Starting phenix.real_space_refine on Fri Mar 6 08:33:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zce_14628/03_2026/7zce_14628.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zce_14628/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zce_14628/03_2026/7zce_14628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zce_14628/03_2026/7zce_14628.map" model { file = "/net/cci-nas-00/data/ceres_data/7zce_14628/03_2026/7zce_14628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zce_14628/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 27 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 dihedrals: 27 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 dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.24, per 1000 atoms: 0.21 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: 2.82 Conformation dependent library (CDL) restraints added in 1.2 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: 1.43 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: 6.57 Time building geometry restraints manager: 3.56 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 - 23.06: 17351 23.06 - 46.11: 1057 46.11 - 69.17: 140 69.17 - 92.22: 44 92.22 - 115.28: 39 Dihedral angle restraints: 18631 sinusoidal: 7894 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 18628 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: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 27.680 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 15.542 115.277 11609 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 covalent geometry : bond 0.00472 (30156) covalent geometry : angle 0.70067 (41030) SS BOND : bond 0.00281 ( 44) SS BOND : angle 1.35667 ( 88) hydrogen bonds : bond 0.14261 ( 939) hydrogen bonds : angle 5.87151 ( 2580) link_BETA1-4 : bond 0.00422 ( 12) link_BETA1-4 : angle 1.81405 ( 36) link_NAG-ASN : bond 0.00421 ( 39) link_NAG-ASN : angle 2.57385 ( 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 : 0.836 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: 0.2272 time to fit residues: 73.1189 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 : 1.079 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.178689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.107521 restraints weight = 53898.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109537 restraints weight = 33615.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.108859 restraints weight = 22607.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109270 restraints weight = 23189.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109251 restraints weight = 22711.719| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 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 = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30251 Z= 0.145 Angle : 0.634 13.807 41271 Z= 0.309 Chirality : 0.046 0.369 4792 Planarity : 0.005 0.070 5248 Dihedral : 10.531 105.953 5053 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 0.53 % Allowed : 6.94 % Favored : 92.53 % 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: -1.11 (0.14), residues: 3646 helix: 2.43 (0.22), residues: 583 sheet: -0.07 (0.17), residues: 936 loop : -2.11 (0.13), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 765 TYR 0.018 0.001 TYR B1067 PHE 0.020 0.001 PHE C 906 TRP 0.015 0.001 TRP A 353 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00343 (30156) covalent geometry : angle 0.61675 (41030) SS BOND : bond 0.00305 ( 44) SS BOND : angle 1.19999 ( 88) hydrogen bonds : bond 0.05147 ( 939) hydrogen bonds : angle 5.14643 ( 2580) link_BETA1-4 : bond 0.00515 ( 12) link_BETA1-4 : angle 1.84833 ( 36) link_NAG-ASN : bond 0.00422 ( 39) link_NAG-ASN : angle 2.54120 ( 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: 17 poor density : 167 time to evaluate : 1.091 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: 0.7234 (t0) cc_final: 0.7001 (t0) REVERT: B 168 PHE cc_start: 0.6433 (t80) cc_final: 0.6098 (t80) REVERT: B 200 TYR cc_start: 0.7299 (m-80) cc_final: 0.6492 (m-80) REVERT: B 211 ASN cc_start: 0.5991 (m-40) cc_final: 0.5404 (m-40) REVERT: E 38 ARG cc_start: 0.3952 (ttm170) cc_final: 0.3514 (ttt-90) REVERT: E 86 ARG cc_start: 0.4242 (ptt180) cc_final: 0.3843 (tpp80) REVERT: G 82 MET cc_start: 0.0227 (mmt) cc_final: -0.0029 (mmm) REVERT: G 144 LEU cc_start: 0.0575 (pp) cc_final: -0.0499 (mp) outliers start: 