Starting phenix.real_space_refine on Sun Jul 5 09:47:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wwj_32867/07_2026/7wwj_32867.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= 0.038 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 117 5.16 5 C 17157 2.51 5 N 4426 2.21 5 O 5215 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26915 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 839, 6555 Classifications: {'peptide': 839} Link IDs: {'PTRANS': 46, 'TRANS': 792} Chain breaks: 9 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 5.05, per 1000 atoms: 0.19 Number of scatterers: 26915 At special positions: 0 Unit cell: (145.96, 136.12, 222.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5215 8.00 N 4426 7.00 C 17157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 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 S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG D 1 " - " ASN C 801 " " NAG E 1 " - " ASN C1074 " " NAG J 1 " - " ASN C1098 " " NAG K 1 " - " ASN C1134 " " NAG L 1 " - " ASN B 717 " " NAG M 1 " - " ASN B 801 " " NAG N 1 " - " ASN B1074 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B1098 " " NAG Q 1 " - " ASN B1134 " " NAG R 1 " - " ASN A 717 " " NAG S 1 " - " ASN A 801 " " NAG T 1 " - " ASN A1098 " " NAG U 1 " - " ASN A1134 " Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 778.9 milliseconds 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 54 sheets defined 22.3% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.569A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.351A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.644A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLN A 957 " --> pdb=" O ASN A 953 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.150A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.105A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.614A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.336A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.608A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.754A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.637A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.553A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.187A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.700A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.071A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.599A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.737A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.901A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.512A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.692A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.541A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.729A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.209A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.549A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.863A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.615A pdb=" N SER C1147 " --> pdb=" O PRO C1143 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.844A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.696A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'I' and resid 28 through 30 No H-bonds generated for 'chain 'I' and resid 28 through 30' Processing helix chain 'I' and resid 62 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.351A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.571A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.789A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.363A pdb=" N PHE A 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.828A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 5.778A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.414A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.365A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.322A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.143A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 7.184A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.062A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.942A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.237A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.105A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.872A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.078A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.065A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.761A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.378A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.532A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.112A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.615A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.132A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 4.663A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 660 removed outlier: 6.005A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.579A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.762A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC9, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.104A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.831A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.677A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 135 through 141 removed outlier: 10.353A pdb=" N ASP C 138 " --> pdb=" O TYR C 160 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N TYR C 160 