Starting phenix.real_space_refine on Mon Aug 25 04:45:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dli_27502/08_2025/8dli_27502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dli_27502/08_2025/8dli_27502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dli_27502/08_2025/8dli_27502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dli_27502/08_2025/8dli_27502.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dli_27502/08_2025/8dli_27502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dli_27502/08_2025/8dli_27502.map" } resolution = 2.56 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= 0.039 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 111 5.16 5 C 16013 2.51 5 N 4115 2.21 5 O 4915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25154 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8107 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 7 Chain: "B" Number of atoms: 8107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8107 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 56, 'TRANS': 980} Chain breaks: 7 Chain: "C" Number of atoms: 8100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8100 Classifications: {'peptide': 1036} Link IDs: {'PTRANS': 56, 'TRANS': 979} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 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 dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 6.25, per 1000 atoms: 0.25 Number of scatterers: 25154 At special positions: 0 Unit cell: (140, 144, 196, 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 111 16.00 O 4915 8.00 N 4115 7.00 C 16013 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 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 331 " " NAG A1307 " - " ASN A 343 " " NAG A1308 " - " 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 331 " " NAG B1307 " - " ASN B 343 " " NAG B1308 " - " 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: 2.04 Conformation dependent library (CDL) restraints added in 1.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5824 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 43 sheets defined 24.6% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.048A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.665A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.736A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 620 removed outlier: 4.044A 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: 3.613A 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: 3.961A 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 966 removed outlier: 3.733A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.109A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1147 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 4.129A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 386 through 389 Processing helix chain 'B' and resid 404 through 410 removed outlier: 3.883A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE B 410 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.650A pdb=" N ASP B 420 " --> pdb=" O GLY B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 620 removed outlier: 3.994A 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: 3.523A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.502A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.925A 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 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: 4.025A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1147 removed outlier: 3.534A 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: 3.894A 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 386 through 390 removed outlier: 3.775A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 removed outlier: 3.827A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 removed outlier: 3.579A pdb=" N ASP C 420 " --> pdb=" O GLY C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.873A 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: 3.605A 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: 3.953A 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: 3.516A 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: 4.334A 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 removed outlier: 8.022A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.672A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.986A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 84 through 85 current: chain 'A' and resid 116 through 121 removed outlier: 11.376A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.946A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.206A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.312A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.626A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 6.674A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.004A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.818A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.575A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.027A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.615A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.743A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 711 through 728 current: chain 'A' and resid 1059 through 1078 removed outlier: 3.900A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.311A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.786A pdb=" N LYS A 790 " --> pdb=" O ASN C 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.238A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.940A 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: 