Starting phenix.real_space_refine on Sat Jul 4 16:26:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tf3_25860/07_2026/7tf3_25860.cif" } resolution = 2.25 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= -0.000 sd= 0.023 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 92 5.16 5 C 13909 2.51 5 N 3583 2.21 5 O 4289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21873 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6500 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6500 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8089 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 56, 'TRANS': 978} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 4.22, per 1000 atoms: 0.19 Number of scatterers: 21873 At special positions: 0 Unit cell: (141, 147, 174, 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 92 16.00 O 4289 8.00 N 3583 7.00 C 13909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, 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=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.04 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 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=2.03 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG 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 122 " " NAG A1303 " - " ASN A 165 " " NAG A1304 " - " ASN A 234 " " NAG A1305 " - " ASN A 282 " " NAG A1306 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 165 " " NAG B1304 " - " ASN B 234 " " NAG B1305 " - " ASN B 282 " " NAG B1306 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 165 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 331 " " NAG C1307 " - " ASN C 343 " " NAG C1308 " - " ASN C 709 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1074 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 17 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 17 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 912.6 milliseconds 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5070 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 45 sheets defined 26.2% alpha, 33.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.055A pdb=" N VAL A 620 " --> pdb=" O CYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.684A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.925A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.562A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.057A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.975A pdb=" N VAL B 620 " --> pdb=" O CYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.592A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.531A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.922A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.513A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1032 removed outlier: 3.992A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.825A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.664A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.883A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.556A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.914A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.662A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (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 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.946A 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 965 removed outlier: 3.521A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.205A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 removed outlier: 3.553A pdb=" N ASP C1146 " --> pdb=" O GLN C1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 30 removed outlier: 7.937A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.835A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.964A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.730A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.115A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 141 through 144 removed outlier: 7.063A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.678A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.163A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.083A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.705A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.558A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.281A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.661A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB7, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.340A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.109A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.712A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.707A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 133 through 135 removed outlier: 4.237A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.690A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.563A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.984A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.512A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.596A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.504A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.332A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD4, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.107A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.109A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.024A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.556A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.831A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.220A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.838A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.887A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.683A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.239A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.595A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.482A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.290A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2790 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: 5.25 Time building geometry restraints manager: 2.