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.311A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.733A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.599A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.484A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VAL C 524 " --> pdb=" O PHE C 392 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.835A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.835A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'F' and resid 5 through 7 Processing sheet with id=AF1, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.709A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR F 49 " --> pdb=" O SER F 53 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'G' and resid 10 through 12 removed outlier: 8.825A pdb=" N TYR G 32 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ILE G 52 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 13 removed outlier: 3.736A pdb=" N GLU H 105 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 48 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N GLN H 37 " --> pdb=" O LEU H 46 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N LEU H 46 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TYR H 49 " --> pdb=" O SER H 53 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 12 removed outlier: 8.682A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 10 through 12 1115 hydrogen bonds defined for protein. 2985 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: 6.02 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8516 1.34 - 1.46: 6673 1.46 - 1.58: 12180 1.58 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 27519 Sorted by residual: bond pdb=" N CYS C 525 " pdb=" CA CYS C 525 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.25e-02 6.40e+03 9.15e+00 bond pdb=" N LEU C 371 " pdb=" CA LEU C 371 " ideal model delta sigma weight residual 1.453 1.490 -0.037 1.27e-02 6.20e+03 8.37e+00 bond pdb=" N ASP G 90 " pdb=" CA ASP G 90 " ideal model delta sigma weight residual 1.455 1.491 -0.035 1.25e-02 6.40e+03 8.02e+00 bond pdb=" N CYS C 391 " pdb=" CA CYS C 391 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.19e-02 7.06e+03 7.64e+00 bond pdb=" N SER B 758 " pdb=" CA SER B 758 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.18e-02 7.18e+03 7.11e+00 ... (remaining 27514 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 36129 1.48 - 2.96: 1079 2.96 - 4.43: 159 4.43 - 5.91: 32 5.91 - 7.39: 8 Bond angle restraints: 37407 Sorted by residual: angle pdb=" N LEU C 387 " pdb=" CA LEU C 387 " pdb=" C LEU C 387 " ideal model delta sigma weight residual 113.16 108.27 4.89 1.24e+00 6.50e-01 1.55e+01 angle pdb=" C VAL I 11 " pdb=" N LYS I 12 " pdb=" CA LYS I 12 " ideal model delta sigma weight residual 122.36 116.74 5.62 1.60e+00 3.91e-01 1.23e+01 angle pdb=" CA LEU C 371 " pdb=" C LEU C 371 " pdb=" O LEU C 371 " ideal model delta sigma weight residual 121.88 117.92 3.96 1.13e+00 7.83e-01 1.23e+01 angle pdb=" CA LEU C 390 " pdb=" C LEU C 390 " pdb=" O LEU C 390 " ideal model delta sigma weight residual 121.87 118.19 3.68 1.10e+00 8.26e-01 1.12e+01 angle pdb=" N GLY A 757 " pdb=" CA GLY A 757 " pdb=" C GLY A 757 " ideal model delta sigma weight residual 111.21 114.61 -3.40 1.04e+00 9.25e-01 1.07e+01 ... (remaining 37402 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 14720 17.93 - 35.87: 1127 35.87 - 53.80: 173 53.80 - 71.74: 41 71.74 - 89.67: 32 Dihedral angle restraints: 16093 sinusoidal: 6307 harmonic: 9786 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.15 -75.85 1 1.00e+01 1.00e-02 7.25e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 154.29 -61.29 1 1.00e+01 1.00e-02 4.99e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -26.66 -59.34 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 16090 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 3872 0.077 - 0.154: 478 0.154 - 0.231: 9 0.231 - 0.308: 2 0.308 - 0.385: 1 Chirality restraints: 4362 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.71e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 331 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.16 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 4359 not shown) Planarity restraints: 4787 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " 0.040 5.00e-02 4.00e+02 5.97e-02 5.70e+00 pdb=" N PRO C 987 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 985 " -0.039 5.00e-02 4.00e+02 5.89e-02 5.55e+00 pdb=" N PRO C 986 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 986 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 986 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL G 37 " 0.010 2.00e-02 2.50e+03 2.14e-02 4.58e+00 pdb=" C VAL G 37 " -0.037 2.00e-02 2.50e+03 pdb=" O VAL G 37 " 0.014 2.00e-02 2.50e+03 pdb=" N ARG G 38 " 0.012 2.00e-02 2.50e+03 ... (remaining 4784 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2118 2.74 - 3.28: 26664 3.28 - 3.82: 43398 3.82 - 4.36: 49622 4.36 - 4.90: 87842 Nonbonded interactions: 209644 Sorted by model distance: nonbonded pdb=" O GLN G 62 " pdb=" NE2 GLN G 65 " model vdw 2.202 3.120 nonbonded pdb=" OE2 GLU B 773 " pdb=" NE ARG B1019 " model vdw 2.223 3.120 nonbonded pdb=" OG SER F 26 " pdb=" OE1 GLN F 27 " model vdw 2.224 3.040 nonbonded pdb=" OE1 GLN B 115 " pdb=" OG1 THR B 167 " model vdw 2.233 3.040 nonbonded pdb=" OG1 THR A1116 " pdb=" OD1 ASP A1118 " model vdw 2.233 3.040 ... (remaining 209639 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 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' 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' selection = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = chain 