17 outliers final: 10 residues processed: 181 average time/residue: 0.2136 time to fit residues: 61.0176 Evaluate side-chains 159 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 149 time to evaluate : 1.020 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 295 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 133 optimal weight: 9.9990 chunk 169 optimal weight: 0.0470 chunk 191 optimal weight: 0.9980 chunk 323 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** F 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 224 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.177259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.105929 restraints weight = 53953.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.106750 restraints weight = 33985.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.106729 restraints weight = 23215.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.107197 restraints weight = 23824.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107354 restraints weight = 20979.966| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30251 Z= 0.162 Angle : 0.624 11.406 41271 Z= 0.307 Chirality : 0.045 0.374 4792 Planarity : 0.005 0.060 5248 Dihedral : 8.739 103.751 5053 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % 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: -1.21 (0.14), residues: 3646 helix: 2.30 (0.22), residues: 584 sheet: -0.20 (0.17), residues: 922 loop : -2.11 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C1039 TYR 0.021 0.001 TYR C 904 PHE 0.020 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 covalent geometry : bond 0.00389 (30156) covalent geometry : angle 0.60495 (41030) SS BOND : bond 0.00326 ( 44) SS BOND : angle 1.29223 ( 88) hydrogen bonds : bond 0.05491 ( 939) hydrogen bonds : angle 5.02540 ( 2580) link_BETA1-4 : bond 0.00430 ( 12) link_BETA1-4 : angle 1.79396 ( 36) link_NAG-ASN : bond 0.00426 ( 39) link_NAG-ASN : angle 2.58305 ( 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 : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7272 (t0) cc_final: 0.7023 (t0) REVERT: B 200 TYR cc_start: 0.7303 (m-80) cc_final: 0.6432 (m-80) REVERT: B 211 ASN cc_start: 0.6071 (m-40) cc_final: 0.5622 (m-40) REVERT: B 1041 ASP cc_start: 0.8295 (t0) cc_final: 0.7947 (t0) REVERT: C 123 ASN cc_start: 0.4526 (p0) cc_final: 0.4145 (p0) REVERT: C 130 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7392 (ttmt) REVERT: C 401 VAL cc_start: 0.4228 (OUTLIER) cc_final: 0.4013 (p) REVERT: E 33 TYR cc_start: 0.6444 (m-80) cc_final: 0.6176 (m-80) REVERT: E 38 ARG cc_start: 0.3903 (ttm170) cc_final: 0.3484 (ttt-90) REVERT: E 86 ARG cc_start: 0.4242 (ptt180) cc_final: 0.3778 (tpp80) REVERT: F 93 TYR cc_start: 0.3597 (OUTLIER) cc_final: 0.3001 (t80) REVERT: F 224 GLN cc_start: 0.2321 (OUTLIER) cc_final: 0.1890 (tp40) outliers start: 30 outliers final: 18 residues processed: 185 average time/residue: 0.1738 time to fit residues: 53.5564 Evaluate side-chains 167 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 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 931 ILE Chi-restraints excluded: chain B residue 1017 GLU Chi-restraints excluded: chain B residue 1082 CYS 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 369 random chunks: chunk 342 optimal weight: 0.1980 chunk 325 optimal weight: 6.9990 chunk 360 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 311 optimal weight: 30.0000 chunk 77 optimal weight: 0.0000 chunk 180 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 63 optimal weight: 0.0060 chunk 72 optimal weight: 3.9990 overall best weight: 1.4404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4344 r_free = 0.4344 target = 0.177521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.105799 restraints weight = 53429.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.107562 restraints weight = 33057.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.107009 restraints weight = 22070.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.107327 restraints weight = 22983.