Starting phenix.real_space_refine on Fri Mar 6 01:43:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wwj_32867/03_2026/7wwj_32867.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wwj_32867/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wwj_32867/03_2026/7wwj_32867.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wwj_32867/03_2026/7wwj_32867.map" model { file = "/net/cci-nas-00/data/ceres_data/7wwj_32867/03_2026/7wwj_32867.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wwj_32867/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 15 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 dihedrals: 15 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 dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.51, per 1000 atoms: 0.24 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: 1.99 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.33 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: 5.93 Time building geometry restraints manager: 2.65 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: 15504 17.93 - 35.87: 1179 35.87 - 53.80: 222 53.80 - 71.74: 59 71.74 - 89.67: 32 Dihedral angle restraints: 16996 sinusoidal: 7210 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 16993 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: 14.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 25.840 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 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 : 13.498 89.673 10568 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 covalent geometry : bond 0.00343 (27519) covalent geometry : angle 0.60471 (37407) SS BOND : bond 0.00277 ( 42) SS BOND : angle 0.78275 ( 84) hydrogen bonds : bond 0.13134 ( 1089) hydrogen bonds : angle 6.37647 ( 2985) link_BETA1-4 : bond 0.00384 ( 14) link_BETA1-4 : angle 0.98014 ( 42) link_NAG-ASN : bond 0.00492 ( 29) link_NAG-ASN : angle 2.61550 ( 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 : 1.113 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: 0.1779 time to fit residues: 68.6772 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 : 0.982 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.075514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.048171 restraints weight = 94410.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050156 restraints weight = 43891.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.051449 restraints weight = 28238.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.052245 restraints weight = 21623.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052759 restraints weight = 18397.320| |-----------------------------------------------------------------------------| r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 27604 Z= 0.251 Angle : 0.636 10.068 37620 Z= 0.324 Chirality : 0.047 0.400 4362 Planarity : 0.004 0.059 4758 Dihedral : 7.022 59.966 4504 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.68 % Allowed : 6.80 % Favored : 92.52 % 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: 2.14 (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 0.026 0.002 PHE B 490 TRP 0.011 0.001 TRP I 47 HIS 0.007 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00587 (27519) covalent geometry : angle 0.62176 (37407) SS BOND : bond 0.00326 ( 42) SS BOND : angle 1.03360 ( 84) hydrogen bonds : bond 0.05408 ( 1089) hydrogen bonds : angle 5.38516 ( 2985) link_BETA1-4 : bond 0.00275 ( 14) link_BETA1-4 : angle 1.16020 ( 42) link_NAG-ASN : bond 0.00468 ( 29) link_NAG-ASN : angle 2.66194 ( 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 217 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9113 (mtm) cc_final: 0.8521 (mtm) REVERT: A 1002 GLN cc_start: 0.8375 (tm-30) cc_final: 0.7863 (tm-30) REVERT: B 357 ARG cc_start: 0.7047 (OUTLIER) cc_final: 0.6682 (tpp80) REVERT: B 1002 GLN cc_start: 0.8329 (tm-30) cc_final: 0.8068 (tm-30) REVERT: B 1050 MET cc_start: 0.8744 (ptm) cc_final: 0.8532 (ptm) REVERT: C 153 MET cc_start: 0.7306 (ppp) cc_final: 0.6670 (ppp) REVERT: C 776 LYS cc_start: 0.9368 (tppt) cc_final: 0.9138 (tmmt) REVERT: C 988 GLU cc_start: 0.8878 (mp0) cc_final: 0.8651 (pm20) REVERT: G 3 GLN cc_start: 0.8770 (mm110) cc_final: 0.8281 (mm-40) REVERT: H 27 GLN cc_start: 0.7741 (tm-30) cc_final: 0.7079 (tm-30) REVERT: H 90 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.6892 (pp30) REVERT: H 104 LEU cc_start: 0.9057 (tp) cc_final: 0.8831 (tp) REVERT: I 19 LYS cc_start: 0.8714 (tptp) cc_final: 