'F' selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) } ncs_group { reference = chain 'G' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.690 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.070 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:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 27604 Z= 0.179 Angle : 0.618 9.658 37620 Z= 0.327 Chirality : 0.046 0.385 4362 Planarity : 0.004 0.060 4758 Dihedral : 13.342 89.673 9665 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3303 helix: 2.16 (0.22), residues: 639 sheet: 0.25 (0.17), residues: 906 loop : -0.87 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 983 TYR 0.016 0.001 TYR A1067 PHE 0.018 0.001 PHE B 135 TRP 0.011 0.001 TRP H 35 HIS 0.003 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.18 (27519) covalent geometry : angle 0.60471 / 0.32 (37407) SS BOND : bond 0.00277 / 0.21 ( 42) SS BOND : angle 0.78275 / 0.53 ( 84) hydrogen bonds : bond 0.13134 / 8.67 ( 1089) hydrogen bonds : angle 6.37647 / 4.51 ( 2985) link_BETA1-4 : bond 0.00384 / 0.25 ( 14) link_BETA1-4 : angle 0.98014 / 0.67 ( 42) link_NAG-ASN : bond 0.00492 / 0.32 ( 29) link_NAG-ASN : angle 2.61550 / 1.80 ( 87) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 241 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 571 ASP cc_start: 0.8826 (m-30) cc_final: 0.8485 (t0) REVERT: A 985 ASP cc_start: 0.7975 (p0) cc_final: 0.7544 (p0) REVERT: A 1002 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 197 ILE cc_start: 0.9242 (mm) cc_final: 0.8887 (mm) REVERT: B 867 ASP cc_start: 0.7983 (p0) cc_final: 0.7751 (p0) REVERT: B 1002 GLN cc_start: 0.8236 (tm-30) cc_final: 0.7849 (tm-30) REVERT: C 90 VAL cc_start: 0.8472 (t) cc_final: 0.8243 (t) REVERT: C 153 MET cc_start: 0.7306 (ppp) cc_final: 0.6762 (ppp) REVERT: G 3 GLN cc_start: 0.8758 (mm110) cc_final: 0.8273 (mm-40) REVERT: G 46 GLU cc_start: 0.8543 (pm20) cc_final: 0.8291 (pm20) REVERT: G 106 ASP cc_start: 0.8659 (m-30) cc_final: 0.8443 (m-30) REVERT: H 27 GLN cc_start: 0.7590 (tm-30) cc_final: 0.7000 (tm-30) REVERT: H 104 LEU cc_start: 0.8809 (tp) cc_final: 0.8477 (tp) REVERT: I 13 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8805 (mmmt) REVERT: I 19 LYS cc_start: 0.8710 (tptp) cc_final: 0.8278 (tppt) REVERT: I 73 ASP cc_start: 0.8215 (t0) cc_final: 0.7930 (t0) REVERT: I 87 ARG cc_start: 0.8567 (ptp90) cc_final: 0.8275 (ptp90) outliers start: 0 outliers final: 0 residues processed: 241 average time/residue: 0.1581 time to fit residues: 61.0641 Evaluate side-chains 177 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 197 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 121 ASN A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN B 935 GLN ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.075674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.048358 restraints weight = 94458.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.050340 restraints weight = 43942.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.051625 restraints weight = 28295.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.052377 restraints weight = 21700.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052932 restraints weight = 18536.390| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 27604 Z= 0.252 Angle : 0.638 10.047 37620 Z= 0.325 Chirality : 0.047 0.382 4362 Planarity : 0.004 0.060 4758 Dihedral : 4.274 19.997 3601 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.71 % Allowed : 6.70 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3303 helix: 2.13 (0.21), residues: 648 sheet: 0.24 (0.17), residues: 851 loop : -0.99 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 61 TYR 0.022 0.002 TYR B1067 PHE 0.025 0.002 PHE C 559 TRP 0.011 0.001 TRP I 47 HIS 0.007 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.25 (27519) covalent geometry : angle 0.62471 / 0.32 (37407) SS BOND : bond 0.00345 / 0.24 ( 42) SS BOND : angle 1.03085 / 0.67 ( 84) hydrogen bonds : bond 0.05370 / 3.55 ( 1089) hydrogen bonds : angle 5.38367 / 3.80 ( 2985) link_BETA1-4 : bond 0.00291 / 0.20 ( 14) link_BETA1-4 : angle 1.05882 / 0.70 ( 42) link_NAG-ASN : bond 0.00463 / 0.29 ( 29) link_NAG-ASN : angle 2.61842 / 1.81 ( 87) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9130 (mtm) cc_final: 0.8538 (mtm) REVERT: A 1002 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 357 ARG cc_start: 0.7044 (OUTLIER) cc_final: 0.6678 (tpp80) REVERT: B 1002 GLN cc_start: 0.8332 (tm-30) cc_final: 0.8070 (tm-30) REVERT: B 1050 MET cc_start: 0.8748 (ptm) cc_final: 0.8533 (ptm) REVERT: C 153 MET cc_start: 0.7300 (ppp) cc_final: 0.6663 (ppp) REVERT: C 776 LYS cc_start: 0.9369 (tppt) cc_final: 0.9137 (tmmt) REVERT: C 988 GLU cc_start: 0.8882 (mp0) cc_final: 0.8650 (pm20) REVERT: G 3 GLN cc_start: 0.8768 (mm110) cc_final: 0.8278 (mm-40) REVERT: H 27 GLN cc_start: 0.7742 (tm-30) cc_final: 0.7079 (tm-30) REVERT: H 90 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.6897 (pp30) REVERT: H 104 LEU cc_start: 0.9059 (tp) cc_final: 0.8836 (tp) REVERT: I 19 LYS cc_start: 0.8715 (tptp) cc_final: 0.8266 (tptp) REVERT: I 73 ASP cc_start: 0.8200 (t0) cc_final: 0.7919 (t0) REVERT: I 82 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8691 (mm-30) outliers start: 21 outliers final: 15 residues processed: 209 average time/residue: 0.1588 time to fit residues: 54.0773 Evaluate side-chains 186 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 169 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 357 ARG Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 51 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 261 optimal weight: 4.9990 chunk 242 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 294 optimal weight: 3.9990 chunk 296 optimal weight: 8.9990 chunk 317 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 217 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.076207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.048876 restraints weight = 93596.