Starting phenix.real_space_refine on Sat Jul 4 16:25:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.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/7tey_25855/07_2026/7tey_25855.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tey_25855/07_2026/7tey_25855.map" } 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= 0.024 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 13904 2.51 5 N 3584 2.21 5 O 4287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21867 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "B" Number of atoms: 6496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6496 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 44, 'TRANS': 789} Chain breaks: 8 Chain: "C" Number of atoms: 8091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8091 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: 4.92, per 1000 atoms: 0.22 Number of scatterers: 21867 At special positions: 0 Unit cell: (140, 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 4287 8.00 N 3584 7.00 C 13904 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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: 1.82 Conformation dependent library (CDL) restraints added in 997.8 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: 5064 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 44 sheets defined 26.1% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.052A 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: 3.700A 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: 3.913A 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: 3.564A 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: 4.062A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 removed outlier: 3.595A pdb=" N ASP A1146 " --> pdb=" O GLN A1142 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.952A 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: 3.615A 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 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.910A 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: 3.539A 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: 4.038A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.533A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.897A 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 389 removed outlier: 3.646A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.886A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.564A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.892A 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: 3.656A 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: 3.956A 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: 4.229A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 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: 7.897A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.829A 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: 3.568A pdb=" N ARG C 567 " --> pdb=" O PHE A 43 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.259A 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: 3.963A 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: 3.605A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 9.396A 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: 7.067A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.889A 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: 6.650A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.006A 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: 5.080A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.506A 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: 6.051A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.314A 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: 6.694A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.800A 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: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.941A 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: 6.505A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.556A 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: 4.283A 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: 3.660A 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: 8.324A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.114A 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: 3.741A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL B 126 " --> pdb=" O SER B 172 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 9.751A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 8.932A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 140 through 144 removed outlier: 6.713A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ARG B 246 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 143 " --> pdb=" O ARG B 246 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.674A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.560A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.973A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.624A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.499A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.320A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.211A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 48 through 55 removed outlier: 4.146A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.021A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.452A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 141 through 144 removed outlier: 6.857A 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: 6.913A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.205A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.817A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.574A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.219A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.449A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.278A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 1006 hydrogen bonds defined for protein. 