0.8264 (tptp) REVERT: I 73 ASP cc_start: 0.8200 (t0) cc_final: 0.7919 (t0) REVERT: I 82 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8690 (mm-30) outliers start: 20 outliers final: 16 residues processed: 208 average time/residue: 0.1721 time to fit residues: 58.2076 Evaluate side-chains 187 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 90 ASP 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: 2.9990 chunk 242 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 294 optimal weight: 8.9990 chunk 296 optimal weight: 20.0000 chunk 317 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 chunk 217 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** H 90 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.075727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.048422 restraints weight = 93820.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.050410 restraints weight = 43532.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.051708 restraints weight = 28016.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.052522 restraints weight = 21429.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.052971 restraints weight = 18211.345| |-----------------------------------------------------------------------------| r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 27604 Z= 0.193 Angle : 0.586 10.375 37620 Z= 0.297 Chirality : 0.045 0.399 4362 Planarity : 0.004 0.054 4758 Dihedral : 6.507 58.574 4504 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.92 % Allowed : 9.45 % Favored : 89.63 % 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: 0.01 (0.14), residues: 3303 helix: 2.26 (0.21), residues: 652 sheet: 0.23 (0.17), residues: 840 loop : -0.98 (0.14), residues: 1811 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 61 TYR 0.021 0.001 TYR B1067 PHE 0.021 0.001 PHE C 559 TRP 0.008 0.001 TRP H 35 HIS 0.008 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00448 (27519) covalent geometry : angle 0.57203 (37407) SS BOND : bond 0.00293 ( 42) SS BOND : angle 0.90762 ( 84) hydrogen bonds : bond 0.05070 ( 1089) hydrogen bonds : angle 5.15919 ( 2985) link_BETA1-4 : bond 0.00266 ( 14) link_BETA1-4 : angle 1.09485 ( 42) link_NAG-ASN : bond 0.00422 ( 29) link_NAG-ASN : angle 2.54614 ( 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 220 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 193 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 869 MET cc_start: 0.9127 (mtm) cc_final: 0.8539 (mtm) REVERT: A 987 PRO cc_start: 0.8058 (OUTLIER) cc_final: 0.7823 (Cg_endo) REVERT: A 1002 GLN cc_start: 0.8378 (tm-30) cc_final: 0.7883 (tm-30) REVERT: B 1002 GLN cc_start: 0.8297 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 1050 MET cc_start: 0.8792 (ptm) cc_final: 0.8586 (ptm) REVERT: C 153 MET cc_start: 0.7291 (ppp) cc_final: 0.6738 (ppp) REVERT: G 3 GLN cc_start: 0.8773 (mm110) cc_final: 0.8289 (mm-40) REVERT: G 100 THR cc_start: 0.8753 (m) cc_final: 0.8517 (t) REVERT: H 27 GLN cc_start: 0.7797 (tm-30) cc_final: 0.7092 (tm-30) REVERT: H 90 GLN cc_start: 0.7779 (OUTLIER) cc_final: 0.6595 (pp30) REVERT: I 73 ASP cc_start: 0.8292 (t0) cc_final: 0.7986 (t0) REVERT: I 81 MET cc_start: 0.8219 (ttt) cc_final: 0.7819 (ttt) REVERT: I 82 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8570 (mm-30) outliers start: 27 outliers final: 15 residues processed: 209 average time/residue: 0.1644 time to fit residues: 56.5756 Evaluate side-chains 189 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 987 PRO 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 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 F residue 58 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 84 optimal weight: 0.0000 chunk 184 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 179 optimal weight: 1.9990 chunk 235 optimal weight: 2.9990 chunk 178 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 253 optimal weight: 0.3980 chunk 229 optimal weight: 1.9990 chunk 245 optimal weight: 0.6980 overall best weight: 0.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** 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 = 0.3554 r_free = 0.3554 target = 0.077155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.050365 restraints weight = 92802.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.052390 restraints weight = 42910.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.053703 restraints weight = 27508.