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 6619 1.34 - 1.46: 5557 1.46 - 1.58: 10054 1.58 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22346 Sorted by residual: bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.96e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.53e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.40e+00 bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 6.12e+00 ... (remaining 22341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.92: 29186 1.92 - 3.84: 1110 3.84 - 5.75: 89 5.75 - 7.67: 26 7.67 - 9.59: 8 Bond angle restraints: 30419 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 116.44 -5.74 1.22e+00 6.72e-01 2.22e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.37 -5.67 1.22e+00 6.72e-01 2.16e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.00 -5.30 1.22e+00 6.72e-01 1.89e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.97 -7.87 2.00e+00 2.50e-01 1.55e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.36 -4.43 1.20e+00 6.94e-01 1.36e+01 ... (remaining 30414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 11899 17.93 - 35.86: 805 35.86 - 53.79: 115 53.79 - 71.73: 44 71.73 - 89.66: 25 Dihedral angle restraints: 12888 sinusoidal: 5033 harmonic: 7855 Sorted by residual: dihedral pdb=" CA LEU C 517 " pdb=" C LEU C 517 " pdb=" N LEU C 518 " pdb=" CA LEU C 518 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -57.50 -28.50 1 1.00e+01 1.00e-02 1.16e+01 dihedral pdb=" CA ASP C 994 " pdb=" CB ASP C 994 " pdb=" CG ASP C 994 " pdb=" OD1 ASP C 994 " ideal model delta sinusoidal sigma weight residual -30.00 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 12885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2712 0.059 - 0.117: 774 0.117 - 0.175: 140 0.175 - 0.234: 23 0.234 - 0.292: 5 Chirality restraints: 3654 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 17 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 17 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CG LEU C 277 " pdb=" CB LEU C 277 " pdb=" CD1 LEU C 277 " pdb=" CD2 LEU C 277 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.46e+00 ... (remaining 3651 not shown) Planarity restraints: 3898 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.50e-02 5.61e+00 pdb=" CG TRP A 886 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TRP A 886 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 886 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 886 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 902 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.56e+00 pdb=" C MET C 902 " 0.041 2.00e-02 2.50e+03 pdb=" O MET C 902 " -0.015 2.00e-02 2.50e+03 pdb=" N ALA C 903 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.015 2.00e-02 2.50e+03 1.47e-02 5.41e+00 pdb=" CG TRP C 886 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP C 886 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 886 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 886 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.003 2.00e-02 2.50e+03 ... (remaining 3895 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5876 2.81 - 3.33: 18476 3.33 - 3.85: 37465 3.85 - 4.38: 43155 4.38 - 4.90: 73914 Nonbonded interactions: 178886 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.313 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.329 3.040 ... (remaining 178881 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 20.750 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 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:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22436 Z= 0.247 Angle : 0.858 14.917 30655 Z= 0.452 Chirality : 0.057 0.292 3654 Planarity : 0.006 0.055 3860 Dihedral : 13.076 89.657 7716 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.15), residues: 2651 helix: 1.28 (0.19), residues: 607 sheet: 0.71 (0.20), residues: 582 loop : -0.74 (0.14), residues: 1462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 44 TYR 0.035 0.003 TYR C1067 PHE 0.034 0.002 PHE A 275 TRP 0.040 0.003 TRP A 886 HIS 0.004 0.001 HIS C1083 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.25 (22346) covalent geometry : angle 0.82346 / 0.45 (30419) SS BOND : bond 0.00334 / 0.21 ( 34) SS BOND : angle 1.29406 / 0.76 ( 68) hydrogen bonds : bond 0.12160 / 7.90 ( 958) hydrogen bonds : angle 7.34017 / 5.05 ( 2790) link_BETA1-4 : bond 0.00802 / 0.51 ( 18) link_BETA1-4 : angle 1.60192 / 1.20 ( 54) link_NAG-ASN : bond 0.00773 / 0.50 ( 38) link_NAG-ASN : angle 3.82542 / 2.49 ( 114) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7716 (tp) cc_final: 0.7495 (mp) REVERT: A 205 SER cc_start: 0.8576 (t) cc_final: 0.8375 (m) REVERT: A 240 THR cc_start: 0.7857 (m) cc_final: 0.7220 (t) REVERT: A 697 MET cc_start: 0.8976 (ptt) cc_final: 0.8767 (ptt) REVERT: A 994 ASP cc_start: 