2793 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: 5.57 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6755 1.34 - 1.46: 5506 1.46 - 1.59: 9960 1.59 - 1.71: 0 1.71 - 1.83: 116 Bond restraints: 22337 Sorted by residual: bond pdb=" C1 NAG P 1 " pdb=" O5 NAG P 1 " ideal model delta sigma weight residual 1.406 1.464 -0.058 2.00e-02 2.50e+03 8.36e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 6.90e+00 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 6.90e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.457 -0.051 2.00e-02 2.50e+03 6.42e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.455 -0.049 2.00e-02 2.50e+03 5.99e+00 ... (remaining 22332 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 29139 1.89 - 3.77: 1124 3.77 - 5.66: 99 5.66 - 7.54: 32 7.54 - 9.43: 7 Bond angle restraints: 30401 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 110.70 116.38 -5.68 1.22e+00 6.72e-01 2.17e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.28 -5.58 1.22e+00 6.72e-01 2.09e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 116.09 -5.39 1.22e+00 6.72e-01 1.95e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.84 -7.74 2.00e+00 2.50e-01 1.50e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.42 -4.49 1.20e+00 6.94e-01 1.40e+01 ... (remaining 30396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 11894 17.92 - 35.84: 806 35.84 - 53.76: 116 53.76 - 71.68: 47 71.68 - 89.60: 25 Dihedral angle restraints: 12888 sinusoidal: 5039 harmonic: 7849 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 180.00 159.57 20.43 0 5.00e+00 4.00e-02 1.67e+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 -58.25 -27.75 1 1.00e+01 1.00e-02 1.10e+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 -86.93 56.93 1 2.00e+01 2.50e-03 1.09e+01 ... (remaining 12885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 3072 0.081 - 0.163: 539 0.163 - 0.244: 33 0.244 - 0.325: 2 0.325 - 0.407: 1 Chirality restraints: 3647 Sorted by residual: chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.13e+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 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 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 -2.13 -0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3644 not shown) Planarity restraints: 3899 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 886 " -0.016 2.00e-02 2.50e+03 1.63e-02 6.63e+00 pdb=" CG TRP C 886 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP C 886 " -0.022 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 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 886 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 886 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 886 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 886 " 0.017 2.00e-02 2.50e+03 1.59e-02 6.35e+00 pdb=" CG TRP A 886 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP A 886 " 0.021 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 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 886 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 886 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 886 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 551 " 0.012 2.00e-02 2.50e+03 2.35e-02 5.51e+00 pdb=" C VAL C 551 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL C 551 " 0.015 2.00e-02 2.50e+03 pdb=" N LEU C 552 " 0.014 2.00e-02 2.50e+03 ... (remaining 3896 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 6022 2.81 - 3.34: 18440 3.34 - 3.86: 37594 3.86 - 4.38: 43056 4.38 - 4.90: 73807 Nonbonded interactions: 178919 Sorted by model distance: nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.293 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.294 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.297 3.040 nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.303 3.040 nonbonded pdb=" OE1 GLN C 115 " pdb=" OG1 THR C 167 " model vdw 2.303 3.040 ... (remaining 178914 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.060 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.060 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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 0.068 22427 Z= 0.247 Angle : 0.851 15.349 30637 Z= 0.449 Chirality : 0.057 0.407 3647 Planarity : 0.006 0.054 3861 Dihedral : 13.169 89.598 7722 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: 0.06 (0.15), residues: 2651 helix: 1.22 (0.19), residues: 612 sheet: 0.75 (0.20), residues: 581 loop : -0.78 (0.14), residues: 1458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 19 TYR 0.036 0.003 TYR C1067 PHE 0.036 0.002 PHE A 275 TRP 0.043 0.003 TRP C 886 HIS 0.005 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 (22337) covalent geometry : angle 0.81934 / 0.44 (30401) SS BOND : bond 0.00288 / 0.19 ( 34) SS BOND : angle 1.21401 / 0.72 ( 68) hydrogen bonds : bond 0.11897 / 8.26 ( 953) hydrogen bonds : angle 7.35085 / 5.16 ( 2793) link_BETA1-4 : bond 0.00683 / 0.44 ( 18) link_BETA1-4 : angle 1.57074 / 1.08 ( 54) link_NAG-ASN : bond 0.00788 / 0.52 ( 38) link_NAG-ASN : angle 3.69572 / 2.42 ( 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 310 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8105 (tm-30) cc_final: 0.7771 (tp-100) REVERT: A 88 ASP cc_start: 0.8420 (m-30) cc_final: 0.8216 (m-30) REVERT: A 205 SER cc_start: 0.8476 (t) cc_final: 0.8241 (m) REVERT: A 591 SER cc_start: 0.8322 (m) cc_final: 0.7938 (p) REVERT: B 54 LEU cc_start: 0.7467 (mm) cc_final: 0.7187 (mp) REVERT: B 287 ASP cc_start: 0.7968 (t0) cc_final: 0.7667 (m-30) REVERT: B 553 THR cc_start: 0.6995 (p) cc_final: 0.6781 (p) REVERT: B 592 PHE cc_start: 0.7294 (p90) cc_final: 0.6884 (p90) REVERT: B 1029 MET cc_start: 0.9141 (tpp) cc_final: 0.8886 (tpp) REVERT: C 129 LYS cc_start: 0.6968 (mtmt) cc_final: 0.6218 (mmtm) REVERT: C 347 PHE cc_start: 0.6661 (m-10) cc_final: 0.6396 (m-10) REVERT: C 396 TYR cc_start: 0.6830 (m-80) cc_final: 0.6576 (m-80) REVERT: C 421 TYR cc_start: 0.8323 (m-10) cc_final: 0.8022 (m-10) REVERT: C 436 TRP cc_start: 0.7005 (p90) cc_final: 0.6577 (p90) REVERT: C 437 ASN cc_start: 0.6398 (t0) cc_final: 0.6174 (m-40) REVERT: C 453 TYR cc_start: 0.7156 (p90) cc_final: 0.6633 (p90) REVERT: C 508 TYR cc_start: 0.7844 (m-80) cc_final: 0.7041 (m-80) outliers start: 0 outliers final: 2 residues processed: 310 average time/residue: 0.6062 time to fit residues: 215.9402 Evaluate side-chains 156 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain C residue 40 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 8.9990 chunk 111 optimal weight: 10.0000 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 926 GLN B 901 GLN B 955 ASN B1002 GLN B1011 GLN C 321 GLN C 556 ASN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.152846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.089337 restraints weight = 33787.084| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.56 r_work: 0.3075 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 22427 Z= 0.205 Angle : 0.636 18.670 30637 Z= 0.315 Chirality : 0.047 0.273 3647 Planarity : 0.005 0.045 3861 Dihedral : 4.601 33.857 2880 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.52 % Allowed : 7.27 % Favored : 91.21 % 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: 0.48 (0.15), residues: 2651 helix: 2.07 (0.20), residues: 621 sheet: 0.69 (0.20), residues: 612 loop : -0.65 (0.15), residues: 1418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.025 0.002 TYR C1067 PHE 0.026 0.002 PHE C 238 TRP 0.024 0.002 TRP C 886 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.20 (22337) covalent geometry : angle 0.59002 / 0.31 (30401) SS BOND : bond 0.00213 / 0.15 ( 34) SS BOND : angle 0.80226 / 0.55 ( 68) hydrogen bonds : bond 0.04880 / 3.31 ( 953) hydrogen bonds : angle 5.99495 / 4.18 ( 2793) link_BETA1-4 : bond 0.00279 / 0.18 ( 18) link_BETA1-4 : angle 1.11582 / 0.74 ( 54) link_NAG-ASN : bond 0.00685 / 0.46 ( 38) link_NAG-ASN : angle 3.85254 / 2.37 ( 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 213 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8393 (tm-30) cc_final: 0.7907 (tm-30) REVERT: A 88 ASP cc_start: 0.8640 (m-30) cc_final: 0.8424 (m-30) REVERT: A 200 TYR cc_start: 0.7725 (m-80) cc_final: 0.7263 (t80) REVERT: A 205 SER cc_start: 0.8797 (t) cc_final: 0.8505 (m) REVERT: A 569 ILE cc_start: 0.8690 (mp) cc_final: 0.8441 (tp) REVERT: A 591 SER cc_start: 0.8668 (m) cc_final: 0.7728 (p) REVERT: A 868 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.7740 (tp30) REVERT: A 1010 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8384 (mp10) REVERT: B 565 PHE cc_start: 0.7295 (OUTLIER) cc_final: 0.6632 (p90) REVERT: C 129 LYS cc_start: 0.6867 (mtmt) cc_final: 0.6246 (mmtt) REVERT: C 347 PHE cc_start: 0.6638 (m-10) cc_final: 0.6293 (m-10) REVERT: C 421 TYR cc_start: 0.8145 (m-10) cc_final: 0.7897 (m-10) REVERT: C 434 ILE cc_start: 0.6198 (OUTLIER) cc_final: 0.5953 (mt) REVERT: C 436 TRP cc_start: 0.6571 (p90) cc_final: 0.5746 (p90) REVERT: C 508 TYR cc_start: 0.7530 (m-80) cc_final: 0.7119 (m-80) REVERT: C 740 MET cc_start: 0.8639 (OUTLIER) cc_final: 0.8056 (ttt) outliers start: 36 outliers final: 11 residues processed: 196 average time/residue: 0.5340 time to fit residues: 122.9218 Evaluate side-chains 167 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 38 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 216 optimal weight: 6.9990 chunk 265 optimal weight: 0.9990 chunk 194 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 0.0670 chunk 252 optimal weight: 5.9990 chunk 114 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 chunk 24 optimal weight: 0.2980 overall best weight: 0.5920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 239 GLN A 762 GLN