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.054514 restraints weight = 20998.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.054963 restraints weight = 17840.026| |-----------------------------------------------------------------------------| r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 27604 Z= 0.113 Angle : 0.550 9.923 37620 Z= 0.277 Chirality : 0.045 0.387 4362 Planarity : 0.004 0.056 4758 Dihedral : 5.994 58.565 4504 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.02 % Allowed : 10.81 % Favored : 88.17 % 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: 0.19 (0.14), residues: 3303 helix: 2.47 (0.21), residues: 644 sheet: 0.43 (0.17), residues: 823 loop : -0.91 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 61 TYR 0.020 0.001 TYR B1067 PHE 0.015 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 covalent geometry : bond 0.00252 (27519) covalent geometry : angle 0.53462 (37407) SS BOND : bond 0.00245 ( 42) SS BOND : angle 1.33276 ( 84) hydrogen bonds : bond 0.04499 ( 1089) hydrogen bonds : angle 4.88439 ( 2985) link_BETA1-4 : bond 0.00370 ( 14) link_BETA1-4 : angle 1.00083 ( 42) link_NAG-ASN : bond 0.00415 ( 29) link_NAG-ASN : angle 2.34554 ( 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 227 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8659 (pp30) cc_final: 0.8210 (pp30) REVERT: A 1002 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7823 (tm-30) REVERT: B 773 GLU cc_start: 0.8765 (tp30) cc_final: 0.8272 (tp30) REVERT: B 1002 GLN cc_start: 0.8268 (tm-30) cc_final: 0.8039 (tm-30) REVERT: B 1050 MET cc_start: 0.8742 (ptm) cc_final: 0.8538 (ptm) REVERT: C 988 GLU cc_start: 0.8612 (pm20) cc_final: 0.8383 (pm20) REVERT: G 3 GLN cc_start: 0.8748 (mm110) cc_final: 0.8267 (mm-40) REVERT: G 90 ASP cc_start: 0.6740 (OUTLIER) cc_final: 0.6512 (p0) REVERT: G 98 ARG cc_start: 0.6343 (OUTLIER) cc_final: 0.4984 (tmm-80) REVERT: H 27 GLN cc_start: 0.7920 (tm-30) cc_final: 0.7189 (tm-30) REVERT: I 63 LYS cc_start: 0.9150 (pttm) cc_final: 0.8839 (pttm) REVERT: I 73 ASP cc_start: 0.8313 (t0) cc_final: 0.7926 (t0) REVERT: I 81 MET cc_start: 0.8254 (ttt) cc_final: 0.7984 (ttt) outliers start: 30 outliers final: 17 residues processed: 218 average time/residue: 0.1687 time to fit residues: 59.6174 Evaluate side-chains 195 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 245 HIS Chi-restraints excluded: chain B residue 587 ILE 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 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 90 ASP 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 104 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 38 optimal weight: 8.9990 chunk 275 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 302 optimal weight: 30.0000 chunk 183 optimal weight: 4.9990 chunk 84 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 224 optimal weight: 0.6980 chunk 79 optimal weight: 3.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 GLN C 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.076455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.049577 restraints weight = 93725.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.051565 restraints weight = 43714.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.052849 restraints weight = 28213.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.053639 restraints weight = 21642.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054151 restraints weight = 18451.580| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27604 Z= 0.162 Angle : 0.562 10.173 37620 Z= 0.283 Chirality : 0.045 0.387 4362 Planarity : 0.004 0.064 4758 Dihedral : 5.686 55.604 4504 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.73 % Allowed : 11.35 % Favored : 86.91 % 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: 0.21 (0.14), residues: 3303 helix: 2.47 (0.21), residues: 647 sheet: 0.41 (0.17), residues: 833 loop : -0.89 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 61 TYR 0.025 0.001 TYR G 32 PHE 0.018 0.001 PHE C 559 TRP 0.008 0.001 TRP I 47 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00377 (27519) covalent geometry : angle 0.54792 (37407) SS BOND : bond 0.00251 ( 42) SS BOND : angle 1.02141 ( 84) hydrogen bonds : bond 0.04648 ( 1089) hydrogen bonds : angle 4.90558 ( 2985) link_BETA1-4 : bond 0.00249 ( 14) link_BETA1-4 : angle 1.08389 ( 42) link_NAG-ASN : bond 0.00386 ( 29) link_NAG-ASN : angle 2.38281 ( 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 237 