0.8067 (t70) cc_final: 0.7837 (t0) REVERT: B 190 ARG cc_start: 0.7063 (mpt-90) cc_final: 0.6608 (mmm160) REVERT: B 858 LEU cc_start: 0.8335 (mt) cc_final: 0.8033 (pt) REVERT: B 987 PRO cc_start: 0.8297 (Cg_exo) cc_final: 0.8087 (Cg_endo) REVERT: B 1029 MET cc_start: 0.9123 (tpp) cc_final: 0.8555 (tpp) REVERT: C 269 TYR cc_start: 0.7308 (m-80) cc_final: 0.7037 (m-80) REVERT: C 270 LEU cc_start: 0.7449 (mt) cc_final: 0.6742 (mt) REVERT: C 351 TYR cc_start: 0.7831 (p90) cc_final: 0.7463 (p90) REVERT: C 378 LYS cc_start: 0.8273 (ttmt) cc_final: 0.8022 (ttpp) REVERT: C 408 ARG cc_start: 0.7751 (ptt90) cc_final: 0.7249 (ptm160) REVERT: C 453 TYR cc_start: 0.5453 (p90) cc_final: 0.5151 (p90) REVERT: C 586 ASP cc_start: 0.7260 (t70) cc_final: 0.6987 (t0) REVERT: C 858 LEU cc_start: 0.8638 (mp) cc_final: 0.8169 (tp) REVERT: C 1029 MET cc_start: 0.9296 (tpp) cc_final: 0.9078 (tpp) outliers start: 0 outliers final: 2 residues processed: 288 average time/residue: 0.5815 time to fit residues: 190.5967 Evaluate side-chains 137 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 135 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ILE Chi-restraints excluded: chain C residue 574 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 0.0570 chunk 111 optimal weight: 10.0000 overall best weight: 0.6100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 755 GLN A 926 GLN A 954 GLN A1002 GLN A1071 HIS B 901 GLN B 955 ASN B1011 GLN C 580 GLN C 606 ASN C 954 GLN C1002 GLN C1010 GLN C1071 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.137550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084979 restraints weight = 37769.287| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.53 r_work: 0.3127 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22436 Z= 0.123 Angle : 0.571 10.556 30655 Z= 0.289 Chirality : 0.044 0.243 3654 Planarity : 0.004 0.044 3860 Dihedral : 4.794 105.770 2880 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.69 % Allowed : 7.39 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.16), residues: 2651 helix: 2.22 (0.21), residues: 616 sheet: 0.73 (0.21), residues: 607 loop : -0.57 (0.15), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 319 TYR 0.027 0.001 TYR A 170 PHE 0.019 0.001 PHE C 238 TRP 0.017 0.001 TRP B 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (22346) covalent geometry : angle 0.54220 / 0.28 (30419) SS BOND : bond 0.00150 / 0.09 ( 34) SS BOND : angle 0.94790 / 0.58 ( 68) hydrogen bonds : bond 0.04374 / 2.82 ( 958) hydrogen bonds : angle 5.96331 / 4.07 ( 2790) link_BETA1-4 : bond 0.00281 / 0.18 ( 18) link_BETA1-4 : angle 1.01557 / 0.69 ( 54) link_NAG-ASN : bond 0.00558 / 0.37 ( 38) link_NAG-ASN : angle 2.86874 / 1.88 ( 114) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 143 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7632 (tp) cc_final: 0.7272 (mp) REVERT: A 200 TYR cc_start: 0.6518 (OUTLIER) cc_final: 0.5713 (t80) REVERT: A 205 SER cc_start: 0.8784 (t) cc_final: 0.8529 (m) REVERT: A 240 THR cc_start: 0.7812 (m) cc_final: 0.7342 (t) REVERT: A 990 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7590 (tm-30) REVERT: A 994 ASP cc_start: 0.8658 (t70) cc_final: 0.8450 (t0) REVERT: B 580 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.6771 (mt0) REVERT: B 858 LEU cc_start: 0.8566 (mt) cc_final: 0.7888 (pt) REVERT: B 987 PRO cc_start: 0.8201 (Cg_exo) cc_final: 0.7875 (Cg_endo) REVERT: B 1092 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8704 (mt-10) REVERT: C 200 TYR cc_start: 0.6819 (OUTLIER) cc_final: 0.6463 (t80) REVERT: C 269 TYR cc_start: 0.7583 (m-80) cc_final: 0.6985 (m-80) REVERT: C 378 LYS cc_start: 0.8123 (ttmt) cc_final: 0.7734 (ttpp) REVERT: C 408 ARG cc_start: 0.7699 (ptt90) cc_final: 0.7345 (ppt170) REVERT: C 436 TRP cc_start: 0.6312 (OUTLIER) cc_final: 0.5088 (p-90) REVERT: C 586 ASP cc_start: 0.7349 (t70) cc_final: 0.6829 (t0) REVERT: C 964 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8767 (mtmt) REVERT: C 987 PRO cc_start: 0.8630 (Cg_exo) cc_final: 0.8256 (Cg_endo) REVERT: C 1029 MET cc_start: 0.9482 (tpp) cc_final: 0.9208 (tpp) outliers start: 40 outliers final: 14 residues processed: 166 average time/residue: 0.5011 time to fit residues: 96.5304 Evaluate side-chains 136 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 582 LEU Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 216 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 194 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 252 optimal weight: 0.6980 chunk 114 optimal weight: 0.0020 chunk 78 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 190 optimal weight: 3.9990 chunk 242 optimal weight: 0.5980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN C 52 GLN C 99 ASN C1010 GLN C1142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.136969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.084338 restraints weight = 37561.180| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.51 r_work: 0.3116 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22436 Z= 0.116 Angle : 0.546 10.205 30655 Z= 0.272 Chirality : 0.044 0.257 3654 Planarity : 0.004 0.050 3860 Dihedral : 4.230 21.104 2876 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.82 % Allowed : 8.36 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.16), residues: 2651 helix: 2.56 (0.21), residues: 617 sheet: 0.74 (0.20), residues: 620 loop : -0.47 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 102 TYR 0.024 0.001 TYR A 170 PHE 0.017 0.001 