4.089A 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 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 85 current: chain 'B' and resid 116 through 121 removed outlier: 6.798A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 156 through 172 current: chain 'B' and resid 259 through 260 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.746A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 325 through 328 removed outlier: 3.519A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 354 through 358 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 354 through 358 current: chain 'B' and resid 508 through 516 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.075A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 701 through 704 removed outlier: 3.647A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 711 through 728 current: chain 'B' and resid 1059 through 1078 removed outlier: 3.904A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.341A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD3, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.122A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.664A 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: 4.109A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.977A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL C 126 " --> pdb=" O SER C 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 156 through 163 removed outlier: 9.921A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.320A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.190A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.876A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.744A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 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: 3.528A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.929A 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: 6.228A 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: 6.415A 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 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 711 through 728 current: chain 'C' and resid 1059 through 1078 removed outlier: 3.840A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.276A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 1120 through 1122 924 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.27 Time building geometry restraints manager: 2.75 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: 7878 1.34 - 1.46: 6408 1.46 - 1.59: 11293 1.59 - 1.71: 0 1.71 - 1.83: 138 Bond restraints: 25717 Sorted by residual: bond pdb=" C1 NAG C1304 " pdb=" O5 NAG C1304 " ideal model delta sigma weight residual 1.406 1.467 -0.061 2.00e-02 2.50e+03 9.45e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.69e+00 bond pdb=" C1 NAG B1303 " pdb=" O5 NAG B1303 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" C1 NAG J 1 " pdb=" O5 NAG J 1 " ideal model delta sigma weight residual 1.406 1.458 -0.052 2.00e-02 2.50e+03 6.79e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.456 -0.050 2.00e-02 2.50e+03 6.31e+00 ... (remaining 25712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 33409 1.84 - 3.68: 1426 3.68 - 5.53: 117 5.53 - 7.37: 40 7.37 - 9.21: 11 Bond angle restraints: 35003 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 110.70 116.57 -5.87 1.22e+00 6.72e-01 2.32e+01 angle pdb=" N PRO B 986 " pdb=" CA PRO B 986 " pdb=" C PRO B 986 " ideal model delta sigma weight residual 110.70 115.96 -5.26 1.22e+00 6.72e-01 1.86e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 115.87 -5.17 1.22e+00 6.72e-01 1.80e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 122.34 -4.41 1.20e+00 6.94e-01 1.35e+01 angle pdb=" CA GLU C 583 " pdb=" CB GLU C 583 " pdb=" CG GLU C 583 " ideal model delta sigma weight residual 114.10 121.33 -7.23 2.00e+00 2.50e-01 1.31e+01 ... (remaining 34998 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 14830 17.80 - 35.60: 1021 35.60 - 53.39: 178 53.39 - 71.19: 66 71.19 - 88.99: 28 Dihedral angle restraints: 16123 sinusoidal: 7079 harmonic: 9044 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 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -57.45 -28.55 1 1.00e+01 1.00e-02 1.17e+01 dihedral pdb=" CA LEU B 517 " pdb=" C LEU B 517 " pdb=" N LEU B 518 " pdb=" CA LEU B 518 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 16120 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 3195 0.065 - 0.130: 826 0.130 - 0.195: 114 0.195 - 0.260: 9 0.260 - 0.325: 3 Chirality restraints: 4147 Sorted by residual: 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 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+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 -2.07 -0.33 2.00e-01 2.50e+01 2.64e+00 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 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 4144 not shown) Planarity restraints: 4501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 716 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C ILE B 716 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE B 716 " -0.026 2.00e-02 2.50e+03 pdb=" N ASN B 717 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 716 " -0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C ILE C 716 " 0.068 2.00e-02 2.50e+03 pdb=" O ILE C 716 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN C 717 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 716 " 0.020 2.00e-02 2.50e+03 3.92e-02 1.54e+01 pdb=" C ILE A 716 " -0.068 2.00e-02 2.50e+03 pdb=" O ILE A 716 " 0.025 2.00e-02 2.50e+03 pdb=" N ASN A 717 " 0.023 2.00e-02 2.50e+03 ... (remaining 4498 