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.107458 restraints weight = 20819.849| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30251 Z= 0.139 Angle : 0.603 13.254 41271 Z= 0.294 Chirality : 0.045 0.374 4792 Planarity : 0.004 0.054 5248 Dihedral : 8.308 102.351 5053 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.24 % Allowed : 12.29 % Favored : 86.47 % 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: -1.18 (0.14), residues: 3646 helix: 2.41 (0.22), residues: 582 sheet: -0.24 (0.17), residues: 923 loop : -2.09 (0.13), residues: 2141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 357 TYR 0.023 0.001 TYR G 52 PHE 0.015 0.001 PHE G 58 TRP 0.016 0.001 TRP A 353 HIS 0.004 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00331 (30156) covalent geometry : angle 0.58422 (41030) SS BOND : bond 0.00274 ( 44) SS BOND : angle 1.19690 ( 88) hydrogen bonds : bond 0.05126 ( 939) hydrogen bonds : angle 4.91342 ( 2580) link_BETA1-4 : bond 0.00427 ( 12) link_BETA1-4 : angle 1.81889 ( 36) link_NAG-ASN : bond 0.00419 ( 39) link_NAG-ASN : angle 2.54717 ( 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 : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8440 (mtt) cc_final: 0.8089 (mtt) REVERT: B 53 ASP cc_start: 0.7311 (t0) cc_final: 0.7044 (t0) REVERT: B 200 TYR cc_start: 0.7316 (m-80) cc_final: 0.6418 (m-80) REVERT: B 211 ASN cc_start: 0.6253 (m-40) cc_final: 0.5804 (m-40) REVERT: B 495 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5294 (m-10) REVERT: B 1041 ASP cc_start: 0.8304 (t0) cc_final: 0.7926 (t0) REVERT: C 123 ASN cc_start: 0.4660 (p0) cc_final: 0.4343 (p0) REVERT: C 130 LYS cc_start: 0.7562 (mtpt) cc_final: 0.7313 (ttmt) REVERT: C 401 VAL cc_start: 0.4385 (OUTLIER) cc_final: 0.4168 (p) REVERT: E 38 ARG cc_start: 0.3886 (ttm170) cc_final: 0.3522 (ttt-90) REVERT: E 86 ARG cc_start: 0.4264 (ptt180) cc_final: 0.3827 (tpp80) REVERT: F 93 TYR cc_start: 0.3471 (OUTLIER) cc_final: 0.2859 (t80) outliers start: 40 outliers final: 21 residues processed: 193 average time/residue: 0.1788 time to fit residues: 57.8700 Evaluate side-chains 168 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 401 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 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: 0.7980 chunk 353 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 0.3980 chunk 208 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 363 optimal weight: 0.3980 chunk 49 optimal weight: 4.9990 chunk 290 optimal weight: 0.8980 chunk 181 optimal weight: 0.0670 chunk 344 optimal weight: 8.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4362 r_free = 0.4362 target = 0.179204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.106008 restraints weight = 53792.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109609 restraints weight = 33726.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110401 restraints weight = 21166.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.110184 restraints weight = 19653.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.110577 restraints weight = 19606.398| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30251 Z= 0.099 Angle : 0.572 11.796 41271 Z= 0.278 Chirality : 0.044 0.369 4792 Planarity : 0.004 0.055 5248 Dihedral : 7.802 98.832 5053 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 1.43 % Allowed : 13.44 % Favored : 85.13 % 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: -1.04 (0.14), residues: 3646 helix: 2.58 (0.22), residues: 585 sheet: -0.18 (0.17), residues: 924 loop : -2.00 (0.13), residues: 2137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.016 0.001 TYR A 170 PHE 0.012 0.001 PHE G 58 TRP 0.013 0.001 TRP B 105 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00218 (30156) covalent geometry : angle 0.55394 (41030) SS BOND : bond 0.00289 ( 44) SS BOND : angle 1.02798 ( 88) hydrogen bonds : bond 0.04141 ( 939) hydrogen bonds : angle 4.65531 ( 2580) link_BETA1-4 : bond 0.00454 ( 12) link_BETA1-4 : angle 1.80242 ( 36) link_NAG-ASN : bond 0.00410 ( 39) link_NAG-ASN : angle 2.46070 ( 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 218 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 172 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8297 (mtt) cc_final: 0.7906 (mtt) REVERT: B 53 ASP cc_start: 0.7321 (t0) cc_final: 0.7114 (t0) REVERT: B 200 TYR cc_start: 0.7205 (m-80) cc_final: 0.6373 (m-80) REVERT: B 211 ASN cc_start: 0.6211 (m-40) cc_final: 0.5727 (m-40) REVERT: B 380 TYR cc_start: 0.6343 (m-80) cc_final: 0.5657 (m-80) REVERT: B 983 ARG cc_start: 0.8115 (ttp80) cc_final: 0.7852 (ttp80) REVERT: B 1005 GLN cc_start: 0.8411 (mm-40) cc_final: 0.8177 (mm110) REVERT: B 1041 ASP cc_start: 0.8251 (t0) cc_final: 0.7768 (t0) REVERT: C 123 ASN cc_start: 0.4814 (p0) cc_final: 0.4487 (p0) REVERT: C 130 LYS cc_start: 0.7697 (mtpt) cc_final: 0.7251 (ttmt) REVERT: C 134 PHE cc_start: 0.4661 (m-80) cc_final: 0.3356 (m-80) REVERT: C 401 VAL cc_start: 0.4318 (OUTLIER) cc_final: 0.4090 (p) REVERT: E 33 TYR cc_start: 0.6394 (m-80) cc_final: 0.6190 (m-80) REVERT: E 38 ARG cc_start: 0.3828 (ttm170) cc_final: 0.3489 (ttt-90) REVERT: E 86 ARG cc_start: 0.4286 (ptt180) cc_final: 0.3846 (tpp80) REVERT: F 93 TYR cc_start: 0.3521 (OUTLIER) cc_final: 0.2902 (t80) outliers start: 46 outliers final: 26 residues processed: 212 average time/residue: 0.1695 time to fit residues: 60.1756 Evaluate side-chains 176 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 148 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 560 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 778 THR Chi-restraints excluded: chain A residue 909 ILE Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 512 VAL 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 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 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 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: 2.9990 chunk 4 optimal weight: 2.9990 chunk 314 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 134 optimal weight: 8.9990 chunk 361 optimal weight: 20.0000 chunk 150 optimal weight: 4.9990 chunk 267 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1135 ASN ** C 122 ASN ** 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 = 0.4347 r_free = 0.4347 target = 0.177854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.107521 restraints weight = 53542.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.107599 restraints weight = 35737.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.107487 restraints weight = 28108.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.107710 restraints weight = 24544.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.108015 restraints weight = 22838.214| |-----------------------------------------------------------------------------| r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30251 Z= 0.130 Angle : 0.594 14.545 41271 Z= 0.288 Chirality : 0.044 0.367 4792 Planarity : 0.004 0.053 5248 Dihedral : 7.702 97.503 5053 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 1.77 % Allowed : 14.03 % Favored : 84.19 % 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: -1.05 (0.14), residues: 3646 helix: 2.50 (0.22), residues: 590 sheet: -0.13 (0.17), residues: 921 loop : -2.02 (0.13), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 97 TYR 0.019 0.001 TYR C 904 PHE 0.031 0.001 PHE A 168 TRP 0.012 0.001 TRP B 105 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00309 (30156) covalent geometry : angle 0.57579 (41030) SS BOND : bond 0.00276 ( 44) SS BOND : angle 1.30457 ( 88) hydrogen bonds : bond 0.04691 ( 939) hydrogen bonds : angle 4.67932 ( 2580) link_BETA1-4 : bond 0.00430 ( 12) link_BETA1-4 : angle 1.77505 ( 36) link_NAG-ASN : bond 0.00370 ( 39) link_NAG-ASN : angle 2.45729 ( 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 205 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 148 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7422 (t0) cc_final: 0.7181 (t0) REVERT: B 168 PHE cc_start: 0.6337 (t80) cc_final: 0.6017 (t80) REVERT: B 200 TYR cc_start: 0.7322 (m-80) cc_final: 0.6389 (m-80) REVERT: B 544 ASN cc_start: 0.8371 (OUTLIER) cc_final: 0.8076 (m110) REVERT: B 1041 ASP cc_start: 0.8336 (t0) cc_final: 0.7808 (t0) REVERT: C 123 ASN cc_start: 0.4947 (p0) cc_final: 0.4611 (p0) REVERT: C 130 LYS cc_start: 0.7590 (mtpt) cc_final: 0.7090 (ttmt) REVERT: C 134 PHE cc_start: 0.4818 (m-80) cc_final: 0.3386 (m-80) REVERT: C 226 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8491 (tt) REVERT: C 401 VAL cc_start: 0.4485 (OUTLIER) cc_final: 0.4228 (p) REVERT: C 948 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7304 (mt) REVERT: E 38 ARG cc_start: 0.3807 (ttm170) cc_final: 0.3464 (ttt-90) REVERT: E 86 ARG cc_start: 0.4304 (ptt180) cc_final: 0.3879 (tpp80) REVERT: F 93 TYR cc_start: 0.3671 (OUTLIER) cc_final: 0.3010 (t80) outliers start: 57 outliers final: 39 residues processed: 199 average time/residue: 0.1730 time to fit residues: 58.2983 Evaluate side-chains 185 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 