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.050894 restraints weight = 43301.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052199 restraints weight = 27755.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.053002 restraints weight = 21246.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.053519 restraints weight = 18085.748| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 27604 Z= 0.162 Angle : 0.570 10.371 37620 Z= 0.289 Chirality : 0.045 0.383 4362 Planarity : 0.004 0.054 4758 Dihedral : 4.166 20.076 3601 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.68 % Allowed : 9.59 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.14), residues: 3303 helix: 2.30 (0.21), residues: 653 sheet: 0.29 (0.17), residues: 845 loop : -0.95 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 61 TYR 0.021 0.001 TYR B1067 PHE 0.019 0.001 PHE C 559 TRP 0.009 0.001 TRP H 35 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (27519) covalent geometry : angle 0.55735 / 0.29 (37407) SS BOND : bond 0.00275 / 0.19 ( 42) SS BOND : angle 0.85941 / 0.56 ( 84) hydrogen bonds : bond 0.04903 / 3.25 ( 1089) hydrogen bonds : angle 5.09894 / 3.60 ( 2985) link_BETA1-4 : bond 0.00178 / 0.11 ( 14) link_BETA1-4 : angle 0.94007 / 0.63 ( 42) link_NAG-ASN : bond 0.00399 / 0.26 ( 29) link_NAG-ASN : angle 2.43515 / 1.69 ( 87) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 195 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9106 (mtm) cc_final: 0.8521 (mtm) REVERT: A 1002 GLN cc_start: 0.8361 (tm-30) cc_final: 0.7876 (tm-30) REVERT: B 1002 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8066 (tm-30) REVERT: B 1050 MET cc_start: 0.8785 (ptm) cc_final: 0.8576 (ptm) REVERT: C 153 MET cc_start: 0.7281 (ppp) cc_final: 0.6710 (ppp) REVERT: C 1050 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.8534 (ptm) REVERT: G 3 GLN cc_start: 0.8770 (mm110) cc_final: 0.8286 (mm-40) REVERT: H 27 GLN cc_start: 0.7806 (tm-30) cc_final: 0.7112 (tm-30) REVERT: I 73 ASP cc_start: 0.8303 (t0) cc_final: 0.7985 (t0) REVERT: I 81 MET cc_start: 0.8218 (ttt) cc_final: 0.7822 (ttt) REVERT: I 82 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8578 (mm-30) outliers start: 20 outliers final: 12 residues processed: 205 average time/residue: 0.1616 time to fit residues: 54.3355 Evaluate side-chains 187 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 174 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 84 optimal weight: 0.0770 chunk 184 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 179 optimal weight: 0.4980 chunk 235 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 253 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.076377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.049575 restraints weight = 92990.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.051555 restraints weight = 43235.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052838 restraints weight = 27819.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.053644 restraints weight = 21272.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.054076 restraints weight = 18092.963| |-----------------------------------------------------------------------------| r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 27604 Z= 0.158 Angle : 0.565 10.117 37620 Z= 0.286 Chirality : 0.045 0.383 4362 Planarity : 0.004 0.053 4758 Dihedral : 4.133 20.318 3601 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.12 % Allowed : 10.64 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % 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: 0.12 (0.14), residues: 3303 helix: 2.39 (0.21), residues: 644 sheet: 0.34 (0.17), residues: 832 loop : -0.92 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 98 TYR 0.023 0.001 TYR G 32 PHE 0.019 0.001 PHE C 559 TRP 0.007 0.001 TRP I 47 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 (27519) covalent geometry : angle 0.55049 / 0.28 (37407) SS BOND : bond 0.00337 / 0.20 ( 42) SS BOND : angle 1.36949 / 1.05 ( 84) hydrogen bonds : bond 0.04755 / 3.16 ( 1089) hydrogen bonds : angle 4.97570 / 3.51 ( 2985) link_BETA1-4 : bond 0.00234 / 0.15 ( 14) link_BETA1-4 : angle 0.96526 / 0.65 ( 42) link_NAG-ASN : bond 0.00381 / 0.24 ( 29) link_NAG-ASN : angle 2.36668 / 1.65 ( 87) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8687 (pp30) cc_final: 0.8227 (pp30) REVERT: A 1002 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7865 (tm-30) REVERT: B 773 GLU cc_start: 0.8787 (tp30) cc_final: 0.8303 (tp30) REVERT: B 1002 GLN cc_start: 0.8269 (tm-30) cc_final: 0.8049 (tm-30) REVERT: C 988 GLU cc_start: 0.8601 (pm20) cc_final: 0.8384 (pm20) REVERT: C 1050 MET cc_start: 0.8816 (ptp) cc_final: 0.8542 (ptm) REVERT: G 3 GLN cc_start: 0.8758 (mm110) cc_final: 0.8279 (mm-40) REVERT: G 98 ARG cc_start: 0.6392 (OUTLIER) cc_final: 0.4992 (tmm-80) REVERT: H 27 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7141 (tm-30) REVERT: I 73 ASP cc_start: 0.8315 (t0) cc_final: 0.7940 (t0) REVERT: I 81 MET cc_start: 0.8291 (ttt) cc_final: 0.8011 (ttt) outliers start: 33 outliers final: 21 residues processed: 215 average time/residue: 0.1547 time to fit residues: 54.5011 Evaluate side-chains 197 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 175 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 7.9990 chunk 275 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 chunk 302 optimal weight: 20.0000 chunk 183 optimal weight: 4.9990 chunk 84 optimal weight: 0.0370 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN C 121 ASN C 992 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.075908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.049044 restraints weight = 93827.