PHE B 238 TRP 0.014 0.001 TRP B 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (22346) covalent geometry : angle 0.51989 / 0.27 (30419) SS BOND : bond 0.00121 / 0.08 ( 34) SS BOND : angle 0.67709 / 0.42 ( 68) hydrogen bonds : bond 0.04056 / 2.61 ( 958) hydrogen bonds : angle 5.59283 / 3.82 ( 2790) link_BETA1-4 : bond 0.00350 / 0.21 ( 18) link_BETA1-4 : angle 0.96680 / 0.65 ( 54) link_NAG-ASN : bond 0.00549 / 0.37 ( 38) link_NAG-ASN : angle 2.69185 / 1.75 ( 114) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 134 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7660 (tp) cc_final: 0.7281 (mp) REVERT: A 200 TYR cc_start: 0.6651 (OUTLIER) cc_final: 0.5840 (t80) REVERT: A 205 SER cc_start: 0.8844 (t) cc_final: 0.8585 (m) REVERT: A 240 THR cc_start: 0.7890 (m) cc_final: 0.7676 (t) REVERT: A 994 ASP cc_start: 0.8699 (t70) cc_final: 0.8439 (t0) REVERT: B 571 ASP cc_start: 0.8334 (m-30) cc_final: 0.7877 (t70) REVERT: B 580 GLN cc_start: 0.7264 (OUTLIER) cc_final: 0.6677 (mt0) REVERT: B 858 LEU cc_start: 0.8710 (mt) cc_final: 0.7971 (pt) REVERT: B 987 PRO cc_start: 0.8184 (Cg_exo) cc_final: 0.7880 (Cg_endo) REVERT: B 1092 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8647 (mt-10) REVERT: B 1141 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7806 (tm) REVERT: C 135 PHE cc_start: 0.7077 (t80) cc_final: 0.6842 (t80) REVERT: C 200 TYR cc_start: 0.6702 (OUTLIER) cc_final: 0.6402 (t80) REVERT: C 269 TYR cc_start: 0.7527 (m-80) cc_final: 0.6710 (m-10) REVERT: C 309 GLU cc_start: 0.7739 (mp0) cc_final: 0.7153 (pm20) REVERT: C 378 LYS cc_start: 0.8196 (ttmt) cc_final: 0.7726 (ttpp) REVERT: C 408 ARG cc_start: 0.7722 (ptt90) cc_final: 0.7387 (ppt170) REVERT: C 436 TRP cc_start: 0.6287 (OUTLIER) cc_final: 0.5010 (p-90) REVERT: C 453 TYR cc_start: 0.4058 (p90) cc_final: 0.3835 (p90) REVERT: C 586 ASP cc_start: 0.7258 (t70) cc_final: 0.6830 (t0) REVERT: C 646 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.8126 (ttp80) REVERT: C 740 MET cc_start: 0.9128 (tpp) cc_final: 0.8796 (ttt) REVERT: C 964 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8769 (mtmt) REVERT: C 987 PRO cc_start: 0.8578 (Cg_exo) cc_final: 0.8201 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7834 (tm-30) REVERT: C 1029 MET cc_start: 0.9474 (tpp) cc_final: 0.9191 (tpp) outliers start: 43 outliers final: 14 residues processed: 165 average time/residue: 0.4840 time to fit residues: 93.8632 Evaluate side-chains 134 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 113 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 120 optimal weight: 0.0870 chunk 143 optimal weight: 1.9990 chunk 176 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 268 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 243 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 8.9990 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 125 ASN A 239 GLN B 580 GLN B 955 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.136726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.083588 restraints weight = 37378.451| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.58 r_work: 0.3100 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22436 Z= 0.120 Angle : 0.530 10.251 30655 Z= 0.265 Chirality : 0.044 0.260 3654 Planarity : 0.004 0.040 3860 Dihedral : 4.185 19.387 2876 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.65 % Allowed : 9.46 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.16), residues: 2651 helix: 2.67 (0.21), residues: 618 sheet: 0.61 (0.20), residues: 609 loop : -0.40 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 237 TYR 0.023 0.001 TYR A 170 PHE 0.013 0.001 PHE C 238 TRP 0.012 0.001 TRP C 886 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (22346) covalent geometry : angle 0.50440 / 0.26 (30419) SS BOND : bond 0.00106 / 0.07 ( 34) SS BOND : angle 0.63327 / 0.39 ( 68) hydrogen bonds : bond 0.03963 / 2.56 ( 958) hydrogen bonds : angle 5.41358 / 3.71 ( 2790) link_BETA1-4 : bond 0.00334 / 0.21 ( 18) link_BETA1-4 : angle 0.94513 / 0.64 ( 54) link_NAG-ASN : bond 0.00542 / 0.36 ( 38) link_NAG-ASN : angle 2.62000 / 1.70 ( 114) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 118 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7636 (tp) cc_final: 0.7244 (mp) REVERT: A 200 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.5863 (t80) REVERT: A 205 SER cc_start: 0.8846 (t) cc_final: 0.8605 (m) REVERT: A 228 ASP cc_start: 0.7555 (t0) cc_final: 0.7031 (t70) REVERT: A 240 THR cc_start: 0.8089 (m) cc_final: 0.7847 (t) REVERT: A 324 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.6562 (pm20) REVERT: A 994 ASP cc_start: 0.8729 (t70) cc_final: 0.8482 (t0) REVERT: B 52 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8388 (tp-100) REVERT: B 580 GLN cc_start: 0.7160 (OUTLIER) cc_final: 0.6536 (mt0) REVERT: B 592 PHE cc_start: 0.7252 (p90) cc_final: 0.6961 (p90) REVERT: B 858 LEU cc_start: 0.8842 (mt) cc_final: 0.8046 (pt) REVERT: B 987 PRO cc_start: 0.8112 (Cg_exo) cc_final: 0.7866 (Cg_endo) REVERT: B 1092 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8696 (mt-10) REVERT: B 1141 LEU cc_start: 0.8131 (OUTLIER) cc_final: 0.7851 (tm) REVERT: C 127 VAL cc_start: 0.7649 (OUTLIER) cc_final: 0.7446 (p) REVERT: C 135 PHE cc_start: 0.6976 (t80) cc_final: 0.6695 (t80) REVERT: C 200 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.6428 (t80) REVERT: C 269 TYR cc_start: 0.7456 (m-80) cc_final: 0.6621 (m-10) REVERT: C 309 GLU cc_start: 0.7790 (mp0) cc_final: 0.7151 (pm20) REVERT: C 378 LYS cc_start: 0.8213 (ttmt) cc_final: 0.7761 (ttpp) REVERT: C 408 ARG cc_start: 0.7707 (ptt90) cc_final: 0.7175 (ptp90) REVERT: C 436 TRP cc_start: 0.6290 (OUTLIER) cc_final: 0.4938 (p-90) REVERT: C 586 ASP cc_start: 0.7118 (t70) cc_final: 0.6591 (t0) REVERT: C 646 ARG cc_start: 0.8561 (OUTLIER) cc_final: 0.8080 (ttp80) REVERT: C 964 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8850 (mtmt) REVERT: C 987 PRO cc_start: 0.8566 (Cg_exo) cc_final: 0.8192 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7889 (tm-30) REVERT: C 1029 MET cc_start: 0.9470 (tpp) cc_final: 0.9211 (tpp) outliers start: 39 outliers final: 12 residues processed: 146 average time/residue: 0.4827 time to fit residues: 83.2137 Evaluate side-chains 133 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 207 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 209 optimal weight: 20.0000 chunk 95 optimal weight: 0.0570 chunk 179 optimal weight: 8.9990 chunk 152 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 237 optimal weight: 0.0770 chunk 268 optimal weight: 2.9990 chunk 149 optimal weight: 0.7980 overall best weight: 1.3860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 764 ASN B 824 ASN C 121 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.134788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.081431 restraints weight = 37180.653| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.59 r_work: 0.3061 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22436 Z= 0.177 Angle : 0.563 10.084 30655 Z= 0.283 Chirality : 0.045 0.267 3654 Planarity : 0.004 0.044 3860 Dihedral : 4.298 19.731 2876 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.73 % Allowed : 9.67 % Favored : 88.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.16), residues: 2651 helix: 2.65 (0.21), residues: 618 sheet: 0.43 (0.20), residues: 650 loop : -0.44 (0.16), residues: 1383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 237 TYR 0.025 0.002 TYR A 170 PHE 0.034 0.002 PHE A 238 TRP 0.014 0.001 TRP C 886 HIS 0.003 0.001 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (22346) covalent geometry : angle 0.53771 / 0.28 (30419) SS BOND : bond 0.00152 / 0.10 ( 34) SS BOND : angle 0.68936 / 0.43 ( 68) hydrogen bonds : bond 0.04323 / 2.78 ( 958) hydrogen bonds : angle 5.48722 / 3.78 ( 2790) link_BETA1-4 : bond 0.00266 / 0.16 ( 18) link_BETA1-4 : angle 1.00401 / 0.67 ( 54) link_NAG-ASN : bond 0.00546 / 0.35 ( 38) link_NAG-ASN : angle 2.71938 / 1.77 ( 114) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 117 time to evaluate : 0.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7699 (tp) cc_final: 0.7274 (mp) REVERT: A 200 TYR cc_start: 0.6955 (OUTLIER) cc_final: 0.6123 (t80) REVERT: A 324 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6648 (pm20) REVERT: A 586 ASP cc_start: 0.7127 (OUTLIER) cc_final: 0.6799 (m-30) REVERT: A 994 ASP cc_start: 0.8762 (t70) cc_final: 0.8507 (t0) REVERT: B 269 TYR cc_start: 0.7430 (m-80) cc_final: 0.7040 (m-80) REVERT: B 987 PRO cc_start: 0.8054 (Cg_exo) cc_final: 0.7799 (Cg_endo) REVERT: C 127 VAL cc_start: 0.7640 (OUTLIER) cc_final: 0.7437 (p) REVERT: C 135 PHE cc_start: 0.6998 (t80) cc_final: 0.6689 (t80) REVERT: C 200 TYR cc_start: 0.6711 (t80) cc_final: 0.6500 (t80) REVERT: C 378 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7773 (ttpp) REVERT: C 436 TRP cc_start: 0.6222 (OUTLIER) cc_final: 0.4826 (p-90) REVERT: C 586 ASP cc_start: 0.7209 (t70) cc_final: 0.6631 (t0) REVERT: C 646 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: C 740 MET cc_start: 0.9172 (tpp) cc_final: 0.8780 (ttt) REVERT: C 964 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8808 (ttmt) REVERT: C 987 PRO cc_start: 0.8609 (Cg_exo) cc_final: 0.8231 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7904 (tm-30) outliers start: 41 outliers final: 18 residues processed: 147 average time/residue: 0.4519 time to fit residues: 78.5602 Evaluate side-chains 133 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 92 optimal weight: 0.9980 chunk 110 optimal weight: 8.9990 chunk 204 optimal weight: 9.9990 chunk 192 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 187 optimal weight: 10.0000 chunk 36 optimal weight: 0.4980 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 0.4980 chunk 211 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.135305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.082356 restraints weight = 37316.829| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.53 r_work: 0.3083 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22436 Z= 0.122 Angle : 0.544 12.716 30655 Z= 0.271 Chirality : 0.044 0.265 3654 Planarity : 0.003 0.039 3860 Dihedral : 4.214 21.015 2876 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.60 % Allowed : 10.26 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.16), residues: 2651 helix: 2.73 (0.21), residues: 618 sheet: 0.48 (0.20), residues: 630 loop : -0.42 (0.16), residues: 1403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 237 TYR 0.024 0.001 TYR B 170 PHE 0.020 0.001 PHE B 238 TRP 0.009 0.001 TRP C 886 HIS 0.002 0.000 HIS C 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22346) covalent geometry : angle 0.51241 / 0.26 (30419) SS BOND : bond 0.00121 / 0.07 ( 34) SS BOND : angle 0.62572 / 0.39 ( 68) hydrogen bonds : bond 0.03951 / 2.54 ( 958) hydrogen bonds : angle 5.33983 / 3.67 ( 2790) link_BETA1-4 : bond 0.00355 / 0.22 ( 18) link_BETA1-4 : angle 0.90686 / 0.62 ( 54) link_NAG-ASN : bond 0.00935 / 0.47 ( 38) link_NAG-ASN : angle 2.97372 / 1.95 ( 114) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 115 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7692 (tp) cc_final: 0.7233 (mp) REVERT: A 200 TYR cc_start: 0.6924 (OUTLIER) cc_final: 0.6120 (t80) REVERT: A 324 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6668 (pm20) REVERT: A 586 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6762 (m-30) REVERT: A 964 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8477 (mttt) REVERT: A 994 ASP cc_start: 0.8749 (t70) cc_final: 0.8499 (t0) REVERT: B 269 TYR cc_start: 0.7349 (m-80) cc_final: 0.7024 (m-80) REVERT: B 580 GLN cc_start: 0.7357 (OUTLIER) cc_final: 0.6804 (mt0) REVERT: B 987 PRO cc_start: 0.7966 (Cg_exo) cc_final: 0.7733 (Cg_endo) REVERT: C 135 PHE cc_start: 0.6977 (t80) cc_final: 0.6675 (t80) REVERT: C 309 GLU cc_start: 0.7832 (mp0) cc_final: 0.7290 (pm20) REVERT: C 378 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7769 (ttpp) REVERT: C 436 TRP cc_start: 0.6190 (OUTLIER) cc_final: 0.4879 (p-90) REVERT: C 586 ASP cc_start: 0.7156 (t70) cc_final: 0.6605 (t0) REVERT: C 646 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: C 964 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8754 (mtmt) REVERT: C 987 PRO cc_start: 0.8547 (Cg_exo) cc_final: 0.8167 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7875 (tm-30) outliers start: 38 outliers final: 18 residues processed: 140 average time/residue: 0.4847 time to fit residues: 80.3085 Evaluate side-chains 135 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 109 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 580 GLN Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 194 optimal weight: 0.8980 chunk 213 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 58 optimal weight: 0.5980 chunk 257 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 178 optimal weight: 0.0060 chunk 29 optimal weight: 5.9990 chunk 173 optimal weight: 3.9990 chunk 237 optimal weight: 0.3980 chunk 32 optimal weight: 3.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C1010 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 = 0.4108 r_free = 0.4108 target = 0.135808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.083236 restraints weight = 37529.857| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.49 r_work: 0.3096 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22436 Z= 0.106 Angle : 0.524 11.060 30655 Z= 0.261 Chirality : 0.044 0.262 3654 Planarity : 0.003 0.040 3860 Dihedral : 4.082 20.042 2876 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.52 % Allowed : 10.47 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), residues: 2651 helix: 2.82 (0.21), residues: 624 sheet: 0.50 (0.20), residues: 628 loop : -0.35 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.026 0.001 TYR C 170 PHE 0.025 0.001 PHE B 201 TRP 0.008 0.001 TRP C 886 HIS 0.002 0.000 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (22346) covalent geometry : angle 0.49430 / 0.25 (30419) SS BOND : bond 0.00095 / 0.06 ( 34) SS BOND : angle 0.57544 / 0.37 ( 68) hydrogen bonds : bond 0.03733 / 2.40 ( 958) hydrogen bonds : angle 5.17815 / 3.56 ( 2790) link_BETA1-4 : bond 0.00361 / 0.23 ( 18) link_BETA1-4 : angle 0.87691 / 0.59 ( 54) link_NAG-ASN : bond 0.00743 / 0.40 ( 38) link_NAG-ASN : angle 2.81989 / 1.83 ( 114) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7664 (tp) cc_final: 0.7195 (mp) REVERT: A 200 TYR cc_start: 0.6956 (OUTLIER) cc_final: 0.6158 (t80) REVERT: A 324 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.6642 (pm20) REVERT: A 586 ASP cc_start: 0.6966 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: A 964 LYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8477 (mttt) REVERT: A 994 ASP cc_start: 0.8740 (t70) cc_final: 0.8489 (t0) REVERT: B 269 TYR cc_start: 0.7353 (m-80) cc_final: 0.7044 (m-80) REVERT: B 748 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8406 (pm20) REVERT: C 135 PHE cc_start: 0.6936 (t80) cc_final: 0.6673 (t80) REVERT: C 309 GLU cc_start: 0.7859 (mp0) cc_final: 0.7307 (pm20) REVERT: C 378 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7825 (ttpp) REVERT: C 436 TRP cc_start: 0.6208 (OUTLIER) cc_final: 0.4901 (p-90) REVERT: C 586 ASP cc_start: 0.7139 (t70) cc_final: 0.6583 (t0) REVERT: C 646 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7991 (ttp80) REVERT: C 740 MET cc_start: 0.9109 (tpp) cc_final: 0.8606 (ttt) REVERT: C 964 LYS cc_start: 0.9008 (OUTLIER) cc_final: 0.8695 (ttmt) REVERT: C 987 PRO cc_start: 0.8501 (Cg_exo) cc_final: 0.8125 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7897 (tm-30) outliers start: 36 outliers final: 17 residues processed: 141 average time/residue: 0.4860 time to fit residues: 81.3526 Evaluate side-chains 133 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 175 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 0.9980 chunk 235 optimal weight: 1.9990 chunk 165 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 196 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN A 824 ASN A1142 GLN B 580 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.134576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.081530 restraints weight = 37153.345| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.53 r_work: 0.3064 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22436 Z= 0.149 Angle : 0.549 11.753 30655 Z= 0.275 Chirality : 0.045 0.265 3654 Planarity : 0.004 0.061 3860 Dihedral : 