141 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 398 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 544 ASN 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 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 401 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 780 GLU 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 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: 1.9990 chunk 154 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 219 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 83 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 226 optimal weight: 0.3980 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN B1135 ASN ** C 122 ASN ** 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 = 0.4360 r_free = 0.4360 target = 0.179014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.109075 restraints weight = 53711.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.109981 restraints weight = 32741.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.109503 restraints weight = 21523.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110039 restraints weight = 23788.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.110166 restraints weight = 20884.290| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3389 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3389 r_free = 0.3389 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3389 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 30251 Z= 0.101 Angle : 0.571 13.666 41271 Z= 0.276 Chirality : 0.044 0.365 4792 Planarity : 0.004 0.055 5248 Dihedral : 7.443 94.852 5053 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 1.59 % Allowed : 14.84 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.14), residues: 3646 helix: 2.57 (0.22), residues: 597 sheet: -0.10 (0.17), residues: 920 loop : -1.96 (0.13), residues: 2129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 97 TYR 0.019 0.001 TYR A 170 PHE 0.023 0.001 PHE A 168 TRP 0.012 0.001 TRP B 105 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00227 (30156) covalent geometry : angle 0.55336 (41030) SS BOND : bond 0.00207 ( 44) SS BOND : angle 1.10307 ( 88) hydrogen bonds : bond 0.04081 ( 939) hydrogen bonds : angle 4.54952 ( 2580) link_BETA1-4 : bond 0.00487 ( 12) link_BETA1-4 : angle 1.76685 ( 36) link_NAG-ASN : bond 0.00392 ( 39) link_NAG-ASN : angle 2.38335 ( 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 207 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 156 time to evaluate : 1.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.8329 (mtt) cc_final: 0.7941 (mtt) REVERT: B 53 ASP cc_start: 0.7358 (t0) cc_final: 0.7141 (t70) REVERT: B 200 TYR cc_start: 0.7177 (m-80) cc_final: 0.6317 (m-80) REVERT: B 211 ASN cc_start: 0.6230 (m-40) cc_final: 0.5665 (m-40) REVERT: B 983 ARG cc_start: 0.8098 (ttp80) cc_final: 0.7822 (ttp80) REVERT: B 1005 GLN cc_start: 0.8360 (mm-40) cc_final: 0.8160 (mm-40) REVERT: B 1041 ASP cc_start: 0.8302 (t0) cc_final: 0.7790 (t0) REVERT: C 123 ASN cc_start: 0.4978 (p0) cc_final: 0.4646 (p0) REVERT: C 130 LYS cc_start: 0.7620 (mtpt) cc_final: 0.7136 (ttmt) REVERT: C 134 PHE cc_start: 0.4678 (m-80) cc_final: 0.3332 (m-80) REVERT: C 226 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8503 (tt) REVERT: C 401 VAL cc_start: 0.4305 (OUTLIER) cc_final: 0.4063 (p) REVERT: C 948 LEU cc_start: 0.7363 (OUTLIER) cc_final: 0.7044 (mt) REVERT: E 38 ARG cc_start: 0.3783 (ttm170) cc_final: 0.3424 (ttt-90) REVERT: E 86 ARG cc_start: 0.4142 (ptt180) cc_final: 0.3709 (tpp80) REVERT: E 195 ARG cc_start: 0.4426 (ptm160) cc_final: 0.4003 (ttm110) REVERT: F 93 TYR cc_start: 0.3650 (OUTLIER) cc_final: 0.3037 (t80) outliers start: 51 outliers final: 37 residues processed: 198 average time/residue: 0.1855 time to fit residues: 61.4218 Evaluate side-chains 192 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 151 time to evaluate : 1.198 ------------------------------------------------------------------------------- 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 909 ILE Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 433 VAL 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 128 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 342 PHE Chi-restraints excluded: chain C residue 401 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 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 780 GLU 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 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: 2.9990 chunk 26 optimal weight: 8.9990 chunk 93 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 186 optimal weight: 3.9990 chunk 363 optimal weight: 0.4980 chunk 241 optimal weight: 20.0000 chunk 198 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 422 ASN C 955 ASN C1106 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.175697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.105674 restraints weight = 53623.