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8705 (pp30) cc_final: 0.8290 (pp30) REVERT: A 1002 GLN cc_start: 0.8355 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 740 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8207 (tmm) REVERT: B 1002 GLN cc_start: 0.8266 (tm-30) cc_final: 0.8052 (tm-30) REVERT: B 1050 MET cc_start: 0.8773 (ptm) cc_final: 0.8572 (ptm) REVERT: C 153 MET cc_start: 0.7283 (ppp) cc_final: 0.6802 (ppp) REVERT: F 107 LYS cc_start: 0.7297 (mppt) cc_final: 0.6912 (mptt) REVERT: G 3 GLN cc_start: 0.8760 (mm110) cc_final: 0.8283 (mm-40) REVERT: H 27 GLN cc_start: 0.7929 (tm-30) cc_final: 0.7141 (tm-30) REVERT: H 103 LYS cc_start: 0.8665 (tppt) cc_final: 0.8254 (tttm) REVERT: I 73 ASP cc_start: 0.8342 (t0) cc_final: 0.8068 (t0) REVERT: I 81 MET cc_start: 0.8294 (ttt) cc_final: 0.7997 (ttt) REVERT: I 82 GLU cc_start: 0.8907 (mm-30) cc_final: 0.8627 (mm-30) REVERT: I 87 ARG cc_start: 0.8718 (ptp90) cc_final: 0.8489 (ptp90) outliers start: 51 outliers final: 30 residues processed: 223 average time/residue: 0.1615 time to fit residues: 59.0694 Evaluate side-chains 207 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 176 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 194 optimal weight: 9.9990 chunk 143 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 206 optimal weight: 8.9990 chunk 303 optimal weight: 0.0270 chunk 292 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 288 optimal weight: 0.9980 chunk 198 optimal weight: 2.9990 overall best weight: 2.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN C 121 ASN G 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.075253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.048127 restraints weight = 93988.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.050093 restraints weight = 43679.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051368 restraints weight = 28114.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.052180 restraints weight = 21542.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.052675 restraints weight = 18294.963| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 27604 Z= 0.204 Angle : 0.587 10.266 37620 Z= 0.298 Chirality : 0.045 0.394 4362 Planarity : 0.004 0.060 4758 Dihedral : 5.588 54.042 4504 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.73 % Allowed : 12.61 % Favored : 85.66 % 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: 2.38 (0.21), residues: 649 sheet: 0.34 (0.18), residues: 840 loop : -0.91 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 98 TYR 0.022 0.001 TYR G 32 PHE 0.021 0.001 PHE C 559 TRP 0.009 0.001 TRP G 36 HIS 0.004 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00479 (27519) covalent geometry : angle 0.57346 (37407) SS BOND : bond 0.00377 ( 42) SS BOND : angle 0.96309 ( 84) hydrogen bonds : bond 0.04917 ( 1089) hydrogen bonds : angle 5.00026 ( 2985) link_BETA1-4 : bond 0.00239 ( 14) link_BETA1-4 : angle 1.11497 ( 42) link_NAG-ASN : bond 0.00394 ( 29) link_NAG-ASN : angle 2.44880 ( 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 236 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 185 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8686 (pp30) cc_final: 0.8297 (pp30) REVERT: A 1002 GLN cc_start: 0.8377 (tm-30) cc_final: 0.7862 (tm-30) REVERT: B 740 MET cc_start: 0.9101 (OUTLIER) cc_final: 0.8254 (tmm) REVERT: B 1002 GLN cc_start: 0.8287 (tm-30) cc_final: 0.8075 (tm-30) REVERT: B 1050 MET cc_start: 0.8783 (ptm) cc_final: 0.8583 (ptm) REVERT: C 153 MET cc_start: 0.7311 (ppp) cc_final: 0.6811 (ppp) REVERT: C 988 GLU cc_start: 0.8740 (pm20) cc_final: 0.8508 (pm20) REVERT: F 55 GLU cc_start: 0.7941 (tt0) cc_final: 0.7211 (mt-10) REVERT: F 107 LYS cc_start: 0.7379 (mppt) cc_final: 0.6961 (mptt) REVERT: G 3 GLN cc_start: 0.8787 (mm110) cc_final: 0.8312 (mm-40) REVERT: G 98 ARG cc_start: 0.6362 (OUTLIER) cc_final: 0.5088 (tmm-80) REVERT: H 27 GLN cc_start: 0.7985 (tm-30) cc_final: 0.7192 (tm-30) REVERT: I 19 LYS cc_start: 0.8704 (tptp) cc_final: 0.8245 (tptp) REVERT: I 62 GLN cc_start: 0.8695 (pp30) cc_final: 0.8444 (pp30) REVERT: I 73 ASP cc_start: 0.8354 (t0) cc_final: 0.8100 (t0) REVERT: I 81 MET cc_start: 0.8254 (ttt) cc_final: 0.7684 (ttt) REVERT: I 82 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8559 (mm-30) outliers start: 51 outliers final: 40 residues processed: 220 average time/residue: 0.1629 time to fit residues: 58.7731 Evaluate side-chains 212 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 1.017 ------------------------------------------------------------------------------- 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 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 104 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 139 optimal weight: 6.9990 chunk 200 optimal weight: 20.0000 chunk 202 optimal weight: 3.9990 chunk 219 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 262 optimal weight: 1.9990 chunk 234 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3488 r_free = 0.3488 target = 0.075452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.048372 restraints weight = 93392.