / 3.98 ( 2580) link_BETA1-4 : bond 0.00422 / 0.27 ( 12) link_BETA1-4 : angle 1.81405 / 1.22 ( 36) link_NAG-ASN : bond 0.00421 / 0.30 ( 39) link_NAG-ASN : angle 2.57385 / 1.68 ( 117) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 200 TYR cc_start: 0.7022 (m-80) cc_final: 0.6257 (m-80) REVERT: C 123 ASN cc_start: 0.4455 (p0) cc_final: 0.4215 (p0) REVERT: E 38 ARG cc_start: 0.3949 (ttm170) cc_final: 0.3512 (ttt-90) REVERT: E 86 ARG cc_start: 0.4310 (ptt180) cc_final: 0.3735 (tpp80) REVERT: E 169 TRP cc_start: 0.7123 (m100) cc_final: 0.6547 (m-10) REVERT: G 66 ARG cc_start: 0.2448 (ptt180) cc_final: 0.1807 (tpt90) REVERT: G 82 MET cc_start: 0.0145 (mmt) cc_final: -0.1059 (mmm) outliers start: 1 outliers final: 0 residues processed: 209 average time/residue: 0.2297 time to fit residues: 74.3788 Evaluate side-chains 148 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 197 optimal weight: 0.5980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN E 3 GLN E 110 GLN F 73 ASN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 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 = 0.4356 r_free = 0.4356 target = 0.178655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108124 restraints weight = 53899.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109096 restraints weight = 34230.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108400 restraints weight = 25628.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.108741 restraints weight = 24155.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.108906 restraints weight = 22889.908| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3365 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3365 r_free = 0.3365 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3365 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.0778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30251 Z= 0.145 Angle : 0.625 13.597 41271 Z= 0.307 Chirality : 0.045 0.352 4792 Planarity : 0.005 0.070 5248 Dihedral : 4.470 29.640 3982 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.56 % Allowed : 7.09 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.12 (0.14), residues: 3646 helix: 2.41 (0.22), residues: 584 sheet: -0.09 (0.17), residues: 929 loop : -2.10 (0.13), residues: 2133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 357 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.001 PHE C 906 TRP 0.016 0.001 TRP A 353 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.14 (30156) covalent geometry : angle 0.60844 / 0.30 (41030) SS BOND : bond 0.00300 / 0.19 ( 44) SS BOND : angle 1.19993 / 0.79 ( 88) hydrogen bonds : bond 0.05097 / 3.35 ( 939) hydrogen bonds : angle 5.13528 / 3.47 ( 2580) link_BETA1-4 : bond 0.00448 / 0.29 ( 12) link_BETA1-4 : angle 1.57947 / 1.07 ( 36) link_NAG-ASN : bond 0.00425 / 0.30 ( 39) link_NAG-ASN : angle 2.46318 / 1.59 ( 117) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7247 (t0) cc_final: 0.7005 (t0) REVERT: B 168 PHE cc_start: 0.6453 (t80) cc_final: 0.6111 (t80) REVERT: B 200 TYR cc_start: 0.7258 (m-80) cc_final: 0.6481 (m-80) REVERT: B 211 ASN cc_start: 0.5987 (m-40) cc_final: 0.5388 (m-40) REVERT: C 401 VAL cc_start: 0.4403 (OUTLIER) cc_final: 0.4107 (t) REVERT: E 38 ARG cc_start: 0.3930 (ttm170) cc_final: 0.3493 (ttt-90) REVERT: E 86 ARG cc_start: 0.4248 (ptt180) cc_final: 0.3840 (tpp80) REVERT: G 82 MET cc_start: 0.0315 (mmt) cc_final: 0.0027 (mmm) REVERT: G 144 LEU cc_start: 0.0579 (pp) cc_final: -0.0504 (mp) outliers start: 18 outliers final: 10 residues processed: 181 average time/residue: 0.2145 time to fit residues: 61.6553 Evaluate side-chains 160 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain E residue 2 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 288 optimal weight: 4.9990 chunk 155 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 295 optimal weight: 1.9990 chunk 129 optimal weight: 20.0000 chunk 353 optimal weight: 2.9990 chunk 133 optimal weight: 10.0000 chunk 169 optimal weight: 0.1980 chunk 191 optimal weight: 0.6980 chunk 323 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN ** G 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 172 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.177311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106593 restraints weight = 53903.