B1002 GLN C 121 ASN C 580 GLN C1010 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.154122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.091179 restraints weight = 33808.009| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.53 r_work: 0.3110 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22427 Z= 0.116 Angle : 0.564 15.862 30637 Z= 0.277 Chirality : 0.045 0.355 3647 Planarity : 0.004 0.039 3861 Dihedral : 4.295 23.324 2876 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.73 % Allowed : 8.49 % Favored : 89.78 % 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: 0.80 (0.16), residues: 2651 helix: 2.55 (0.21), residues: 621 sheet: 0.81 (0.20), residues: 617 loop : -0.52 (0.15), residues: 1413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 190 TYR 0.026 0.001 TYR A 170 PHE 0.028 0.001 PHE C 238 TRP 0.013 0.001 TRP C 104 HIS 0.003 0.000 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (22337) covalent geometry : angle 0.52127 / 0.27 (30401) SS BOND : bond 0.00092 / 0.06 ( 34) SS BOND : angle 0.63338 / 0.42 ( 68) hydrogen bonds : bond 0.04176 / 2.82 ( 953) hydrogen bonds : angle 5.63019 / 3.91 ( 2793) link_BETA1-4 : bond 0.00385 / 0.25 ( 18) link_BETA1-4 : angle 0.97385 / 0.69 ( 54) link_NAG-ASN : bond 0.00708 / 0.46 ( 38) link_NAG-ASN : angle 3.50561 / 2.13 ( 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 199 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8343 (tm-30) cc_final: 0.7845 (tm-30) REVERT: A 66 HIS cc_start: 0.5945 (OUTLIER) cc_final: 0.5448 (t-90) REVERT: A 200 TYR cc_start: 0.7714 (m-80) cc_final: 0.7302 (t80) REVERT: A 205 SER cc_start: 0.8774 (t) cc_final: 0.8510 (m) REVERT: A 569 ILE cc_start: 0.8653 (mp) cc_final: 0.8401 (tp) REVERT: A 591 SER cc_start: 0.8838 (m) cc_final: 0.8616 (p) REVERT: A 868 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7718 (tp30) REVERT: A 900 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8814 (mtm) REVERT: B 287 ASP cc_start: 0.8006 (t0) cc_final: 0.7743 (m-30) REVERT: B 565 PHE cc_start: 0.7376 (OUTLIER) cc_final: 0.6846 (p90) REVERT: C 129 LYS cc_start: 0.6917 (mtmt) cc_final: 0.6172 (mmtt) REVERT: C 421 TYR cc_start: 0.8170 (m-10) cc_final: 0.7920 (m-10) REVERT: C 434 ILE cc_start: 0.6200 (OUTLIER) cc_final: 0.5941 (mt) REVERT: C 436 TRP cc_start: 0.6362 (p90) cc_final: 0.6027 (p90) REVERT: C 619 GLU cc_start: 0.7825 (mp0) cc_final: 0.7621 (mp0) REVERT: C 740 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8034 (ttt) REVERT: C 1141 LEU cc_start: 0.7673 (OUTLIER) cc_final: 0.7351 (tm) outliers start: 41 outliers final: 17 residues processed: 186 average time/residue: 0.4582 time to fit residues: 102.1579 Evaluate side-chains 168 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 3 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 133 optimal weight: 0.0470 chunk 37 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 143 optimal weight: 0.5980 chunk 176 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 overall best weight: 1.9284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 762 GLN A 824 ASN B 245 HIS B 824 ASN B1002 GLN C 580 GLN C 779 GLN C 824 ASN C1010 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.150647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.087223 restraints weight = 33746.974| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.53 r_work: 0.3038 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 22427 Z= 0.230 Angle : 0.608 11.139 30637 Z= 0.304 Chirality : 0.047 0.336 3647 Planarity : 0.004 0.043 3861 Dihedral : 4.536 21.179 2876 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.86 % Allowed : 8.87 % Favored : 89.27 % 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: 0.59 (0.16), residues: 2651 helix: 2.35 (0.20), residues: 629 sheet: 0.47 (0.21), residues: 611 loop : -0.55 (0.15), residues: 1411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1014 TYR 0.024 0.002 TYR C1067 PHE 0.027 0.002 PHE C 238 TRP 0.014 0.002 TRP C 886 HIS 0.023 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.23 (22337) covalent geometry : angle 0.57853 / 0.30 (30401) SS BOND : bond 0.00218 / 0.16 ( 34) SS BOND : angle 0.69709 / 0.48 ( 68) hydrogen bonds : bond 0.04916 / 3.35 ( 953) hydrogen bonds : angle 5.76022 / 4.00 ( 2793) link_BETA1-4 : bond 0.00318 / 0.21 ( 18) link_BETA1-4 : angle 1.14079 / 0.75 ( 54) link_NAG-ASN : bond 0.00700 / 0.47 ( 38) link_NAG-ASN : angle 3.00930 / 1.90 ( 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 196 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 152 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8394 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 200 TYR cc_start: 0.7778 (m-80) cc_final: 0.7238 (t80) REVERT: A 569 ILE cc_start: 0.8632 (mp) cc_final: 0.8323 (tp) REVERT: A 591 SER cc_start: 0.8795 (m) cc_final: 0.8435 (p) REVERT: A 858 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8784 (mt) REVERT: A 868 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7774 (tp30) REVERT: B 560 LEU cc_start: 0.8469 (mp) cc_final: 0.8221 (mp) REVERT: B 565 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6921 (p90) REVERT: B 983 ARG cc_start: 0.7708 (ttm170) cc_final: 0.7505 (mtp180) REVERT: C 129 LYS cc_start: 0.6926 (mtmt) cc_final: 