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6444 2.80 - 3.32: 21194 3.32 - 3.85: 43005 3.85 - 4.37: 49555 4.37 - 4.90: 85019 Nonbonded interactions: 205217 Sorted by model distance: nonbonded pdb=" OH TYR B 37 " pdb=" O LEU B 54 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP B 420 " pdb=" OH TYR C 369 " model vdw 2.285 3.040 nonbonded pdb=" OG1 THR C 323 " pdb=" OE1 GLU C 324 " model vdw 2.287 3.040 nonbonded pdb=" OE1 GLN B 52 " pdb=" OG1 THR B 274 " model vdw 2.288 3.040 ... (remaining 205212 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 552 or resid 554 through 1308)) selection = (chain 'B' and (resid 14 through 552 or resid 554 through 1308)) selection = chain 'C' } 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.400 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 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 25819 Z= 0.240 Angle : 0.854 15.282 35267 Z= 0.459 Chirality : 0.057 0.325 4147 Planarity : 0.006 0.058 4459 Dihedral : 12.958 88.988 10173 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.07 % Allowed : 3.38 % Favored : 96.55 % 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 aren not related in a simple way. whole: -0.02 (0.14), residues: 3060 helix: 1.01 (0.18), residues: 675 sheet: 0.81 (0.19), residues: 686 loop : -0.78 (0.13), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 995 TYR 0.029 0.002 TYR A1067 PHE 0.031 0.002 PHE C 275 TRP 0.028 0.002 TRP A 886 HIS 0.006 0.001 HIS B1118 Details of bonding type rmsd covalent geometry : bond 0.00497 (25717) covalent geometry : angle 0.82840 (35003) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.26814 ( 84) hydrogen bonds : bond 0.11675 ( 924) hydrogen bonds : angle 6.95635 ( 2571) link_BETA1-4 : bond 0.00622 ( 18) link_BETA1-4 : angle 1.33503 ( 54) link_NAG-ASN : bond 0.00721 ( 42) link_NAG-ASN : angle 3.43602 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 250 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.7984 (t80) cc_final: 0.7254 (t80) REVERT: A 1029 MET cc_start: 0.9325 (tpp) cc_final: 0.9042 (tpp) REVERT: B 201 PHE cc_start: 0.8955 (t80) cc_final: 0.8301 (t80) REVERT: B 239 GLN cc_start: 0.8316 (tt0) cc_final: 0.7791 (tt0) REVERT: B 387 LEU cc_start: 0.8247 (mt) cc_final: 0.7739 (mp) REVERT: B 993 ILE cc_start: 0.9390 (mt) cc_final: 0.9060 (mp) REVERT: B 1029 MET cc_start: 0.9310 (tpp) cc_final: 0.8931 (tpp) REVERT: C 229 LEU cc_start: 0.7935 (tp) cc_final: 0.7707 (tt) REVERT: C 392 PHE cc_start: 0.7192 (m-80) cc_final: 0.6861 (m-80) REVERT: C 453 TYR cc_start: 0.6072 (p90) cc_final: 0.5676 (p90) outliers start: 2 outliers final: 2 residues processed: 252 average time/residue: 0.7134 time to fit residues: 206.7428 Evaluate side-chains 107 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 105 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 979 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 211 ASN A 388 ASN A 926 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B1002 GLN ** B1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C 960 ASN C1010 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.118831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.073497 restraints weight = 70188.484| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.73 r_work: 0.3141 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 25819 Z= 0.184 Angle : 0.586 11.061 35267 Z= 0.296 Chirality : 0.045 0.255 4147 Planarity : 0.005 0.060 4459 Dihedral : 6.609 59.914 4592 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 0.92 % Allowed : 7.38 % Favored : 91.70 % 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 aren not related in a simple way. whole: 0.34 (0.14), residues: 3060 helix: 1.80 (0.20), residues: 691 sheet: 0.69 (0.21), residues: 580 loop : -0.56 (0.13), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 357 TYR 0.017 0.001 TYR A1067 PHE 0.018 0.002 PHE B 515 TRP 0.019 0.002 TRP C 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00413 (25717) covalent geometry : angle 0.56116 (35003) SS BOND : bond 0.00232 ( 42) SS BOND : angle 0.79251 ( 84) hydrogen bonds : bond 0.04470 ( 924) hydrogen bonds : angle 5.77861 ( 2571) link_BETA1-4 : bond 0.00216 ( 18) link_BETA1-4 : angle 1.13251 ( 54) link_NAG-ASN : bond 0.00577 ( 42) link_NAG-ASN : angle 2.78440 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 988 GLU cc_start: 0.9382 (mp0) cc_final: 0.8964 (mp0) REVERT: B 201 PHE cc_start: 0.8727 (t80) cc_final: 0.8320 (t80) REVERT: B 237 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6762 (mtm-85) REVERT: B 239 GLN cc_start: 0.7994 (tt0) cc_final: 0.7780 (tp40) REVERT: B 387 LEU cc_start: 0.7906 (mt) cc_final: 0.7334 (mp) REVERT: B 950 ASP cc_start: 0.9045 (m-30) cc_final: 0.8805 (m-30) REVERT: B 993 ILE cc_start: 0.9361 (mt) cc_final: 0.9082 (mp) REVERT: B 1029 MET cc_start: 0.9636 (tpp) cc_final: 0.9168 (tpp) REVERT: C 421 TYR cc_start: 0.8451 (m-10) cc_final: 0.8212 (m-10) outliers start: 25 outliers final: 9 residues processed: 133 average time/residue: 0.6015 time to fit residues: 93.7592 Evaluate side-chains 103 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 52 optimal weight: 7.9990 chunk 190 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 164 optimal weight: 0.7980 chunk 9 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 121 optimal weight: 0.9990 chunk 140 optimal weight: 20.