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.051006 restraints weight = 43864.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.052273 restraints weight = 28348.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.053070 restraints weight = 21782.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.053495 restraints weight = 18524.491| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 27604 Z= 0.192 Angle : 0.579 10.307 37620 Z= 0.293 Chirality : 0.045 0.387 4362 Planarity : 0.004 0.065 4758 Dihedral : 4.170 23.691 3601 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 1.77 % Allowed : 11.76 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.14), residues: 3303 helix: 2.40 (0.21), residues: 643 sheet: 0.32 (0.18), residues: 832 loop : -0.93 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 61 TYR 0.019 0.001 TYR B1067 PHE 0.020 0.001 PHE C 559 TRP 0.007 0.001 TRP I 47 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.19 (27519) covalent geometry : angle 0.56591 / 0.29 (37407) SS BOND : bond 0.00282 / 0.20 ( 42) SS BOND : angle 1.04450 / 0.74 ( 84) hydrogen bonds : bond 0.04861 / 3.23 ( 1089) hydrogen bonds : angle 4.99294 / 3.52 ( 2985) link_BETA1-4 : bond 0.00227 / 0.15 ( 14) link_BETA1-4 : angle 1.01402 / 0.68 ( 42) link_NAG-ASN : bond 0.00386 / 0.25 ( 29) link_NAG-ASN : angle 2.38873 / 1.67 ( 87) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 188 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8707 (pp30) cc_final: 0.8295 (pp30) REVERT: A 1002 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7873 (tm-30) REVERT: B 740 MET cc_start: 0.9062 (OUTLIER) cc_final: 0.8231 (tmm) REVERT: B 1002 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8064 (tm-30) REVERT: C 153 MET cc_start: 0.7282 (ppp) cc_final: 0.6800 (ppp) REVERT: C 378 LYS cc_start: 0.8229 (tptp) cc_final: 0.7958 (tptp) REVERT: C 983 ARG cc_start: 0.8510 (tpp80) cc_final: 0.8302 (tpp80) REVERT: F 107 LYS cc_start: 0.7301 (mppt) cc_final: 0.6920 (mptt) REVERT: G 3 GLN cc_start: 0.8777 (mm110) cc_final: 0.8301 (mm-40) REVERT: G 95 TYR cc_start: 0.7744 (m-10) cc_final: 0.6549 (m-10) REVERT: G 98 ARG cc_start: 0.6146 (OUTLIER) cc_final: 0.5247 (tmm-80) REVERT: H 27 GLN cc_start: 0.7924 (tm-30) cc_final: 0.7140 (tm-30) REVERT: I 73 ASP cc_start: 0.8282 (t0) cc_final: 0.8006 (t0) REVERT: I 81 MET cc_start: 0.8264 (ttt) cc_final: 0.7962 (ttt) REVERT: I 82 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8610 (mm-30) REVERT: I 87 ARG cc_start: 0.8690 (ptp90) cc_final: 0.8461 (ptp90) outliers start: 52 outliers final: 32 residues processed: 225 average time/residue: 0.1675 time to fit residues: 61.8186 Evaluate side-chains 209 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 278 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 206 optimal weight: 8.9990 chunk 303 optimal weight: 0.9980 chunk 292 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 288 optimal weight: 0.5980 chunk 198 optimal weight: 7.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN G 59 ASN H 90 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.075441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.048161 restraints weight = 94039.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.050140 restraints weight = 43781.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.051428 restraints weight = 28256.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052170 restraints weight = 21672.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.052718 restraints weight = 18562.385| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27604 Z= 0.185 Angle : 0.580 10.261 37620 Z= 0.294 Chirality : 0.045 0.387 4362 Planarity : 0.004 0.060 4758 Dihedral : 4.189 25.639 3601 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.77 % Allowed : 12.64 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.15), residues: 3303 helix: 2.37 (0.21), residues: 649 sheet: 0.29 (0.18), residues: 831 loop : -0.91 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 50 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE C 559 TRP 0.008 0.001 TRP C 436 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 (27519) covalent geometry : angle 0.56746 / 0.29 (37407) SS BOND : bond 0.00296 / 0.21 ( 42) SS BOND : angle 0.91679 / 0.61 ( 84) hydrogen bonds : bond 0.04832 / 3.21 ( 1089) hydrogen bonds : angle 5.00063 / 3.52 ( 2985) link_BETA1-4 : bond 0.00243 / 0.16 ( 14) link_BETA1-4 : angle 1.00144 / 0.67 ( 42) link_NAG-ASN : bond 0.00374 / 0.24 ( 29) link_NAG-ASN : angle 2.36495 / 1.66 ( 87) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 190 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8688 (pp30) cc_final: 0.8292 (pp30) REVERT: A 1002 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7856 (tm-30) REVERT: B 740 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8239 (tmm) REVERT: B 1002 GLN cc_start: 0.8294 (tm-30) cc_final: 0.8079 (tm-30) REVERT: C 153 MET cc_start: 0.7322 (ppp) cc_final: 0.6833 (ppp) REVERT: C 378 LYS cc_start: 0.8205 (tptp) cc_final: 0.7987 (tptp) REVERT: F 107 LYS