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.106990 restraints weight = 32918.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.106893 restraints weight = 23968.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107481 restraints weight = 22740.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107575 restraints weight = 22220.490| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30251 Z= 0.161 Angle : 0.617 11.466 41271 Z= 0.304 Chirality : 0.045 0.349 4792 Planarity : 0.005 0.059 5248 Dihedral : 4.509 28.533 3982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 0.93 % Allowed : 10.42 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.14), residues: 3646 helix: 2.31 (0.22), residues: 584 sheet: -0.19 (0.17), residues: 919 loop : -2.09 (0.13), residues: 2143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.021 0.001 TYR C 904 PHE 0.019 0.001 PHE B 906 TRP 0.019 0.001 TRP A 353 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (30156) covalent geometry : angle 0.60044 / 0.30 (41030) SS BOND : bond 0.00324 / 0.21 ( 44) SS BOND : angle 1.28267 / 0.85 ( 88) hydrogen bonds : bond 0.05465 / 3.58 ( 939) hydrogen bonds : angle 5.01924 / 3.39 ( 2580) link_BETA1-4 : bond 0.00380 / 0.24 ( 12) link_BETA1-4 : angle 1.58531 / 1.07 ( 36) link_NAG-ASN : bond 0.00438 / 0.30 ( 39) link_NAG-ASN : angle 2.44307 / 1.58 ( 117) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 159 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7255 (t0) cc_final: 0.7020 (t0) REVERT: B 200 TYR cc_start: 0.7229 (m-80) cc_final: 0.6376 (m-80) REVERT: B 211 ASN cc_start: 0.6055 (m-40) cc_final: 0.5599 (m-40) REVERT: B 1041 ASP cc_start: 0.8253 (t0) cc_final: 0.7934 (t0) REVERT: C 123 ASN cc_start: 0.4414 (p0) cc_final: 0.4057 (p0) REVERT: C 130 LYS cc_start: 0.7747 (mtpt) cc_final: 0.7468 (ttmt) REVERT: E 33 TYR cc_start: 0.6492 (m-80) cc_final: 0.6252 (m-80) REVERT: E 38 ARG cc_start: 0.3859 (ttm170) cc_final: 0.3447 (ttt-90) REVERT: E 86 ARG cc_start: 0.4227 (ptt180) cc_final: 0.3740 (tpp80) REVERT: F 93 TYR cc_start: 0.3582 (OUTLIER) cc_final: 0.2968 (t80) REVERT: F 224 GLN cc_start: 0.2252 (OUTLIER) cc_final: 0.1866 (tp40) REVERT: G 172 GLN cc_start: -0.2566 (OUTLIER) cc_final: -0.2967 (tt0) outliers start: 30 outliers final: 17 residues processed: 186 average time/residue: 0.1953 time to fit residues: 60.2252 Evaluate side-chains 164 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 93 TYR Chi-restraints excluded: chain F residue 224 GLN Chi-restraints excluded: chain G residue 172 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 342 optimal weight: 0.9980 chunk 325 optimal weight: 0.5980 chunk 360 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 311 optimal weight: 40.0000 chunk 77 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 63 optimal weight: 0.0010 chunk 72 optimal weight: 3.9990 overall best weight: 1.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 710 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 907 ASN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.177771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.107231 restraints weight = 53456.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.108029 restraints weight = 34343.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107436 restraints weight = 24358.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.107738 restraints weight = 25336.