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050372 restraints weight = 43715.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.051676 restraints weight = 28127.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.052417 restraints weight = 21514.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.052971 restraints weight = 18391.636| |-----------------------------------------------------------------------------| r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 27604 Z= 0.156 Angle : 0.564 10.096 37620 Z= 0.286 Chirality : 0.045 0.388 4362 Planarity : 0.004 0.055 4758 Dihedral : 5.413 54.127 4504 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.67 % Allowed : 13.15 % Favored : 85.18 % 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: 0.18 (0.15), residues: 3303 helix: 2.49 (0.21), residues: 643 sheet: 0.34 (0.17), residues: 840 loop : -0.88 (0.14), residues: 1820 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 0.004 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00365 (27519) covalent geometry : angle 0.55070 (37407) SS BOND : bond 0.00326 ( 42) SS BOND : angle 1.13499 ( 84) hydrogen bonds : bond 0.04631 ( 1089) hydrogen bonds : angle 4.91176 ( 2985) link_BETA1-4 : bond 0.00288 ( 14) link_BETA1-4 : angle 1.04482 ( 42) link_NAG-ASN : bond 0.00368 ( 29) link_NAG-ASN : angle 2.35787 ( 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 237 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.028 Fit side-chains revert: symmetry clash REVERT: A 957 GLN cc_start: 0.8649 (pp30) cc_final: 0.8266 (pp30) REVERT: A 983 ARG cc_start: 0.8891 (tmm-80) cc_final: 0.8521 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8348 (tm-30) cc_final: 0.7836 (tm-30) REVERT: B 740 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8188 (tmm) REVERT: B 1002 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 1050 MET cc_start: 0.8794 (ptm) cc_final: 0.8584 (ptm) REVERT: C 153 MET cc_start: 0.7378 (ppp) cc_final: 0.6892 (ppp) REVERT: C 378 LYS cc_start: 0.8082 (tptp) cc_final: 0.7772 (tptp) REVERT: C 405 ASP cc_start: 0.8408 (m-30) cc_final: 0.8205 (m-30) REVERT: C 988 GLU cc_start: 0.8740 (pm20) cc_final: 0.8519 (pm20) REVERT: F 107 LYS cc_start: 0.7411 (mppt) cc_final: 0.6984 (mptt) REVERT: G 3 GLN cc_start: 0.8794 (mm110) cc_final: 0.8320 (mm-40) REVERT: G 98 ARG cc_start: 0.6090 (OUTLIER) cc_final: 0.5111 (tmm-80) REVERT: H 27 GLN cc_start: 0.7980 (tm-30) cc_final: 0.7195 (tm-30) REVERT: I 19 LYS cc_start: 0.8701 (tptp) cc_final: 0.8239 (tptp) REVERT: I 73 ASP cc_start: 0.8355 (t0) cc_final: 0.8087 (t0) REVERT: I 81 MET cc_start: 0.8095 (ttt) cc_final: 0.7623 (ttt) REVERT: I 82 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8521 (mm-30) outliers start: 49 outliers final: 37 residues processed: 222 average time/residue: 0.1643 time to fit residues: 59.8636 Evaluate side-chains 215 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 740 MET 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 395 VAL 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 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 104 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 333 random chunks: chunk 59 optimal weight: 2.9990 chunk 330 optimal weight: 9.9990 chunk 198 optimal weight: 20.0000 chunk 85 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 314 optimal weight: 4.9990 chunk 207 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 252 optimal weight: 4.9990 chunk 272 optimal weight: 2.9990 chunk 209 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 603 ASN C 957 GLN G 39 GLN H 90 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.074112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.047237 restraints weight = 93820.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.049140 restraints weight = 44071.