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104985 restraints weight = 32879.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.104575 restraints weight = 25872.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.105127 restraints weight = 25717.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.105279 restraints weight = 24216.945| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3312 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3312 r_free = 0.3312 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3312 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 30251 Z= 0.196 Angle : 0.647 13.862 41271 Z= 0.317 Chirality : 0.046 0.366 4792 Planarity : 0.004 0.053 5248 Dihedral : 7.658 96.063 5053 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.69 % Favored : 91.31 % Rotamer: Outliers : 1.65 % Allowed : 15.37 % Favored : 82.98 % 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: -1.16 (0.14), residues: 3646 helix: 2.26 (0.21), residues: 596 sheet: -0.24 (0.17), residues: 938 loop : -2.05 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C1107 TYR 0.029 0.001 TYR B 904 PHE 0.017 0.001 PHE C 93 TRP 0.015 0.001 TRP C 886 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00478 (30156) covalent geometry : angle 0.62886 (41030) SS BOND : bond 0.00327 ( 44) SS BOND : angle 1.44710 ( 88) hydrogen bonds : bond 0.05856 ( 939) hydrogen bonds : angle 4.85364 ( 2580) link_BETA1-4 : bond 0.00420 ( 12) link_BETA1-4 : angle 1.81799 ( 36) link_NAG-ASN : bond 0.00397 ( 39) link_NAG-ASN : angle 2.49586 ( 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 201 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 148 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 ASP cc_start: 0.7452 (t0) cc_final: 0.7228 (t0) REVERT: B 200 TYR cc_start: 0.7235 (m-80) cc_final: 0.6224 (m-80) REVERT: B 1041 ASP cc_start: 0.8389 (t0) cc_final: 0.8039 (t0) REVERT: C 123 ASN cc_start: 0.4938 (p0) cc_final: 0.4641 (p0) REVERT: C 130 LYS cc_start: 0.7862 (mtpt) cc_final: 0.7069 (mtpp) REVERT: C 134 PHE cc_start: 0.4827 (m-80) cc_final: 0.3761 (m-80) REVERT: C 226 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8556 (tt) REVERT: C 401 VAL cc_start: 0.4433 (OUTLIER) cc_final: 0.4181 (p) REVERT: E 38 ARG cc_start: 0.3559 (ttm170) cc_final: 0.3288 (ttt-90) REVERT: E 86 ARG cc_start: 0.3945 (ptt180) cc_final: 0.3633 (tpp80) REVERT: E 195 ARG cc_start: 0.4408 (ptm160) cc_final: 0.3972 (ttm110) REVERT: F 93 TYR cc_start: 0.3649 (OUTLIER) cc_final: 0.2915 (t80) outliers start: 53 outliers final: 42 residues processed: 195 average time/residue: 0.1717 time to fit residues: 56.1981 Evaluate side-chains 186 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 141 time to evaluate : 1.045 ------------------------------------------------------------------------------- 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 1136 THR Chi-restraints excluded: chain A residue 1137 VAL Chi-restraints excluded: chain B residue 235 ILE 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 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 401 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 599 THR Chi-restraints excluded: chain C residue 663 ASP Chi-restraints excluded: chain C residue 780 GLU 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 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: 4.9990 chunk 180 optimal weight: 3.9990 chunk 294 optimal weight: 0.1980 chunk 60 optimal weight: 0.4980 chunk 315 optimal weight: 0.4980 chunk 191 optimal weight: 0.9990 chunk 224 optimal weight: 3.9990 chunk 354 optimal weight: 30.0000 chunk 263 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 321 optimal weight: 20.