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107856 restraints weight = 23109.122| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30251 Z= 0.133 Angle : 0.595 13.208 41271 Z= 0.291 Chirality : 0.045 0.351 4792 Planarity : 0.004 0.053 5248 Dihedral : 4.418 29.134 3982 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 1.24 % Allowed : 12.48 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 3646 helix: 2.42 (0.22), residues: 583 sheet: -0.20 (0.17), residues: 913 loop : -2.06 (0.13), residues: 2150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 357 TYR 0.022 0.001 TYR G 52 PHE 0.017 0.001 PHE G 58 TRP 0.017 0.001 TRP A 353 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (30156) covalent geometry : angle 0.57838 / 0.29 (41030) SS BOND : bond 0.00265 / 0.17 ( 44) SS BOND : angle 1.16806 / 0.78 ( 88) hydrogen bonds : bond 0.05042 / 3.31 ( 939) hydrogen bonds : angle 4.89489 / 3.31 ( 2580) link_BETA1-4 : bond 0.00381 / 0.24 ( 12) link_BETA1-4 : angle 1.55777 / 1.06 ( 36) link_NAG-ASN : bond 0.00412 / 0.29 ( 39) link_NAG-ASN : angle 2.37341 / 1.52 ( 117) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8424 (mtt) cc_final: 0.8073 (mtt) REVERT: B 53 ASP cc_start: 0.7333 (t0) cc_final: 0.7069 (t0) REVERT: B 200 TYR cc_start: 0.7314 (m-80) cc_final: 0.6436 (m-80) REVERT: B 211 ASN cc_start: 0.6246 (m-40) cc_final: 0.5791 (m-40) REVERT: B 495 TYR cc_start: 0.5532 (OUTLIER) cc_final: 0.4738 (m-10) REVERT: B 1041 ASP cc_start: 0.8320 (t0) cc_final: 0.7935 (t0) REVERT: C 123 ASN cc_start: 0.4539 (p0) cc_final: 0.4218 (p0) REVERT: C 130 LYS cc_start: 0.7636 (mtpt) cc_final: 0.7362 (ttmt) REVERT: E 38 ARG cc_start: 0.3852 (ttm170) cc_final: 0.3487 (ttt-90) REVERT: E 86 ARG cc_start: 0.4277 (ptt180) cc_final: 0.3802 (tpp80) REVERT: F 93 TYR cc_start: 0.3449 (OUTLIER) cc_final: 0.2812 (t80) outliers start: 40 outliers final: 22 residues processed: 192 average time/residue: 0.1876 time to fit residues: 60.1407 Evaluate side-chains 167 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 167 optimal weight: 0.9990 chunk 353 optimal weight: 8.9990 chunk 149 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 208 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 363 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 290 optimal weight: 0.9990 chunk 181 optimal weight: 2.9990 chunk 344 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 955 ASN C1106 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.175931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107119 restraints weight = 53614.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104470 restraints weight = 32604.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.104230 restraints weight = 31779.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104780 restraints weight = 27177.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.105035 restraints weight = 23338.444| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30251 Z= 0.188 Angle : 0.637 12.057 41271 Z= 0.313 Chirality : 0.046 0.352 4792 Planarity : 0.005 0.054 5248 Dihedral : 4.570 28.550 3982 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 1.93 % Allowed : 13.38 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.26 (0.14), residues: 3646 helix: 2.23 (0.21), residues: 588 sheet: -0.31 (0.17), residues: 932 loop : -2.10 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.020 0.001 TYR C 904 PHE 0.020 0.001 PHE A 87 TRP 0.016 0.001 TRP B 105 HIS 0.008 0.001 HIS B 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.19 (30156) covalent geometry : angle 0.62034 / 0.31 (41030) SS BOND : bond 0.00327 / 0.21 ( 44) SS BOND : angle 1.35622 / 0.92 ( 88) hydrogen bonds : bond 0.05791 / 3.80 ( 939) hydrogen bonds : angle 4.96753 / 3.35 ( 2580) link_BETA1-4 : bond 0.00341 / 0.21 ( 12) link_BETA1-4 : angle 1.60654 / 1.08 ( 36) link_NAG-ASN : bond 0.00425 / 0.29 ( 39) link_NAG-ASN : angle 2.42383 / 1.57 ( 117) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 146 