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.050390 restraints weight = 28519.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.051171 restraints weight = 21857.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.051645 restraints weight = 18582.900| |-----------------------------------------------------------------------------| r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 27604 Z= 0.270 Angle : 0.645 10.467 37620 Z= 0.326 Chirality : 0.046 0.401 4362 Planarity : 0.004 0.054 4758 Dihedral : 5.559 54.123 4504 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.07 % Allowed : 13.43 % Favored : 84.50 % 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: -0.03 (0.15), residues: 3303 helix: 2.14 (0.21), residues: 661 sheet: 0.19 (0.17), residues: 853 loop : -0.98 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 61 TYR 0.020 0.002 TYR B1067 PHE 0.024 0.001 PHE C 559 TRP 0.008 0.001 TRP C 64 HIS 0.005 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00631 (27519) covalent geometry : angle 0.63087 (37407) SS BOND : bond 0.00401 ( 42) SS BOND : angle 1.21578 ( 84) hydrogen bonds : bond 0.05231 ( 1089) hydrogen bonds : angle 5.15035 ( 2985) link_BETA1-4 : bond 0.00267 ( 14) link_BETA1-4 : angle 1.20444 ( 42) link_NAG-ASN : bond 0.00472 ( 29) link_NAG-ASN : angle 2.56757 ( 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 245 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 184 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.8026 (mp) REVERT: A 983 ARG cc_start: 0.8936 (tmm-80) cc_final: 0.8576 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8409 (tm-30) cc_final: 0.7905 (tm-30) REVERT: B 740 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8228 (tmm) REVERT: B 1002 GLN cc_start: 0.8324 (tm-30) cc_final: 0.8087 (tm-30) REVERT: B 1050 MET cc_start: 0.8816 (ptm) cc_final: 0.8609 (ptm) REVERT: C 153 MET cc_start: 0.7442 (ppp) cc_final: 0.6950 (ppp) REVERT: C 378 LYS cc_start: 0.8180 (tptp) cc_final: 0.7819 (tptp) REVERT: C 583 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7906 (pm20) REVERT: F 55 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7440 (mp0) REVERT: F 107 LYS cc_start: 0.7441 (mppt) cc_final: 0.6989 (mptt) REVERT: G 3 GLN cc_start: 0.8765 (mm110) cc_final: 0.8287 (mm-40) REVERT: G 98 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5787 (tmm-80) REVERT: H 27 GLN cc_start: 0.8001 (tm-30) cc_final: 0.7159 (tm-30) REVERT: H 90 GLN cc_start: 0.7942 (OUTLIER) cc_final: 0.6807 (pp30) REVERT: I 19 LYS cc_start: 0.8729 (tptp) cc_final: 0.8493 (tptm) REVERT: I 63 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8932 (ptpp) REVERT: I 73 ASP cc_start: 0.8354 (t0) cc_final: 0.8093 (t0) REVERT: I 82 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8534 (mm-30) REVERT: I 87 ARG cc_start: 0.8833 (ptp90) cc_final: 0.8543 (ptp90) outliers start: 61 outliers final: 47 residues processed: 230 average time/residue: 0.1555 time to fit residues: 59.2820 Evaluate side-chains 221 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 168 time to evaluate : 0.995 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET 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 896 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 135 PHE 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 957 GLN 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 F residue 104 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 98 ARG Chi-restraints excluded: chain G residue 117 VAL Chi-restraints excluded: chain H residue 90 GLN 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 63 LYS 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: 4.9990 chunk 66 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 170 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 301 optimal weight: 30.0000 chunk 287 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** B 613 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.075803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.049127 restraints weight = 92764.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.051111 restraints weight = 44717.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052407 restraints weight = 29074.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.053226 restraints weight = 22344.