cc_start: 0.7324 (mppt) cc_final: 0.6906 (mptt) REVERT: G 3 GLN cc_start: 0.8802 (mm110) cc_final: 0.8328 (mm-40) REVERT: G 98 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5275 (tmm-80) REVERT: H 27 GLN cc_start: 0.7961 (tm-30) cc_final: 0.7161 (tm-30) REVERT: H 90 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.6836 (pp30) REVERT: I 19 LYS cc_start: 0.8712 (tptp) cc_final: 0.8236 (tptp) REVERT: I 73 ASP cc_start: 0.8296 (t0) cc_final: 0.8009 (t0) REVERT: I 81 MET cc_start: 0.8245 (ttt) cc_final: 0.7672 (ttt) REVERT: I 82 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8577 (mm-30) outliers start: 52 outliers final: 39 residues processed: 225 average time/residue: 0.1578 time to fit residues: 58.6249 Evaluate side-chains 215 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 90 GLN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 16 SER Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 104 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 139 optimal weight: 3.9990 chunk 200 optimal weight: 20.0000 chunk 202 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 192 optimal weight: 7.9990 chunk 262 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 116 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.075469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.048597 restraints weight = 91651.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050552 restraints weight = 42681.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051840 restraints weight = 27397.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.052647 restraints weight = 20822.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053101 restraints weight = 17664.395| |-----------------------------------------------------------------------------| r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 27604 Z= 0.159 Angle : 0.570 10.178 37620 Z= 0.289 Chirality : 0.045 0.385 4362 Planarity : 0.004 0.055 4758 Dihedral : 4.166 24.978 3601 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.63 % Allowed : 13.09 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3303 helix: 2.48 (0.21), residues: 643 sheet: 0.31 (0.17), residues: 839 loop : -0.88 (0.14), residues: 1821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 87 TYR 0.020 0.001 TYR B1067 PHE 0.018 0.001 PHE C 559 TRP 0.008 0.001 TRP C 436 HIS 0.005 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (27519) covalent geometry : angle 0.55719 / 0.29 (37407) SS BOND : bond 0.00335 / 0.21 ( 42) SS BOND : angle 1.06562 / 0.76 ( 84) hydrogen bonds : bond 0.04668 / 3.10 ( 1089) hydrogen bonds : angle 4.93642 / 3.47 ( 2985) link_BETA1-4 : bond 0.00252 / 0.16 ( 14) link_BETA1-4 : angle 0.97257 / 0.65 ( 42) link_NAG-ASN : bond 0.00364 / 0.24 ( 29) link_NAG-ASN : angle 2.31340 / 1.62 ( 87) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 187 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8650 (pp30) cc_final: 0.8262 (pp30) REVERT: A 983 ARG cc_start: 0.8898 (tmm-80) cc_final: 0.8475 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8353 (tm-30) cc_final: 0.7845 (tm-30) REVERT: B 740 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8187 (tmm) REVERT: B 1002 GLN cc_start: 0.8253 (tm-30) cc_final: 0.8023 (tm-30) REVERT: C 153 MET cc_start: 0.7365 (ppp) cc_final: 0.6883 (ppp) REVERT: C 378 LYS cc_start: 0.8143 (tptp) cc_final: 0.7854 (tptp) REVERT: C 983 ARG cc_start: 0.8555 (tpp80) cc_final: 0.8306 (tpp80) REVERT: F 55 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7238 (mt-10) REVERT: G 3 GLN cc_start: 0.8800 (mm110) cc_final: 0.8328 (mm-40) REVERT: G 95 TYR cc_start: 0.7773 (m-10) cc_final: 0.7537 (m-10) REVERT: G 98 ARG cc_start: 0.5997 (OUTLIER) cc_final: 0.5122 (tmm-80) REVERT: H 27 GLN cc_start: 0.7984 (tm-30) cc_final: 0.7167 (tm-30) REVERT: I 19 LYS cc_start: 0.8698 (tptp) cc_final: 0.8224 (tptp) REVERT: I 73 ASP cc_start: 0.8308 (t0) cc_final: 0.8036 (t0) REVERT: I 81 MET cc_start: 0.8129 (ttt) cc_final: 0.7584 (ttt) REVERT: I 82 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8534 (mm-30) outliers start: 48 outliers final: 38 residues processed: 221 average time/residue: 0.1663 time to fit residues: 59.9762 Evaluate side-chains 214 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 174 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 104 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 59 optimal weight: 0.9980 chunk 330 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 85 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 314 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 252 optimal weight: 2.9990 chunk 272 optimal weight: 0.9990 chunk 209 optimal weight: 10.0000 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.075050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.048141 restraints weight = 93208.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.050095 restraints weight = 43434.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.051375 restraints weight = 27907.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052141 restraints weight = 21298.