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 LYS cc_start: 0.8139 (ptmm) cc_final: 0.7619 (ptmm) REVERT: B 53 ASP cc_start: 0.7427 (t0) cc_final: 0.7167 (t0) REVERT: B 200 TYR cc_start: 0.7425 (m-80) cc_final: 0.6449 (m-80) REVERT: B 211 ASN cc_start: 0.6268 (m-40) cc_final: 0.5867 (m-40) REVERT: B 495 TYR cc_start: 0.5566 (OUTLIER) cc_final: 0.4446 (m-10) REVERT: B 1041 ASP cc_start: 0.8348 (t0) cc_final: 0.7953 (t0) REVERT: C 123 ASN cc_start: 0.4719 (p0) cc_final: 0.4419 (p0) REVERT: C 130 LYS cc_start: 0.7638 (mtpt) cc_final: 0.7151 (ttmt) REVERT: C 134 PHE cc_start: 0.4823 (m-80) cc_final: 0.3374 (m-80) REVERT: C 226 LEU cc_start: 0.8733 (OUTLIER) cc_final: 0.8524 (tt) REVERT: E 33 TYR cc_start: 0.6331 (m-80) cc_final: 0.6122 (m-80) REVERT: E 38 ARG cc_start: 0.3803 (ttm170) cc_final: 0.3457 (ttt-90) REVERT: E 86 ARG cc_start: 0.4323 (ptt180) cc_final: 0.3873 (tpp80) REVERT: F 93 TYR cc_start: 0.3490 (OUTLIER) cc_final: 0.2929 (t80) outliers start: 62 outliers final: 42 residues processed: 203 average time/residue: 0.1743 time to fit residues: 59.4230 Evaluate side-chains 185 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 140 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 266 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 314 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 244 optimal weight: 6.9990 chunk 134 optimal weight: 0.0170 chunk 361 optimal weight: 50.0000 chunk 150 optimal weight: 0.9990 chunk 267 optimal weight: 0.7980 chunk 29 optimal weight: 20.0000 overall best weight: 1.5624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 957 GLN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 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 = 0.4333 r_free = 0.4333 target = 0.176703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.107152 restraints weight = 53428.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107066 restraints weight = 33799.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.106376 restraints weight = 25245.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106701 restraints weight = 24376.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.106717 restraints weight = 23480.501| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30251 Z= 0.146 Angle : 0.603 14.104 41271 Z= 0.295 Chirality : 0.045 0.353 4792 Planarity : 0.004 0.052 5248 Dihedral : 4.507 28.734 3982 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 1.84 % Allowed : 14.28 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.21 (0.14), residues: 3646 helix: 2.34 (0.22), residues: 587 sheet: -0.29 (0.17), residues: 927 loop : -2.09 (0.13), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.020 0.001 TYR C 904 PHE 0.016 0.001 PHE A 93 TRP 0.015 0.001 TRP B 105 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (30156) covalent geometry : angle 0.58606 / 0.29 (41030) SS BOND : bond 0.00274 / 0.18 ( 44) SS BOND : angle 1.37642 / 0.93 ( 88) hydrogen bonds : bond 0.05145 / 3.38 ( 939) hydrogen bonds : angle 4.82505 / 3.25 ( 2580) link_BETA1-4 : bond 0.00391 / 0.24 ( 12) link_BETA1-4 : angle 1.57873 / 1.07 ( 36) link_NAG-ASN : bond 0.00406 / 0.28 ( 39) link_NAG-ASN : angle 2.35039 / 1.51 ( 117) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 153 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7414 (t0) cc_final: 0.7163 (t0) REVERT: B 168 PHE cc_start: 0.6367 (t80) cc_final: 0.6019 (t80) REVERT: B 200 TYR cc_start: 0.7364 (m-80) cc_final: 0.6397 (m-80) REVERT: B 380 TYR cc_start: 0.6558 (OUTLIER) cc_final: 0.5862 (m-80) REVERT: B 1041 ASP cc_start: 0.8337 (t0) cc_final: 0.7918 (t0) REVERT: C 123 ASN cc_start: 0.4795 (p0) cc_final: 0.4455 (p0) REVERT: C 130 LYS cc_start: 0.7665 (mtpt) cc_final: 0.7155 (ttmt) REVERT: C 134 PHE cc_start: 0.4725 (m-80) cc_final: 0.3285 (m-80) REVERT: E 38 ARG cc_start: 0.3797 (ttm170) cc_final: 0.3454 (ttt-90) REVERT: E 86 ARG cc_start: 0.4295 (ptt180) cc_final: 