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.053714 restraints weight = 19005.621| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 27604 Z= 0.151 Angle : 0.578 10.032 37620 Z= 0.294 Chirality : 0.045 0.388 4362 Planarity : 0.004 0.056 4758 Dihedral : 5.376 54.098 4504 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.77 % Allowed : 13.83 % Favored : 84.40 % 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: 0.09 (0.15), residues: 3303 helix: 2.34 (0.21), residues: 649 sheet: 0.27 (0.17), residues: 854 loop : -0.93 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 983 TYR 0.021 0.001 TYR B1067 PHE 0.017 0.001 PHE C 559 TRP 0.009 0.001 TRP C 436 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00352 (27519) covalent geometry : angle 0.56510 (37407) SS BOND : bond 0.00363 ( 42) SS BOND : angle 0.99412 ( 84) hydrogen bonds : bond 0.04704 ( 1089) hydrogen bonds : angle 4.98694 ( 2985) link_BETA1-4 : bond 0.00314 ( 14) link_BETA1-4 : angle 1.05603 ( 42) link_NAG-ASN : bond 0.00369 ( 29) link_NAG-ASN : angle 2.37955 ( 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 238 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7982 (mp) REVERT: A 957 GLN cc_start: 0.8653 (pp30) cc_final: 0.8279 (pp30) REVERT: A 983 ARG cc_start: 0.8933 (tmm-80) cc_final: 0.8554 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8367 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 740 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8202 (tmm) REVERT: B 1002 GLN cc_start: 0.8274 (tm-30) cc_final: 0.8033 (tm-30) REVERT: C 153 MET cc_start: 0.7506 (ppp) cc_final: 0.7017 (ppp) REVERT: C 378 LYS cc_start: 0.8163 (tptp) cc_final: 0.7800 (tptp) REVERT: C 405 ASP cc_start: 0.8398 (m-30) cc_final: 0.8193 (m-30) REVERT: F 46 LEU cc_start: 0.9004 (pt) cc_final: 0.8385 (pt) REVERT: F 107 LYS cc_start: 0.7486 (mppt) cc_final: 0.7072 (mptt) REVERT: G 3 GLN cc_start: 0.8785 (mm110) cc_final: 0.8302 (mm-40) REVERT: G 98 ARG cc_start: 0.6154 (OUTLIER) cc_final: 0.5134 (tmm-80) REVERT: H 27 GLN cc_start: 0.8020 (tm-30) cc_final: 0.7222 (tm-30) REVERT: I 19 LYS cc_start: 0.8702 (tptp) cc_final: 0.8474 (tptm) REVERT: I 73 ASP cc_start: 0.8400 (t0) cc_final: 0.8130 (t0) REVERT: I 81 MET cc_start: 0.8171 (ttt) cc_final: 0.7870 (ttt) REVERT: I 82 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8456 (mm-30) REVERT: I 87 ARG cc_start: 0.8824 (ptp90) cc_final: 0.8537 (ptp90) outliers start: 52 outliers final: 43 residues processed: 222 average time/residue: 0.1676 time to fit residues: 60.2236 Evaluate side-chains 219 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 173 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 84 LEU Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 705 VAL Chi-restraints excluded: chain A residue 740 MET 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 592 PHE 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 1010 GLN 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 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 32 TYR Chi-restraints excluded: chain G residue 71 THR 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 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: 0.0570 chunk 265 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 209 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 chunk 325 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 258 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 327 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1064 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.076348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.049670 restraints weight = 92284.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.051660 restraints weight = 44530.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052965 restraints weight = 28993.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.053801 restraints weight = 22262.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.054264 restraints weight = 18877.922| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27604 Z= 0.127 Angle : 0.580 10.149 37620 Z= 0.290 Chirality : 0.045 0.377 4362 Planarity : 0.004 0.095 4758 Dihedral : 5.150 54.460 4504 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.43 % Allowed : 14.21 % Favored : 84.36 % 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: 0.15 (0.15), residues: 3303 helix: 2.37 (0.21), residues: 656 sheet: 0.31 (0.17), residues: 853 loop : -0.90 (0.14), residues: 1794 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 50 TYR 0.019 0.001 TYR B1067 PHE 0.015 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 covalent