0.6302 (mmtt) REVERT: C 238 PHE cc_start: 0.6164 (p90) cc_final: 0.5009 (p90) REVERT: C 434 ILE cc_start: 0.6457 (OUTLIER) cc_final: 0.6201 (mt) REVERT: C 740 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8049 (ttt) outliers start: 44 outliers final: 23 residues processed: 182 average time/residue: 0.4635 time to fit residues: 100.8481 Evaluate side-chains 167 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 226 LEU Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 250 optimal weight: 3.9990 chunk 209 optimal weight: 5.9990 chunk 265 optimal weight: 0.9980 chunk 206 optimal weight: 9.9990 chunk 125 optimal weight: 0.6980 chunk 204 optimal weight: 8.9990 chunk 227 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 153 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 762 GLN B1002 GLN C 978 ASN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.089438 restraints weight = 33597.045| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.48 r_work: 0.3085 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22427 Z= 0.133 Angle : 0.593 29.156 30637 Z= 0.286 Chirality : 0.051 1.311 3647 Planarity : 0.004 0.045 3861 Dihedral : 4.309 20.564 2876 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.82 % Allowed : 9.59 % Favored : 88.59 % 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: 0.77 (0.16), residues: 2651 helix: 2.64 (0.21), residues: 617 sheet: 0.57 (0.21), residues: 568 loop : -0.44 (0.15), residues: 1466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 403 TYR 0.021 0.001 TYR C1067 PHE 0.022 0.001 PHE C 238 TRP 0.018 0.001 TRP C 104 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (22337) covalent geometry : angle 0.53113 / 0.27 (30401) SS BOND : bond 0.00167 / 0.09 ( 34) SS BOND : angle 0.61182 / 0.42 ( 68) hydrogen bonds : bond 0.04181 / 2.83 ( 953) hydrogen bonds : angle 5.52222 / 3.83 ( 2793) link_BETA1-4 : bond 0.00337 / 0.23 ( 18) link_BETA1-4 : angle 0.93682 / 0.66 ( 54) link_NAG-ASN : bond 0.00612 / 0.42 ( 38) link_NAG-ASN : angle 4.30659 / 2.48 ( 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 194 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 151 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8374 (tm-30) cc_final: 0.7793 (tm-30) REVERT: A 200 TYR cc_start: 0.7723 (m-80) cc_final: 0.7236 (t80) REVERT: A 569 ILE cc_start: 0.8692 (mp) cc_final: 0.8360 (tp) REVERT: A 577 ARG cc_start: 0.5398 (OUTLIER) cc_final: 0.5110 (ptp-110) REVERT: A 591 SER cc_start: 0.8889 (m) cc_final: 0.8484 (p) REVERT: A 858 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8801 (mt) REVERT: A 868 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: B 551 VAL cc_start: 0.6834 (t) cc_final: 0.6623 (m) REVERT: B 565 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7034 (p90) REVERT: B 983 ARG cc_start: 0.7729 (ttm170) cc_final: 0.7459 (mtm-85) REVERT: C 52 GLN cc_start: 0.8965 (tm-30) cc_final: 0.8746 (tm-30) REVERT: C 129 LYS cc_start: 0.6838 (mtmt) cc_final: 0.6139 (mmtt) REVERT: C 238 PHE cc_start: 0.6026 (p90) cc_final: 0.4815 (p90) REVERT: C 269 TYR cc_start: 0.7233 (m-80) cc_final: 0.6968 (m-80) REVERT: C 740 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.7999 (ttt) outliers start: 43 outliers final: 23 residues processed: 180 average time/residue: 0.4411 time to fit residues: 95.2220 Evaluate side-chains 166 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 138 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 191 optimal weight: 4.9990 chunk 133 optimal weight: 0.9980 chunk 181 optimal weight: 8.9990 chunk 44 optimal weight: 0.0770 chunk 103 optimal weight: 10.0000 chunk 195 optimal weight: 6.9990 chunk 107 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 overall best weight: 3.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 81 ASN A 125 ASN A 762 GLN B 907 ASN B 955 ASN B1002 GLN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.147149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.084220 restraints weight = 33500.695| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 2.47 r_work: 0.2983 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 22427 Z= 0.419 Angle : 0.788 36.616 30637 Z= 0.385 Chirality : 0.057 1.055 3647 Planarity : 0.005 0.047 3861 Dihedral : 4.978 23.594 2876 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.15 % Allowed : 9.76 % Favored : 88.09 % 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: 0.07 (0.16), residues: 2651 helix: 1.85 (0.20), residues: 634 sheet: -0.04 (0.20), residues: 638 loop : -0.76 (0.15), residues: 1379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B1014 TYR 0.028 0.003 TYR B 269 PHE 0.027 0.003 PHE A 898 TRP 0.015 0.002 TRP C 436 HIS 0.006 0.002 HIS A1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00975 / 0.42 (22337) covalent geometry : angle 0.72745 / 0.37 (30401) SS BOND : bond 0.00483 / 0.35 ( 34) SS BOND : angle 0.88763 / 0.58 ( 68) hydrogen bonds : bond 0.05883 / 4.02 ( 953) hydrogen bonds : angle 6.12627 / 4.26 ( 2793) link_BETA1-4 : bond 0.00412 / 0.24 ( 18) link_BETA1-4 : angle 1.40559 / 0.87 ( 54) link_NAG-ASN : bond 0.00903 / 0.59 ( 38) link_NAG-ASN : angle 4.94716 / 2.83 ( 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 193 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 