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 544 ASN B1135 ASN ** C 122 ASN ** 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 = 0.4353 r_free = 0.4353 target = 0.178477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108624 restraints weight = 53507.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.109182 restraints weight = 33211.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108579 restraints weight = 23195.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.109042 restraints weight = 23728.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.109151 restraints weight = 21687.861| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 30251 Z= 0.103 Angle : 0.582 13.650 41271 Z= 0.282 Chirality : 0.044 0.362 4792 Planarity : 0.004 0.054 5248 Dihedral : 7.337 93.235 5053 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 1.43 % Allowed : 15.96 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.14), residues: 3646 helix: 2.54 (0.22), residues: 593 sheet: -0.08 (0.17), residues: 905 loop : -1.97 (0.13), residues: 2148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C1107 TYR 0.030 0.001 TYR B 904 PHE 0.019 0.001 PHE A 168 TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00230 (30156) covalent geometry : angle 0.56483 (41030) SS BOND : bond 0.00219 ( 44) SS BOND : angle 1.11664 ( 88) hydrogen bonds : bond 0.04277 ( 939) hydrogen bonds : angle 4.57470 ( 2580) link_BETA1-4 : bond 0.00489 ( 12) link_BETA1-4 : angle 1.81130 ( 36) link_NAG-ASN : bond 0.00394 ( 39) link_NAG-ASN : angle 2.37435 ( 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 200 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 154 time to evaluate : 1.097 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: 0.8304 (mtt) cc_final: 0.7904 (mtt) REVERT: B 53 ASP cc_start: 0.7367 (t0) cc_final: 0.7139 (t70) REVERT: B 200 TYR cc_start: 0.7259 (m-80) cc_final: 0.6323 (m-80) REVERT: B 1005 GLN cc_start: 0.8441 (mm-40) cc_final: 0.8220 (mm110) REVERT: B 1041 ASP cc_start: 0.8309 (t0) cc_final: 0.7791 (t0) REVERT: C 123 ASN cc_start: 0.4983 (p0) cc_final: 0.4637 (p0) REVERT: C 130 LYS cc_start: 0.7657 (mtpt) cc_final: 0.7272 (tttt) REVERT: C 134 PHE cc_start: 0.4943 (m-80) cc_final: 0.4348 (m-80) REVERT: C 226 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8480 (tt) REVERT: C 401 VAL cc_start: 0.4421 (OUTLIER) cc_final: 0.4177 (p) REVERT: C 948 LEU cc_start: 0.7295 (OUTLIER) cc_final: 0.6963 (mt) REVERT: E 82 MET cc_start: -0.0038 (mtt) cc_final: -0.0268 (mtt) REVERT: E 86 ARG cc_start: 0.3944 (ptt180) cc_final: 0.3617 (tpp80) REVERT: E 195 ARG cc_start: 0.4342 (ptm160) cc_final: 0.3937 (ttm110) REVERT: F 93 TYR cc_start: 0.3601 (OUTLIER) cc_final: 0.3002 (t80) outliers start: 46 outliers final: 37 residues processed: 194 average time/residue: 0.1724 time to fit residues: 56.0393 Evaluate side-chains 193 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.978 ------------------------------------------------------------------------------- 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 549 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 1137 VAL 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 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 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 401 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 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 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 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: 5.9990 chunk 45 optimal weight: 2.9990 chunk 251 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 328 optimal weight: 30.0000 chunk 78 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 519 HIS B 544 ASN B1135 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** F 234 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 = 0.4310 r_free = 0.4310 target = 0.174678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105734 restraints weight = 53223.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.103346 restraints weight = 35502.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103122 restraints weight = 28831.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.103941 restraints weight = 24892.