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.052673 restraints weight = 18119.495| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 27604 Z= 0.189 Angle : 0.593 10.296 37620 Z= 0.300 Chirality : 0.045 0.389 4362 Planarity : 0.004 0.055 4758 Dihedral : 4.208 21.855 3601 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.80 % Allowed : 13.53 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.15), residues: 3303 helix: 2.46 (0.21), residues: 643 sheet: 0.23 (0.17), residues: 863 loop : -0.88 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 61 TYR 0.020 0.001 TYR B1067 PHE 0.020 0.001 PHE C 559 TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (27519) covalent geometry : angle 0.58117 / 0.30 (37407) SS BOND : bond 0.00353 / 0.22 ( 42) SS BOND : angle 1.02941 / 0.72 ( 84) hydrogen bonds : bond 0.04806 / 3.19 ( 1089) hydrogen bonds : angle 4.96624 / 3.49 ( 2985) link_BETA1-4 : bond 0.00238 / 0.15 ( 14) link_BETA1-4 : angle 1.02242 / 0.68 ( 42) link_NAG-ASN : bond 0.00374 / 0.24 ( 29) link_NAG-ASN : angle 2.35071 / 1.65 ( 87) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 185 time to evaluate : 0.993 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7970 (mp) REVERT: A 957 GLN cc_start: 0.8647 (pp30) cc_final: 0.8265 (pp30) REVERT: A 983 ARG cc_start: 0.8918 (tmm-80) cc_final: 0.8529 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8366 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 740 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8212 (tmm) REVERT: B 1002 GLN cc_start: 0.8283 (tm-30) cc_final: 0.8044 (tm-30) REVERT: C 153 MET cc_start: 0.7403 (ppp) cc_final: 0.6923 (ppp) REVERT: C 378 LYS cc_start: 0.8171 (tptp) cc_final: 0.7847 (tptp) REVERT: C 405 ASP cc_start: 0.8419 (m-30) cc_final: 0.8208 (m-30) REVERT: G 3 GLN cc_start: 0.8789 (mm110) cc_final: 0.8312 (mm-40) REVERT: G 54 ILE cc_start: 0.9291 (tp) cc_final: 0.8962 (mp) REVERT: G 95 TYR cc_start: 0.7794 (m-10) cc_final: 0.7562 (m-10) REVERT: G 98 ARG cc_start: 0.6150 (OUTLIER) cc_final: 0.5379 (tmm-80) REVERT: H 27 GLN cc_start: 0.8002 (tm-30) cc_final: 0.7208 (tm-30) REVERT: I 19 LYS cc_start: 0.8690 (tptp) cc_final: 0.8219 (tptp) REVERT: I 73 ASP cc_start: 0.8326 (t0) cc_final: 0.8067 (t0) REVERT: I 81 MET cc_start: 0.8240 (ttt) cc_final: 0.7659 (ttt) REVERT: I 82 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8525 (mm-30) REVERT: I 87 ARG cc_start: 0.8810 (ptp90) cc_final: 0.8528 (ptp90) outliers start: 53 outliers final: 42 residues processed: 224 average time/residue: 0.1613 time to fit residues: 59.5864 Evaluate side-chains 219 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 174 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 731 MET Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 959 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 68 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 188 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 170 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 301 optimal weight: 30.0000 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.075220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.048335 restraints weight = 92934.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.050294 restraints weight = 43308.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.051569 restraints weight = 27835.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052369 restraints weight = 21279.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.052842 restraints weight = 18041.860| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 27604 Z= 0.175 Angle : 0.587 10.243 37620 Z= 0.296 Chirality : 0.045 0.388 4362 Planarity : 0.004 0.094 4758 Dihedral : 4.189 23.618 3601 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.73 % Allowed : 13.63 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.15), residues: 3303 helix: 2.37 (0.21), residues: 649 sheet: 0.29 (0.17), residues: 854 loop : -0.89 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 50 TYR 0.020 0.001 TYR B1067 PHE 0.019 0.001 PHE C 559 TRP 0.010 0.001 TRP G 111 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.17 (27519) covalent geometry : angle 0.57576 / 0.29 (37407) SS BOND : bond 0.00373 / 0.22 ( 42) SS BOND : angle 0.91155 / 0.61 ( 84) hydrogen bonds : bond 0.04711 / 3.12 ( 1089) hydrogen bonds : angle 4.95100 / 3.48 ( 2985) link_BETA1-4 : bond 0.00246 / 0.16 ( 14) link_BETA1-4 : angle 0.99337 / 0.66 ( 42) link_NAG-ASN : bond 0.00364 / 0.24 ( 29) link_NAG-ASN : angle 2.32574 / 1.64 ( 87) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 189 time to evaluate : 1.073 Fit side-chains revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8648 (pp30) cc_final: 0.8273 (pp30) REVERT: A 983 ARG cc_start: 0.8948 (tmm-80) cc_final: 0.8567 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8369 (tm-30) cc_final: 0.7855 (tm-30) REVERT: B 740 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8200 (tmm) REVERT: B 1002 GLN cc_start: 0.8268 (tm-30) cc_final: 0.8011 (tm-30) REVERT: C 153 MET cc_start: 0.7472 (ppp) cc_final: 0.7001 (ppp) REVERT: C 378 LYS cc_start: 0.8194 (tptp) cc_final: 0.7857 (tptp) REVERT: C 405 ASP cc_start: 0.8409 (m-30) cc_final: 0.8204 (m-30) REVERT: C 583 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7943 (pm20) REVERT: C 983 ARG cc_start: 0.8591 (tpp80) cc_final: 0.8340 (tpp80) REVERT: G 3 GLN cc_start: 0.8798 (mm110) cc_final: 0.8320 (mm-40) REVERT: G 54 ILE cc_start: 0.9310 (tp) cc_final: 0.9020 (mp) REVERT: G 95 TYR cc_start: 0.7774 (m-10) cc_final: 0.7549 (m-10) REVERT: H 27 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7234 (tm-30) REVERT: I 19 LYS cc_start: 0.8714 (tptp) cc_final: 0.8242 (tptp) REVERT: I 73 ASP cc_start: 0.8318 (t0) cc_final: 0.8046 (t0) REVERT: I 81 MET cc_start: 0.8310 (ttt) cc_final: 0.7650 (ttt) REVERT: I 82 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8417 (tp30) outliers start: 51 outliers final: 43 residues processed: 227 average time/residue: 0.1661 time to fit residues: 61.7820 Evaluate side-chains 220 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 180 optimal weight: 2.9990 chunk 101 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 7.9990 chunk 232 optimal weight: 4.9990 chunk 325 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 258 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.076114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.049394 restraints weight = 92303.