142 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8391 (tm-30) cc_final: 0.7755 (tm-30) REVERT: A 81 ASN cc_start: 0.6655 (OUTLIER) cc_final: 0.6303 (m110) REVERT: A 569 ILE cc_start: 0.8608 (mp) cc_final: 0.8290 (tp) REVERT: A 577 ARG cc_start: 0.5407 (OUTLIER) cc_final: 0.5181 (ptp-110) REVERT: A 591 SER cc_start: 0.8799 (m) cc_final: 0.8295 (p) REVERT: A 858 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 868 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: B 565 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.7027 (p90) REVERT: B 983 ARG cc_start: 0.7795 (ttm170) cc_final: 0.7534 (mtm-85) REVERT: C 52 GLN cc_start: 0.8921 (tm-30) cc_final: 0.8641 (tm-30) REVERT: C 129 LYS cc_start: 0.6645 (mtmt) cc_final: 0.6153 (mmtt) REVERT: C 238 PHE cc_start: 0.5990 (p90) cc_final: 0.4827 (p90) REVERT: C 421 TYR cc_start: 0.8158 (m-10) cc_final: 0.7951 (m-10) REVERT: C 427 ASP cc_start: 0.8243 (m-30) cc_final: 0.7938 (t0) REVERT: C 516 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6371 (pp20) REVERT: C 1141 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7267 (tm) outliers start: 51 outliers final: 23 residues processed: 182 average time/residue: 0.4659 time to fit residues: 101.5972 Evaluate side-chains 162 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASN Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 940 SER Chi-restraints excluded: chain C residue 1141 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 247 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 175 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 261 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 125 ASN A 762 GLN B 907 ASN B1002 GLN C 115 GLN C 532 ASN C 955 ASN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.150480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.088107 restraints weight = 33312.138| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.46 r_work: 0.3050 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22427 Z= 0.129 Angle : 0.615 29.344 30637 Z= 0.298 Chirality : 0.050 1.129 3647 Planarity : 0.004 0.042 3861 Dihedral : 4.548 26.749 2876 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.44 % Allowed : 10.69 % Favored : 87.87 % 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: 0.45 (0.16), residues: 2651 helix: 2.40 (0.21), residues: 628 sheet: 0.21 (0.21), residues: 573 loop : -0.60 (0.15), residues: 1450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 567 TYR 0.021 0.001 TYR C1067 PHE 0.025 0.001 PHE B 238 TRP 0.022 0.001 TRP C 104 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (22337) covalent geometry : angle 0.55334 / 0.28 (30401) SS BOND : bond 0.00204 / 0.11 ( 34) SS BOND : angle 0.65679 / 0.44 ( 68) hydrogen bonds : bond 0.04328 / 2.94 ( 953) hydrogen bonds : angle 5.65270 / 3.94 ( 2793) link_BETA1-4 : bond 0.00307 / 0.21 ( 18) link_BETA1-4 : angle 0.93212 / 0.66 ( 54) link_NAG-ASN : bond 0.00727 / 0.46 ( 38) link_NAG-ASN : angle 4.40490 / 2.50 ( 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 175 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.696 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 200 TYR cc_start: 0.8018 (m-80) cc_final: 0.7221 (t80) REVERT: A 221 SER cc_start: 0.8659 (t) cc_final: 0.8282 (p) REVERT: A 231 ILE cc_start: 0.8678 (pt) cc_final: 0.8413 (pp) REVERT: A 569 ILE cc_start: 0.8651 (mp) cc_final: 0.8185 (tp) REVERT: A 591 SER cc_start: 0.8857 (m) cc_final: 0.8421 (p) REVERT: A 858 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8794 (mt) REVERT: A 868 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7710 (tp30) REVERT: B 565 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7209 (p90) REVERT: B 983 ARG cc_start: 0.7828 (ttm170) cc_final: 0.7550 (mtp180) REVERT: C 52 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8617 (tm-30) REVERT: C 129 LYS cc_start: 0.6657 (mtmt) cc_final: 0.6153 (mmtt) REVERT: C 238 PHE cc_start: 0.5890 (p90) cc_final: 0.4668 (p90) REVERT: C 269 TYR cc_start: 0.7293 (m-80) cc_final: 0.7028 (m-80) REVERT: C 516 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.6151 (pp20) outliers start: 34 outliers final: 19 residues processed: 167 average time/residue: 0.4511 time to fit residues: 89.5780 Evaluate side-chains 156 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1010 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 49 optimal weight: 1.9990 chunk 99 optimal weight: 0.0870 chunk 31 optimal weight: 0.9980 chunk 153 optimal weight: 1.9990 chunk 244 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 231 optimal weight: 6.9990 chunk 225 optimal weight: 1.9990 chunk 82 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 207 HIS A 762 GLN B1002 GLN C1010 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.150349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.088013 restraints weight = 33280.773| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 2.48 r_work: 0.3048 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22427 Z= 0.139 Angle : 0.603 32.129 30637 Z= 0.292 Chirality : 0.047 0.593 3647 Planarity : 0.004 0.044 3861 Dihedral : 4.432 24.013 2876 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.27 % Allowed : 10.98 % Favored : 87.75 % 