0.3838 (tpp80) REVERT: F 93 TYR cc_start: 0.3601 (OUTLIER) cc_final: 0.2938 (t80) outliers start: 59 outliers final: 41 residues processed: 206 average time/residue: 0.1811 time to fit residues: 62.7671 Evaluate side-chains 191 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 380 TYR Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 275 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 338 optimal weight: 0.1980 chunk 46 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 298 optimal weight: 0.0670 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 226 optimal weight: 3.9990 overall best weight: 1.0322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 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 = 0.4342 r_free = 0.4342 target = 0.177485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108595 restraints weight = 53545.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.107401 restraints weight = 34418.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107149 restraints weight = 27052.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107447 restraints weight = 25587.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107627 restraints weight = 24035.102| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30251 Z= 0.120 Angle : 0.586 13.712 41271 Z= 0.286 Chirality : 0.044 0.351 4792 Planarity : 0.004 0.057 5248 Dihedral : 4.393 27.893 3982 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.23 % Favored : 91.77 % Rotamer: Outliers : 1.74 % Allowed : 15.18 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.14), residues: 3646 helix: 2.44 (0.22), residues: 593 sheet: -0.25 (0.17), residues: 919 loop : -2.04 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 97 TYR 0.017 0.001 TYR C 904 PHE 0.019 0.001 PHE C 329 TRP 0.016 0.001 TRP B 105 HIS 0.003 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 (30156) covalent geometry : angle 0.56968 / 0.28 (41030) SS BOND : bond 0.00282 / 0.19 ( 44) SS BOND : angle 1.24654 / 0.84 ( 88) hydrogen bonds : bond 0.04679 / 3.08 ( 939) hydrogen bonds : angle 4.68389 / 3.16 ( 2580) link_BETA1-4 : bond 0.00452 / 0.26 ( 12) link_BETA1-4 : angle 1.54846 / 1.05 ( 36) link_NAG-ASN : bond 0.00384 / 0.26 ( 39) link_NAG-ASN : angle 2.28461 / 1.47 ( 117) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8426 (mtt) cc_final: 0.8056 (mtt) REVERT: B 53 ASP cc_start: 0.7416 (t0) cc_final: 0.7213 (t0) REVERT: B 168 PHE cc_start: 0.6314 (t80) cc_final: 0.5969 (t80) REVERT: B 200 TYR cc_start: 0.7215 (m-80) cc_final: 0.6306 (m-80) REVERT: B 1041 ASP cc_start: 0.8335 (t0) cc_final: 0.7867 (t0) REVERT: C 123 ASN cc_start: 0.4846 (p0) cc_final: 0.4513 (p0) REVERT: C 130 LYS cc_start: 0.7781 (mtpt) cc_final: 0.7270 (ttmt) REVERT: C 134 PHE cc_start: 0.4648 (m-80) cc_final: 0.3190 (m-80) REVERT: C 226 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8544 (tt) REVERT: C 948 LEU cc_start: 0.7597 (OUTLIER) cc_final: 0.7211 (mt) REVERT: E 38 ARG cc_start: 0.3764 (ttm170) cc_final: 0.3440 (ttt-90) REVERT: E 86 ARG cc_start: 0.3855 (ptt180) cc_final: 0.3556 (tpp80) REVERT: F 93 TYR cc_start: 0.3518 (OUTLIER) cc_final: 0.2913 (t80) outliers start: 56 outliers final: 39 residues processed: 203 average time/residue: 0.1835 time to fit residues: 62.5261 Evaluate side-chains 191 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 149 time to evaluate : 1.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 132 CYS Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 111 optimal weight: 20.0000 chunk 194 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 114 optimal weight: 9.9990 chunk 143 optimal weight: 30.0000 chunk 186 optimal weight: 5.9990 chunk 363 optimal weight: 0.0000 chunk 241 optimal weight: 30.0000 chunk 198 optimal weight: 2.9990 chunk 57 optimal weight: 0.0570 overall best weight: 1.2108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 172 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 = 0.4339 r_free = 0.4339 target = 0.177231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.108539 restraints weight = 53712.