geometry : bond 0.00297 (27519) covalent geometry : angle 0.56838 (37407) SS BOND : bond 0.00321 ( 42) SS BOND : angle 0.84366 ( 84) hydrogen bonds : bond 0.04386 ( 1089) hydrogen bonds : angle 4.87019 ( 2985) link_BETA1-4 : bond 0.00335 ( 14) link_BETA1-4 : angle 1.00138 ( 42) link_NAG-ASN : bond 0.00367 ( 29) link_NAG-ASN : angle 2.27054 ( 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 236 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7963 (mp) REVERT: A 957 GLN cc_start: 0.8638 (pp30) cc_final: 0.8287 (pp30) REVERT: A 983 ARG cc_start: 0.8929 (tmm-80) cc_final: 0.8589 (tmm-80) REVERT: A 1002 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7818 (tm-30) REVERT: B 740 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8192 (tmm) REVERT: B 1002 GLN cc_start: 0.8233 (tm-30) cc_final: 0.8007 (tm-30) REVERT: C 153 MET cc_start: 0.7474 (ppp) cc_final: 0.6948 (ppp) REVERT: C 378 LYS cc_start: 0.8157 (tptp) cc_final: 0.7803 (tptp) REVERT: C 979 ASP cc_start: 0.8893 (t0) cc_final: 0.8456 (t0) REVERT: C 983 ARG cc_start: 0.7221 (mtm-85) cc_final: 0.6297 (mtm-85) REVERT: F 107 LYS cc_start: 0.7551 (mppt) cc_final: 0.7149 (mptt) REVERT: G 3 GLN cc_start: 0.8817 (mm110) cc_final: 0.8345 (mm-40) REVERT: G 98 ARG cc_start: 0.6178 (OUTLIER) cc_final: 0.5176 (tmm-80) REVERT: H 27 GLN cc_start: 0.8028 (tm-30) cc_final: 0.7208 (tm-30) REVERT: I 73 ASP cc_start: 0.8413 (t0) cc_final: 0.8135 (t0) REVERT: I 81 MET cc_start: 0.8156 (ttt) cc_final: 0.7781 (ttt) REVERT: I 82 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8551 (mm-30) REVERT: I 87 ARG cc_start: 0.8725 (ptp90) cc_final: 0.8432 (ptp90) outliers start: 42 outliers final: 37 residues processed: 221 average time/residue: 0.1645 time to fit residues: 59.1352 Evaluate side-chains 215 residues out of total 2943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.924 ------------------------------------------------------------------------------- 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 740 MET Chi-restraints excluded: chain A residue 869 MET 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 592 PHE 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 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 595 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 104 LEU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 32 TYR Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 98 ARG 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 63 LYS 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: 5.9990 chunk 143 optimal weight: 5.9990 chunk 188 optimal weight: 0.3980 chunk 201 optimal weight: 10.0000 chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 223 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 901 GLN ** 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** C 992 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.074551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.047822 restraints weight = 93375.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.049729 restraints weight = 45723.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050991 restraints weight = 30078.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051766 restraints weight = 23232.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052212 restraints weight = 19870.441| |-----------------------------------------------------------------------------| r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 27604 Z= 0.261 Angle : 0.660 10.320 37620 Z= 0.333 Chirality : 0.046 0.397 4362 Planarity : 0.004 0.084 4758 Dihedral : 5.406 54.301 4504 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.56 % Allowed : 14.55 % Favored : 83.89 % 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: -0.08 (0.15), residues: 3303 helix: 2.10 (0.21), residues: 662 sheet: 0.14 (0.17), residues: 850 loop : -1.01 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG G 67 TYR 0.022 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 covalent geometry : bond 0.00610 (27519) covalent geometry : angle 0.64706 (37407) SS BOND : bond 0.00394 ( 42) SS BOND : angle 1.10000 ( 84) hydrogen bonds : bond 0.05195 ( 1089) hydrogen bonds : angle 5.14428 ( 2985) link_BETA1-4 : bond 0.00269 ( 14) link_BETA1-4 : angle 1.19870 ( 42) link_NAG-ASN : bond 0.00469 ( 29) link_NAG-ASN : angle 2.54387 ( 87) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5295.58 seconds wall clock time: 91 minutes 55.63 seconds (5515.63 seconds total)