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: 0.55 (0.16), residues: 2651 helix: 2.51 (0.21), residues: 629 sheet: 0.25 (0.21), residues: 581 loop : -0.56 (0.15), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.021 0.001 TYR C1067 PHE 0.029 0.001 PHE A 168 TRP 0.029 0.001 TRP C 436 HIS 0.002 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (22337) covalent geometry : angle 0.54403 / 0.28 (30401) SS BOND : bond 0.00132 / 0.09 ( 34) SS BOND : angle 0.61450 / 0.41 ( 68) hydrogen bonds : bond 0.04274 / 2.89 ( 953) hydrogen bonds : angle 5.51919 / 3.85 ( 2793) link_BETA1-4 : bond 0.00323 / 0.22 ( 18) link_BETA1-4 : angle 0.96298 / 0.66 ( 54) link_NAG-ASN : bond 0.00723 / 0.46 ( 38) link_NAG-ASN : angle 4.25897 / 2.40 ( 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 173 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.760 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8341 (tm-30) cc_final: 0.7735 (tm-30) REVERT: A 200 TYR cc_start: 0.7962 (m-80) cc_final: 0.7011 (t80) REVERT: A 221 SER cc_start: 0.8665 (t) cc_final: 0.8299 (p) REVERT: A 231 ILE cc_start: 0.8709 (pt) cc_final: 0.8447 (pp) REVERT: A 569 ILE cc_start: 0.8651 (mp) cc_final: 0.8175 (tp) REVERT: A 591 SER cc_start: 0.8812 (m) cc_final: 0.8388 (p) REVERT: A 858 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8796 (mt) REVERT: A 868 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7735 (tp30) REVERT: B 565 PHE cc_start: 0.7430 (OUTLIER) cc_final: 0.7154 (p90) REVERT: B 983 ARG cc_start: 0.7822 (ttm170) cc_final: 0.7553 (mtp180) REVERT: C 52 GLN cc_start: 0.8894 (tm-30) cc_final: 0.8611 (tm-30) REVERT: C 129 LYS cc_start: 0.6617 (mtmt) cc_final: 0.6091 (mmtt) REVERT: C 238 PHE cc_start: 0.5904 (p90) cc_final: 0.4690 (p90) REVERT: C 269 TYR cc_start: 0.7274 (m-80) cc_final: 0.7018 (m-80) REVERT: C 353 TRP cc_start: 0.7028 (p-90) cc_final: 0.6776 (p-90) REVERT: C 516 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6246 (pp20) outliers start: 30 outliers final: 17 residues processed: 162 average time/residue: 0.4200 time to fit residues: 81.6600 Evaluate side-chains 160 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 260 optimal weight: 0.3980 chunk 201 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 205 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 148 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 250 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 207 HIS A 762 GLN B1002 GLN C 978 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.149685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.087253 restraints weight = 33359.242| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.47 r_work: 0.3033 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22427 Z= 0.179 Angle : 0.621 31.835 30637 Z= 0.300 Chirality : 0.047 0.534 3647 Planarity : 0.004 0.045 3861 Dihedral : 4.464 22.845 2876 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.10 % Allowed : 11.28 % Favored : 87.62 % 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: 0.48 (0.16), residues: 2651 helix: 2.44 (0.21), residues: 628 sheet: 0.18 (0.21), residues: 581 loop : -0.58 (0.15), residues: 1442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 567 TYR 0.022 0.001 TYR C1067 PHE 0.033 0.001 PHE C 65 TRP 0.029 0.002 TRP C 104 HIS 0.003 0.001 HIS C1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (22337) covalent geometry : angle 0.56465 / 0.29 (30401) SS BOND : bond 0.00174 / 0.12 ( 34) SS BOND : angle 0.62911 / 0.41 ( 68) hydrogen bonds : bond 0.04477 / 3.04 ( 953) hydrogen bonds : angle 5.56726 / 3.88 ( 2793) link_BETA1-4 : bond 0.00304 / 0.20 ( 18) link_BETA1-4 : angle 1.00446 / 0.68 ( 54) link_NAG-ASN : bond 0.00701 / 0.45 ( 38) link_NAG-ASN : angle 4.21362 / 2.38 ( 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 162 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8368 (tm-30) cc_final: 0.7763 (tm-30) REVERT: A 221 SER cc_start: 0.8665 (t) cc_final: 0.8266 (p) REVERT: A 231 ILE cc_start: 0.8700 (pt) cc_final: 0.8418 (pp) REVERT: A 569 ILE cc_start: 0.8643 (mp) cc_final: 0.8151 (tp) REVERT: A 591 SER cc_start: 0.8811 (m) cc_final: 0.8379 (p) REVERT: A 858 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8762 (mt) REVERT: A 868 GLU cc_start: 0.8107 (OUTLIER) cc_final: 0.7765 (tp30) REVERT: B 565 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7188 (p90) REVERT: B 983 ARG cc_start: 0.7834 (ttm170) cc_final: 0.7568 (mtp180) REVERT: C 52 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8575 (tm-30) REVERT: C 129 LYS cc_start: 0.6591 (mtmt) cc_final: 0.6112 (mmtt) REVERT: C 238 PHE cc_start: 0.5906 (p90) cc_final: 0.4702 (p90) REVERT: C 269 TYR cc_start: 0.7248 (m-80) cc_final: 0.6991 (m-80) REVERT: C 353 TRP cc_start: 0.6919 (p-90) cc_final: 0.6712 (p-90) REVERT: C 516 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.6240 (pp20) outliers start: 26 outliers final: 19 residues processed: 152 average time/residue: 0.4384 time to fit residues: 79.6394 Evaluate side-chains 158 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 217 optimal weight: 4.9990 chunk 266 optimal weight: 0.0870 chunk 224 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 21 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 163 optimal weight: 0.0570 