4.205 19.792 2876 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.69 % Allowed : 10.55 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2651 helix: 2.78 (0.21), residues: 617 sheet: 0.49 (0.20), residues: 635 loop : -0.37 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 577 TYR 0.023 0.002 TYR A 170 PHE 0.022 0.001 PHE A 79 TRP 0.010 0.001 TRP C 886 HIS 0.002 0.001 HIS A 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (22346) covalent geometry : angle 0.51910 / 0.27 (30419) SS BOND : bond 0.00134 / 0.09 ( 34) SS BOND : angle 0.66012 / 0.40 ( 68) hydrogen bonds : bond 0.04099 / 2.64 ( 958) hydrogen bonds : angle 5.29402 / 3.64 ( 2790) link_BETA1-4 : bond 0.00289 / 0.18 ( 18) link_BETA1-4 : angle 0.94635 / 0.64 ( 54) link_NAG-ASN : bond 0.00666 / 0.38 ( 38) link_NAG-ASN : angle 2.90416 / 1.89 ( 114) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 113 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 117 LEU cc_start: 0.7699 (tp) cc_final: 0.7217 (mp) REVERT: A 200 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.6201 (t80) REVERT: A 324 GLU cc_start: 0.7058 (OUTLIER) cc_final: 0.6621 (pm20) REVERT: A 586 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: A 964 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8532 (mttt) REVERT: A 994 ASP cc_start: 0.8752 (t70) cc_final: 0.8489 (t0) REVERT: B 269 TYR cc_start: 0.7424 (m-80) cc_final: 0.7069 (m-80) REVERT: B 569 ILE cc_start: 0.8561 (OUTLIER) cc_final: 0.8323 (pt) REVERT: B 748 GLU cc_start: 0.8648 (OUTLIER) cc_final: 0.8374 (pm20) REVERT: C 64 TRP cc_start: 0.6510 (t60) cc_final: 0.6076 (t-100) REVERT: C 135 PHE cc_start: 0.6924 (t80) cc_final: 0.6639 (t80) REVERT: C 278 LYS cc_start: 0.8226 (OUTLIER) cc_final: 0.7965 (tttt) REVERT: C 309 GLU cc_start: 0.7915 (mp0) cc_final: 0.7354 (pm20) REVERT: C 378 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7822 (ttpp) REVERT: C 436 TRP cc_start: 0.6271 (OUTLIER) cc_final: 0.4903 (p-90) REVERT: C 586 ASP cc_start: 0.7128 (t70) cc_final: 0.6599 (t0) REVERT: C 646 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7957 (ttp80) REVERT: C 740 MET cc_start: 0.9098 (tpp) cc_final: 0.8608 (ttt) REVERT: C 964 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8745 (ttmt) REVERT: C 987 PRO cc_start: 0.8528 (Cg_exo) cc_final: 0.8153 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7978 (tm-30) outliers start: 40 outliers final: 18 residues processed: 141 average time/residue: 0.4897 time to fit residues: 81.4302 Evaluate side-chains 133 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 105 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 748 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 101 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 266 optimal weight: 0.5980 chunk 166 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN B 580 GLN C 52 GLN C 394 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.132809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.079352 restraints weight = 37325.926| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.54 r_work: 0.3027 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2913 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22436 Z= 0.228 Angle : 0.610 11.894 30655 Z= 0.306 Chirality : 0.047 0.270 3654 Planarity : 0.004 0.040 3860 Dihedral : 4.472 20.929 2876 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.52 % Allowed : 10.89 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.16), residues: 2651 helix: 2.54 (0.21), residues: 623 sheet: 0.29 (0.20), residues: 623 loop : -0.49 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B1107 TYR 0.024 0.002 TYR A 170 PHE 0.020 0.002 PHE C 133 TRP 0.012 0.002 TRP C 886 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.23 (22346) covalent geometry : angle 0.57903 / 0.30 (30419) SS BOND : bond 0.00210 / 0.14 ( 34) SS BOND : angle 0.75383 / 0.47 ( 68) hydrogen bonds : bond 0.04614 / 2.97 ( 958) hydrogen bonds : angle 5.55343 / 3.84 ( 2790) link_BETA1-4 : bond 0.00275 / 0.17 ( 18) link_BETA1-4 : angle 1.00264 / 0.67 ( 54) link_NAG-ASN : bond 0.00685 / 0.39 ( 38) link_NAG-ASN : angle 3.11583 / 2.04 ( 114) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7070 (OUTLIER) cc_final: 0.6199 (t80) REVERT: A 324 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6547 (pm20) REVERT: A 586 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6769 (m-30) REVERT: A 994 ASP cc_start: 0.8813 (t70) cc_final: 0.8563 (t0) REVERT: B 269 TYR cc_start: 0.7520 (m-80) cc_final: 0.7135 (m-80) REVERT: B 1142 GLN cc_start: 0.8382 (tp40) cc_final: 0.8067 (tm-30) REVERT: C 64 TRP cc_start: 0.6565 (t60) cc_final: 0.6142 (t-100) REVERT: C 135 PHE cc_start: 0.6896 (t80) cc_final: 0.6645 (t80) REVERT: C 278 LYS cc_start: 0.8148 (OUTLIER) cc_final: 0.7850 (tttt) REVERT: C 309 GLU cc_start: 0.7952 (mp0) cc_final: 0.7401 (pm20) REVERT: C 378 LYS cc_start: 0.8302 (ttmt) cc_final: 0.7793 (ttpp) REVERT: C 421 TYR cc_start: 0.8085 (m-10) cc_final: 0.7390 (m-10) REVERT: C 436 TRP cc_start: 0.6277 (OUTLIER) cc_final: 0.4941 (p-90) REVERT: C 646 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7997 (ttp80) REVERT: C 740 MET cc_start: 0.9131 (tpp) cc_final: 0.8670 (ttt) REVERT: C 964 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8842 (mtmt) REVERT: C 987 PRO cc_start: 0.8479 (Cg_exo) cc_final: 0.8096 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8012 (tm-30) outliers start: 36 outliers final: 20 residues processed: 144 average time/residue: 0.4881 