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107609 restraints weight = 35149.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.107425 restraints weight = 25164.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107669 restraints weight = 24338.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.107782 restraints weight = 23262.696| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30251 Z= 0.126 Angle : 0.590 13.799 41271 Z= 0.288 Chirality : 0.044 0.348 4792 Planarity : 0.004 0.057 5248 Dihedral : 4.370 28.146 3982 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.80 % Allowed : 15.87 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.14), residues: 3646 helix: 2.44 (0.22), residues: 592 sheet: -0.26 (0.17), residues: 928 loop : -2.05 (0.13), residues: 2126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 97 TYR 0.020 0.001 TYR C 904 PHE 0.035 0.001 PHE A 168 TRP 0.014 0.001 TRP B 105 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (30156) covalent geometry : angle 0.57480 / 0.28 (41030) SS BOND : bond 0.00247 / 0.16 ( 44) SS BOND : angle 1.24202 / 0.85 ( 88) hydrogen bonds : bond 0.04754 / 3.13 ( 939) hydrogen bonds : angle 4.68271 / 3.15 ( 2580) link_BETA1-4 : bond 0.00402 / 0.25 ( 12) link_BETA1-4 : angle 1.53022 / 1.03 ( 36) link_NAG-ASN : bond 0.00384 / 0.26 ( 39) link_NAG-ASN : angle 2.25837 / 1.46 ( 117) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8470 (mtt) cc_final: 0.8088 (mtt) REVERT: B 53 ASP cc_start: 0.7422 (t0) cc_final: 0.7221 (t0) REVERT: B 200 TYR cc_start: 0.7213 (m-80) cc_final: 0.6259 (m-80) REVERT: B 1041 ASP cc_start: 0.8351 (t0) cc_final: 0.7933 (t0) REVERT: C 123 ASN cc_start: 0.4822 (p0) cc_final: 0.4494 (p0) REVERT: C 130 LYS cc_start: 0.7790 (mtpt) cc_final: 0.7431 (tttt) REVERT: C 134 PHE cc_start: 0.4804 (m-80) cc_final: 0.4241 (m-80) REVERT: C 226 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8528 (tt) REVERT: C 948 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7264 (mt) REVERT: E 34 MET cc_start: 0.6909 (mmm) cc_final: 0.6530 (mmm) REVERT: E 38 ARG cc_start: 0.3528 (ttm170) cc_final: 0.3252 (ttt-90) REVERT: E 86 ARG cc_start: 0.3846 (ptt180) cc_final: 0.3552 (tpp80) REVERT: E 195 ARG cc_start: 0.4311 (ptm160) cc_final: 0.3790 (ttm110) REVERT: F 93 TYR cc_start: 0.3614 (OUTLIER) cc_final: 0.2912 (t80) outliers start: 58 outliers final: 45 residues processed: 206 average time/residue: 0.1855 time to fit residues: 63.9111 Evaluate side-chains 197 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 149 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 299 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 211 optimal weight: 9.9990 chunk 180 optimal weight: 5.9990 chunk 294 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 315 optimal weight: 0.0370 chunk 191 optimal weight: 0.4980 chunk 224 optimal weight: 0.7980 chunk 354 optimal weight: 30.0000 chunk 263 optimal weight: 0.9990 chunk 85 optimal weight: 0.4980 chunk 321 optimal weight: 30.0000 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.178612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108600 restraints weight = 53494.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.108148 restraints weight = 32647.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109226 restraints weight = 26388.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.109463 restraints weight = 20861.