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.104014 restraints weight = 23241.218| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 30251 Z= 0.233 Angle : 0.680 13.641 41271 Z= 0.334 Chirality : 0.047 0.365 4792 Planarity : 0.005 0.056 5248 Dihedral : 7.670 95.032 5053 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 1.46 % Allowed : 16.12 % Favored : 82.42 % 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: 2.13 (0.21), residues: 592 sheet: -0.28 (0.17), residues: 943 loop : -2.10 (0.13), residues: 2111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 86 TYR 0.032 0.002 TYR B 904 PHE 0.020 0.002 PHE A 87 TRP 0.017 0.002 TRP B 105 HIS 0.008 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00572 (30156) covalent geometry : angle 0.66112 (41030) SS BOND : bond 0.00394 ( 44) SS BOND : angle 1.65901 ( 88) hydrogen bonds : bond 0.06328 ( 939) hydrogen bonds : angle 4.94712 ( 2580) link_BETA1-4 : bond 0.00444 ( 12) link_BETA1-4 : angle 1.89556 ( 36) link_NAG-ASN : bond 0.00435 ( 39) link_NAG-ASN : angle 2.55816 ( 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 189 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 LYS cc_start: 0.8090 (mmmt) cc_final: 0.7722 (mtmm) REVERT: B 200 TYR cc_start: 0.7252 (m-80) cc_final: 0.6234 (m-80) REVERT: B 1041 ASP cc_start: 0.8406 (t0) cc_final: 0.8007 (t0) REVERT: C 123 ASN cc_start: 0.4815 (p0) cc_final: 0.4535 (p0) REVERT: C 130 LYS cc_start: 0.7931 (mtpt) cc_final: 0.7491 (tttt) REVERT: C 134 PHE cc_start: 0.4888 (m-80) cc_final: 0.4298 (m-80) REVERT: C 226 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8533 (tt) REVERT: C 401 VAL cc_start: 0.4540 (OUTLIER) cc_final: 0.4292 (p) REVERT: E 86 ARG cc_start: 0.3911 (ptt180) cc_final: 0.3594 (tpp80) REVERT: E 195 ARG cc_start: 0.4305 (ptm160) cc_final: 0.3739 (ttm110) REVERT: F 93 TYR cc_start: 0.3657 (OUTLIER) cc_final: 0.2976 (t80) outliers start: 47 outliers final: 39 residues processed: 184 average time/residue: 0.1747 time to fit residues: 53.8948 Evaluate side-chains 179 residues out of total 3214 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 137 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 549 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 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 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 401 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 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 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: 7.9990 chunk 346 optimal weight: 40.0000 chunk 230 optimal weight: 0.0060 chunk 239 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 145 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 316 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 246 optimal weight: 2.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B1135 ASN ** C 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 234 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 = 0.4320 r_free = 0.4320 target = 0.175605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105721 restraints weight = 53639.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.105425 restraints weight = 34553.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.104608 restraints weight = 25914.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.104890 restraints weight = 26777.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.105116 restraints weight = 24311.531| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 30251 Z= 0.171 Angle : 0.628 13.587 41271 Z= 0.307 Chirality : 0.046 0.364 4792 Planarity : 0.004 0.057 5248 Dihedral : 7.578 95.633 5053 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 1.68 % Allowed : 16.24 % Favored : 82.08 % 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: -1.23 (0.14), residues: 3646 helix: 2.25 (0.22), residues: 593 sheet: -0.31 (0.17), residues: 950 loop : -2.09 (0.13), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 86 TYR 0.026 0.001 TYR B 904 PHE 0.017 0.001 PHE A 87 TRP 0.017 0.001 TRP C 886 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd covalent geometry : bond 0.00418 (30156) covalent geometry : angle 0.60924 (41030) SS BOND : bond 0.00299 ( 44) SS BOND : angle 1.44506 ( 88) hydrogen bonds : bond 0.05492 ( 939) hydrogen bonds : angle 4.82217 ( 2580) link_BETA1-4 : bond 0.00423 ( 12) link_BETA1-4 : angle 1.88939 ( 36) link_NAG-ASN : bond 0.00391 ( 39) link_NAG-ASN : angle 2.48586 ( 117) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5932.92 seconds wall clock time: 103 minutes 7.57 seconds (6187.57 seconds total)