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.051359 restraints weight = 44700.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.052651 restraints weight = 29215.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.053478 restraints weight = 22503.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.053936 restraints weight = 19087.556| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27604 Z= 0.144 Angle : 0.593 10.091 37620 Z= 0.298 Chirality : 0.045 0.382 4362 Planarity : 0.004 0.108 4758 Dihedral : 4.174 34.641 3601 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 1.60 % Allowed : 14.07 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.15), residues: 3303 helix: 2.42 (0.21), residues: 649 sheet: 0.34 (0.17), residues: 846 loop : -0.89 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 50 TYR 0.032 0.001 TYR G 32 PHE 0.017 0.001 PHE C 559 TRP 0.010 0.001 TRP I 47 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (27519) covalent geometry : angle 0.58174 / 0.30 (37407) SS BOND : bond 0.00328 / 0.21 ( 42) SS BOND : angle 0.90609 / 0.61 ( 84) hydrogen bonds : bond 0.04534 / 3.00 ( 1089) hydrogen bonds : angle 4.89848 / 3.45 ( 2985) link_BETA1-4 : bond 0.00273 / 0.17 ( 14) link_BETA1-4 : angle 0.96070 / 0.64 ( 42) link_NAG-ASN : bond 0.00358 / 0.24 ( 29) link_NAG-ASN : angle 2.25841 / 1.59 ( 87) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6606 Ramachandran restraints generated. 3303 Oldfield, 0 Emsley, 3303 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8651 (pp30) cc_final: 0.8283 (pp30) REVERT: A 983 ARG cc_start: 0.8949 (tmm-80) cc_final: 0.8609 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7830 (tm-30) REVERT: B 740 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8208 (tmm) REVERT: B 1002 GLN cc_start: 0.8251 (tm-30) cc_final: 0.8006 (tm-30) REVERT: C 153 MET cc_start: 0.7470 (ppp) cc_final: 0.6981 (ppp) REVERT: C 378 LYS cc_start: 0.8171 (tptp) cc_final: 0.7825 (tptp) REVERT: C 583 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.7950 (pm20) REVERT: C 983 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8373 (tpp80) REVERT: F 46 LEU cc_start: 0.8952 (pt) cc_final: 0.8310 (pt) REVERT: G 3 GLN cc_start: 0.8796 (mm110) cc_final: 0.8321 (mm-40) REVERT: H 27 GLN cc_start: 0.8035 (tm-30) cc_final: 0.7218 (tm-30) REVERT: I 73 ASP cc_start: 0.8390 (t0) cc_final: 0.8126 (t0) REVERT: I 81 MET cc_start: 0.8341 (ttt) cc_final: 0.7902 (ttt) REVERT: I 82 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8610 (mm-30) outliers start: 47 outliers final: 42 residues processed: 227 average time/residue: 0.1603 time to fit residues: 59.3040 Evaluate side-chains 217 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 173 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 869 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 587 ILE Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 994 ASP Chi-restraints excluded: chain B residue 1077 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 578 ASP Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 93 SER Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 93 SER Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 51 ILE Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 15 optimal weight: 5.9990 chunk 123 optimal weight: 7.9990 chunk 143 optimal weight: 5.9990 chunk 188 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 118 optimal weight: 7.9990 chunk 13 optimal weight: 0.9980 chunk 223 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 294 optimal weight: 0.1980 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.074563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.047704 restraints weight = 93097.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.049607 restraints weight = 45675.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.050856 restraints weight = 30056.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.051646 restraints weight = 23261.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.052089 restraints weight = 19874.662| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 27604 Z= 0.254 Angle : 0.661 10.560 37620 Z= 0.333 Chirality : 0.046 0.401 4362 Planarity : 0.004 0.109 4758 Dihedral : 4.383 30.819 3601 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.67 % Allowed : 14.24 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.15), residues: 3303 helix: 2.17 (0.21), residues: 655 sheet: 0.11 (0.17), residues: 857 loop : -0.97 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG G 67 TYR 0.042 0.002 TYR G 32 PHE 0.023 0.001 PHE C 559 TRP 0.013 0.001 TRP I 47 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.25 (27519) covalent geometry : angle 0.64832 / 0.33 (37407) SS BOND : bond 0.00394 / 0.25 ( 42) SS BOND : angle 1.12032 / 0.77 ( 84) hydrogen bonds : bond 0.05213 / 3.47 ( 1089) hydrogen bonds : angle 5.13173 / 3.61 ( 2985) link_BETA1-4 : bond 0.00238 / 0.15 ( 14) link_BETA1-4 : angle 1.16071 / 0.76 ( 42) link_NAG-ASN : bond 0.00445 / 0.29 ( 29) link_NAG-ASN : angle 2.47580 / 1.74 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4936.02 seconds wall clock time: 86 minutes 0.70 seconds (5160.70 seconds total)