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.109926 restraints weight = 19910.372| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3386 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30251 Z= 0.099 Angle : 0.570 13.630 41271 Z= 0.278 Chirality : 0.044 0.346 4792 Planarity : 0.004 0.056 5248 Dihedral : 4.206 27.314 3982 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.37 % Allowed : 16.46 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.14), residues: 3646 helix: 2.61 (0.22), residues: 592 sheet: -0.18 (0.17), residues: 907 loop : -1.99 (0.13), residues: 2147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 97 TYR 0.017 0.001 TYR A 170 PHE 0.022 0.001 PHE A 168 TRP 0.012 0.001 TRP B 105 HIS 0.003 0.000 HIS B1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (30156) covalent geometry : angle 0.55581 / 0.27 (41030) SS BOND : bond 0.00212 / 0.13 ( 44) SS BOND : angle 1.16657 / 0.78 ( 88) hydrogen bonds : bond 0.04047 / 2.67 ( 939) hydrogen bonds : angle 4.53878 / 3.05 ( 2580) link_BETA1-4 : bond 0.00419 / 0.25 ( 12) link_BETA1-4 : angle 1.49992 / 1.01 ( 36) link_NAG-ASN : bond 0.00388 / 0.26 ( 39) link_NAG-ASN : angle 2.17080 / 1.39 ( 117) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 1.182 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 869 MET cc_start: 0.8331 (mtt) cc_final: 0.7931 (mtt) REVERT: B 200 TYR cc_start: 0.7199 (m-80) cc_final: 0.6285 (m-80) REVERT: B 211 ASN cc_start: 0.6262 (m-40) cc_final: 0.5871 (m-40) REVERT: B 380 TYR cc_start: 0.6590 (m-80) cc_final: 0.5962 (m-80) REVERT: B 1041 ASP cc_start: 0.8334 (t0) cc_final: 0.7898 (t0) REVERT: C 123 ASN cc_start: 0.4829 (p0) cc_final: 0.4472 (p0) REVERT: C 130 LYS cc_start: 0.7778 (mtpt) cc_final: 0.7285 (tttt) REVERT: C 226 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8551 (tt) REVERT: C 948 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7028 (mt) REVERT: E 82 MET cc_start: 0.0034 (mtt) cc_final: -0.0228 (mtt) REVERT: E 86 ARG cc_start: 0.3856 (ptt180) cc_final: 0.3502 (tpp80) REVERT: E 195 ARG cc_start: 0.4060 (OUTLIER) cc_final: 0.3634 (ttm110) REVERT: F 93 TYR cc_start: 0.3557 (OUTLIER) cc_final: 0.2934 (t80) outliers start: 44 outliers final: 34 residues processed: 200 average time/residue: 0.1888 time to fit residues: 62.8433 Evaluate side-chains 192 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 154 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 260 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 183 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1005 GLN B1135 ASN E 6 GLN F 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.176079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104775 restraints weight = 53290.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.105414 restraints weight = 36282.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.105142 restraints weight = 25379.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.105493 restraints weight = 23030.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.105578 restraints weight = 23003.183| |-----------------------------------------------------------------------------| r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 30251 Z= 0.171 Angle : 0.623 13.579 41271 Z= 0.305 Chirality : 0.046 0.342 4792 Planarity : 0.004 0.058 5248 Dihedral : 4.430 27.925 3982 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 1.49 % Allowed : 16.68 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3646 helix: 2.35 (0.22), residues: 592 sheet: -0.31 (0.17), residues: 953 loop : -2.05 (0.13), residues: 2101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1039 TYR 0.024 0.001 TYR C 904 PHE 0.021 0.001 PHE A 168 TRP 0.015 0.001 TRP B 105 HIS 0.006 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.17 (30156) covalent geometry : angle 0.60679 / 0.30 (41030) SS BOND : bond 0.00355 / 0.22 ( 44) SS BOND : angle 1.63635 / 1.07 ( 88) hydrogen bonds : bond 0.05342 / 3.50 ( 939) hydrogen bonds : angle 4.74768 / 3.19 ( 2580) link_BETA1-4 : bond 0.00369 / 0.24 ( 12) link_BETA1-4 : angle 1.54309 / 1.03 ( 36) link_NAG-ASN : bond 0.00389 / 0.26 ( 39) link_NAG-ASN : angle 2.26205 / 1.48 ( 117) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7292 Ramachandran restraints generated. 