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 207 HIS A 762 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 = 0.4151 r_free = 0.4151 target = 0.151229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.089282 restraints weight = 33337.373| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.47 r_work: 0.3072 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22427 Z= 0.113 Angle : 0.589 31.827 30637 Z= 0.283 Chirality : 0.046 0.486 3647 Planarity : 0.004 0.045 3861 Dihedral : 4.256 21.935 2876 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.14 % Allowed : 11.45 % Favored : 87.41 % 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: 0.66 (0.16), residues: 2651 helix: 2.67 (0.21), residues: 623 sheet: 0.24 (0.21), residues: 577 loop : -0.46 (0.15), residues: 1451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 190 TYR 0.024 0.001 TYR B 170 PHE 0.026 0.001 PHE A 168 TRP 0.037 0.002 TRP C 104 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (22337) covalent geometry : angle 0.53174 / 0.27 (30401) SS BOND : bond 0.00116 / 0.07 ( 34) SS BOND : angle 0.62898 / 0.43 ( 68) hydrogen bonds : bond 0.03960 / 2.68 ( 953) hydrogen bonds : angle 5.33680 / 3.71 ( 2793) link_BETA1-4 : bond 0.00339 / 0.23 ( 18) link_BETA1-4 : angle 0.90383 / 0.63 ( 54) link_NAG-ASN : bond 0.00672 / 0.43 ( 38) link_NAG-ASN : angle 4.14753 / 2.35 ( 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 174 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 147 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 52 GLN cc_start: 0.8345 (tm-30) cc_final: 0.7734 (tm-30) REVERT: A 200 TYR cc_start: 0.7861 (OUTLIER) cc_final: 0.6839 (t80) REVERT: A 221 SER cc_start: 0.8649 (t) cc_final: 0.8295 (p) REVERT: A 231 ILE cc_start: 0.8689 (pt) cc_final: 0.8437 (pp) REVERT: A 569 ILE cc_start: 0.8619 (mp) cc_final: 0.8151 (tp) REVERT: A 591 SER cc_start: 0.8866 (m) cc_final: 0.8393 (p) REVERT: A 773 GLU cc_start: 0.8844 (tt0) cc_final: 0.8574 (tt0) REVERT: A 858 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8775 (mt) REVERT: A 868 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7721 (tp30) REVERT: B 565 PHE cc_start: 0.7401 (OUTLIER) cc_final: 0.7066 (p90) REVERT: B 820 ASP cc_start: 0.8414 (t70) cc_final: 0.7950 (m-30) REVERT: B 983 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7574 (mtp180) REVERT: C 52 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8557 (tm-30) REVERT: C 129 LYS cc_start: 0.6616 (mtmt) cc_final: 0.6105 (mmtt) REVERT: C 238 PHE cc_start: 0.5889 (p90) cc_final: 0.4682 (p90) REVERT: C 269 TYR cc_start: 0.7210 (m-80) cc_final: 0.6936 (m-80) REVERT: C 353 TRP cc_start: 0.6756 (p-90) cc_final: 0.6501 (p-90) REVERT: C 421 TYR cc_start: 0.8111 (m-80) cc_final: 0.7853 (m-80) REVERT: C 516 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6287 (pp20) REVERT: C 740 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8187 (ttt) outliers start: 27 outliers final: 17 residues processed: 165 average time/residue: 0.5214 time to fit residues: 101.8061 Evaluate side-chains 162 residues out of total 2367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 ILE Chi-restraints excluded: chain A residue 200 TYR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 868 GLU Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 619 GLU Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 47 VAL Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 747 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 269 random chunks: chunk 227 optimal weight: 5.9990 chunk 240 optimal weight: 0.4980 chunk 129 optimal weight: 3.9990 chunk 182 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 212 optimal weight: 0.0670 chunk 44 optimal weight: 0.5980 chunk 190 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS A 81 ASN A 207 HIS A 762 GLN C 978 ASN ** C1010 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.151305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.089291 restraints weight = 33358.042| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.46 r_work: 0.3072 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22427 Z= 0.116 Angle : 0.584 31.708 30637 Z= 0.281 Chirality : 0.045 0.440 3647 Planarity : 0.004 0.047 3861 Dihedral : 4.169 20.627 2876 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 11.49 % Favored : 87.45 % 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: 0.71 (0.16), residues: 2651 helix: 2.71 (0.21), residues: 623 sheet: 0.23 (0.21), residues: 581 loop : -0.41 (0.15), residues: 1447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.021 0.001 TYR C1067 PHE 0.034 0.001 PHE C 65 TRP 0.034 0.001 TRP C 436 HIS 0.002 0.000 HIS A1048 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 (22337) covalent geometry : angle 0.52721 / 0.27 (30401) SS BOND : bond 0.00108 / 0.07 ( 34) SS BOND : angle 0.59976 / 0.41 ( 68) hydrogen bonds : bond 0.03910 / 2.64 ( 953) hydrogen bonds : angle 5.24918 / 3.65 ( 2793) link_BETA1-4 : bond 0.00329 / 0.22 ( 18) link_BETA1-4 : angle 0.93690 / 0.65 ( 54) link_NAG-ASN : bond 0.00651 / 0.42 ( 38) link_NAG-ASN : angle 4.09477 / 2.32 ( 114) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12938.16 seconds wall clock time: 219 minutes 53.95 seconds (13193.95 seconds total)