time to fit residues: 82.2715 Evaluate side-chains 138 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 111 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 586 ASP Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 201 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 124 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 3.9990 chunk 217 optimal weight: 4.9990 chunk 180 optimal weight: 4.9990 chunk 244 optimal weight: 0.4980 chunk 119 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 81 ASN A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.132889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.079234 restraints weight = 37364.901| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.57 r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 22436 Z= 0.206 Angle : 0.747 59.200 30655 Z= 0.409 Chirality : 0.046 0.269 3654 Planarity : 0.004 0.043 3860 Dihedral : 4.468 20.873 2876 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.35 % Allowed : 11.31 % Favored : 87.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2651 helix: 2.55 (0.21), residues: 623 sheet: 0.26 (0.20), residues: 623 loop : -0.50 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.023 0.002 TYR A 170 PHE 0.020 0.002 PHE A 898 TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (22346) covalent geometry : angle 0.72302 / 0.40 (30419) SS BOND : bond 0.00166 / 0.11 ( 34) SS BOND : angle 0.74056 / 0.45 ( 68) hydrogen bonds : bond 0.04556 / 2.93 ( 958) hydrogen bonds : angle 5.55092 / 3.83 ( 2790) link_BETA1-4 : bond 0.00253 / 0.15 ( 18) link_BETA1-4 : angle 1.01815 / 0.69 ( 54) link_NAG-ASN : bond 0.00687 / 0.39 ( 38) link_NAG-ASN : angle 3.12549 / 2.05 ( 114) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5302 Ramachandran restraints generated. 2651 Oldfield, 0 Emsley, 2651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.6201 (t80) REVERT: A 324 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6533 (pm20) REVERT: A 994 ASP cc_start: 0.8800 (t70) cc_final: 0.8548 (t0) REVERT: B 269 TYR cc_start: 0.7526 (m-80) cc_final: 0.7152 (m-80) REVERT: B 1142 GLN cc_start: 0.8381 (tp40) cc_final: 0.8066 (tm-30) REVERT: C 64 TRP cc_start: 0.6576 (t60) cc_final: 0.6154 (t-100) REVERT: C 135 PHE cc_start: 0.6890 (t80) cc_final: 0.6638 (t80) REVERT: C 278 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7859 (tttt) REVERT: C 309 GLU cc_start: 0.7951 (mp0) cc_final: 0.7397 (pm20) REVERT: C 378 LYS cc_start: 0.8313 (ttmt) cc_final: 0.7801 (ttpp) REVERT: C 421 TYR cc_start: 0.8100 (m-10) cc_final: 0.7402 (m-10) REVERT: C 436 TRP cc_start: 0.6273 (OUTLIER) cc_final: 0.4936 (p-90) REVERT: C 646 ARG cc_start: 0.8590 (OUTLIER) cc_final: 0.7994 (ttp80) REVERT: C 740 MET cc_start: 0.9139 (tpp) cc_final: 0.8683 (ttt) REVERT: C 964 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8832 (mtmt) REVERT: C 987 PRO cc_start: 0.8470 (Cg_exo) cc_final: 0.8087 (Cg_endo) REVERT: C 990 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8000 (tm-30) outliers start: 32 outliers final: 19 residues processed: 132 average time/residue: 0.5801 time to fit residues: 89.9307 Evaluate side-chains 134 residues out of total 2369 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 221 SER Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 939 SER Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 52 GLN Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 430 THR Chi-restraints excluded: chain C residue 436 TRP Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 702 GLU Chi-restraints excluded: chain C residue 964 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 171 optimal weight: 7.9990 chunk 143 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 166 optimal weight: 20.0000 chunk 214 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 207 optimal weight: 4.9990 chunk 174 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 180 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 196 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN ** C1010 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 = 0.4070 r_free = 0.4070 target = 0.132854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.079261 restraints weight = 37352.833| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.54 r_work: 0.3028 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.161 22436 Z= 0.206 Angle : 0.747 59.200 30655 Z= 0.409 Chirality : 0.046 0.269 3654 Planarity : 0.004 0.043 3860 Dihedral : 4.468 20.873 2876 Min Nonbonded Distance : 1.690 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.10 % Allowed : 11.57 % Favored : 87.34 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.16), residues: 2651 helix: 2.55 (0.21), residues: 623 sheet: 0.26 (0.20), residues: 623 loop : -0.50 (0.16), residues: 1405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 78 TYR 0.023 0.002 TYR A 170 PHE 0.020 0.002 PHE A 898 TRP 0.011 0.001 TRP C 886 HIS 0.003 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (22346) covalent geometry : angle 0.72308 / 0.40 (30419) SS BOND : bond 0.00166 / 0.11 ( 34) SS BOND : angle 0.74056 / 0.45 ( 68) hydrogen bonds : bond 0.04556 / 2.93 ( 958) hydrogen bonds : angle 5.55092 / 3.83 ( 2790) link_BETA1-4 : bond 0.00253 / 0.15 ( 18) link_BETA1-4 : angle 1.01815 / 0.69 ( 54) link_NAG-ASN : bond 0.00687 / 0.39 ( 38) link_NAG-ASN : angle 3.12549 / 2.05 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12310.40 seconds wall clock time: 209 minutes 12.42 seconds (12552.42 seconds total)