3646 Oldfield, 0 Emsley, 3646 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 148 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8556 (mtt) cc_final: 0.8212 (mtt) REVERT: B 200 TYR cc_start: 0.7305 (m-80) cc_final: 0.6276 (m-80) REVERT: B 380 TYR cc_start: 0.6756 (m-80) cc_final: 0.6098 (m-80) REVERT: B 436 TRP cc_start: 0.6794 (m-90) cc_final: 0.6054 (m-90) REVERT: B 1041 ASP cc_start: 0.8357 (t0) cc_final: 0.7853 (t0) REVERT: C 123 ASN cc_start: 0.4932 (p0) cc_final: 0.4606 (p0) REVERT: C 130 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7450 (tttt) REVERT: C 134 PHE cc_start: 0.5009 (m-80) cc_final: 0.4383 (m-80) REVERT: C 226 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8518 (tt) REVERT: E 82 MET cc_start: 0.0049 (mtt) cc_final: -0.0195 (mtt) REVERT: E 86 ARG cc_start: 0.3890 (ptt180) cc_final: 0.3585 (tpp80) REVERT: E 195 ARG cc_start: 0.3973 (OUTLIER) cc_final: 0.3479 (ttm110) REVERT: F 93 TYR cc_start: 0.3657 (OUTLIER) cc_final: 0.3000 (t80) outliers start: 48 outliers final: 40 residues processed: 190 average time/residue: 0.1848 time to fit residues: 58.9218 Evaluate side-chains 188 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 762 GLN Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 495 TYR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 912 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 572 THR Chi-restraints excluded: chain C residue 585 LEU Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1129 VAL Chi-restraints excluded: chain C residue 1132 ILE Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 182 ILE Chi-restraints excluded: chain E residue 195 ARG Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 93 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 115 optimal weight: 6.9990 chunk 346 optimal weight: 20.0000 chunk 230 optimal weight: 0.0000 chunk 239 optimal weight: 10.0000 chunk 244 optimal weight: 10.0000 chunk 145 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 275 optimal weight: 0.9990 chunk 316 optimal weight: 7.9990 chunk 81 optimal weight: 1.9990 chunk 246 optimal weight: 9.9990 overall best weight: 2.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 519 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN ** C 422 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.174190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.102869 restraints weight = 53614.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.103405 restraints weight = 33671.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.103016 restraints weight = 23788.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.103639 restraints weight = 23202.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.103898 restraints weight = 22005.021| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 30251 Z= 0.224 Angle : 0.678 13.485 41271 Z= 0.335 Chirality : 0.047 0.340 4792 Planarity : 0.005 0.062 5248 Dihedral : 4.758 28.541 3982 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 1.56 % Allowed : 16.93 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.14), residues: 3646 helix: 1.99 (0.21), residues: 598 sheet: -0.43 (0.17), residues: 952 loop : -2.15 (0.13), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C1039 TYR 0.028 0.002 TYR C 904 PHE 0.023 0.002 PHE B 168 TRP 0.020 0.002 TRP B 105 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.22 (30156) covalent geometry : angle 0.66128 / 0.33 (41030) SS BOND : bond 0.00373 / 0.24 ( 44) SS BOND : angle 1.74129 / 1.17 ( 88) hydrogen bonds : bond 0.06324 / 4.15 ( 939) hydrogen bonds : angle 5.02287 / 3.38 ( 2580) link_BETA1-4 : bond 0.00367 / 0.24 ( 12) link_BETA1-4 : angle 1.65149 / 1.10 ( 36) link_NAG-ASN : bond 0.00433 / 0.30 ( 39) link_NAG-ASN : angle 2.39445 / 1.57 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5928.20 seconds wall clock time: 103 minutes 15.80 seconds (6195.80 seconds total)