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN B 901 GLN B 955 ASN C 207 HIS C 824 ASN C 913 GLN C 957 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.117563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.071579 restraints weight = 69844.021| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 4.08 r_work: 0.3101 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 25819 Z= 0.201 Angle : 0.570 10.507 35267 Z= 0.287 Chirality : 0.045 0.260 4147 Planarity : 0.004 0.046 4459 Dihedral : 5.886 55.907 4588 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.36 % Allowed : 8.48 % Favored : 90.16 % 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 aren not related in a simple way. whole: 0.40 (0.15), residues: 3060 helix: 1.89 (0.20), residues: 691 sheet: 0.50 (0.20), residues: 628 loop : -0.48 (0.14), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.023 0.001 TYR C 453 PHE 0.021 0.001 PHE B 392 TRP 0.038 0.002 TRP A 104 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00451 (25717) covalent geometry : angle 0.54692 (35003) SS BOND : bond 0.00224 ( 42) SS BOND : angle 0.66649 ( 84) hydrogen bonds : bond 0.04412 ( 924) hydrogen bonds : angle 5.52671 ( 2571) link_BETA1-4 : bond 0.00346 ( 18) link_BETA1-4 : angle 1.13160 ( 54) link_NAG-ASN : bond 0.00592 ( 42) link_NAG-ASN : angle 2.64595 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 108 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 985 ASP cc_start: 0.7286 (p0) cc_final: 0.6933 (p0) REVERT: A 1002 GLN cc_start: 0.8980 (OUTLIER) cc_final: 0.8377 (tm-30) REVERT: B 81 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8268 (t0) REVERT: B 201 PHE cc_start: 0.8814 (t80) cc_final: 0.8372 (t80) REVERT: B 238 PHE cc_start: 0.6134 (p90) cc_final: 0.5872 (p90) REVERT: B 239 GLN cc_start: 0.7936 (tt0) cc_final: 0.7584 (tp-100) REVERT: B 314 GLN cc_start: 0.9193 (tt0) cc_final: 0.8649 (tm-30) REVERT: B 342 PHE cc_start: 0.7029 (m-80) cc_final: 0.6743 (t80) REVERT: B 950 ASP cc_start: 0.9059 (m-30) cc_final: 0.8785 (m-30) REVERT: B 983 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8732 (ttm-80) REVERT: B 1029 MET cc_start: 0.9618 (tpp) cc_final: 0.9342 (tpp) REVERT: C 229 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7907 (tm) REVERT: C 440 ASN cc_start: 0.7053 (p0) cc_final: 0.6665 (m110) REVERT: C 441 LEU cc_start: 0.8453 (mt) cc_final: 0.7914 (tm) outliers start: 37 outliers final: 8 residues processed: 140 average time/residue: 0.5103 time to fit residues: 85.7771 Evaluate side-chains 103 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain B residue 81 ASN Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 983 ARG Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 0 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 267 optimal weight: 4.9990 chunk 146 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 194 optimal weight: 0.7980 chunk 123 optimal weight: 8.9990 chunk 262 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 245 optimal weight: 20.0000 chunk 118 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 824 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 955 ASN B 957 GLN B1002 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.116064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.070509 restraints weight = 69769.054| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 3.89 r_work: 0.3069 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 25819 Z= 0.272 Angle : 0.610 10.401 35267 Z= 0.305 Chirality : 0.046 0.259 4147 Planarity : 0.004 0.047 4459 Dihedral : 5.782 52.949 4588 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.32 % Allowed : 9.88 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.26 (0.15), residues: 3060 helix: 1.84 (0.20), residues: 693 sheet: 0.21 (0.21), residues: 588 loop : -0.50 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 357 TYR 0.021 0.002 TYR A1067 PHE 0.020 0.002 PHE B 515 TRP 0.015 0.002 TRP B 104 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00615 (25717) covalent geometry : angle 0.58737 (35003) SS BOND : bond 0.00252 ( 42) SS BOND : angle 0.67562 ( 84) hydrogen bonds : bond 0.04602 ( 924) hydrogen bonds : angle 5.56377 ( 2571) link_BETA1-4 : bond 0.00279 ( 18) link_BETA1-4 : angle 1.22877 ( 54) link_NAG-ASN : bond 0.00672 ( 42) link_NAG-ASN : angle 2.68923 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 94 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8428 (tm-30) REVERT: B 108 THR cc_start: 0.4713 (OUTLIER) cc_final: 0.4321 (m) REVERT: B 189 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8172 (tm) REVERT: B 201 PHE cc_start: 0.8894 (t80) cc_final: 0.8458 (t80) REVERT: B 238 PHE cc_start: 0.6408 (p90) cc_final: 0.6070 (p90) REVERT: B 239 GLN cc_start: 0.8035 (tt0) cc_final: 0.7807 (tp40) REVERT: B 314 GLN cc_start: 0.9183 (tt0) cc_final: 0.8608 (tm-30) REVERT: B 950 ASP cc_start: 0.9042 (m-30) cc_final: 0.8758 (m-30) REVERT: C 440 ASN cc_start: 0.7194 (p0) cc_final: 0.6772 (m110) REVERT: C 441 LEU cc_start: 0.8512 (mt) cc_final: 0.7964 (tm) outliers start: 36 outliers final: 15 residues processed: 123 average time/residue: 0.5325 time to fit residues: 79.1580 Evaluate side-chains 108 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 143 optimal weight: 6.9990 chunk 64 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 32 optimal weight: 30.0000 chunk 140 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 224 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 231 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN A 955 ASN A1011 GLN B1002 GLN C 955 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.117699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.072586 restraints weight = 69244.319| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 3.91 r_work: 0.3107 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25819 Z= 0.117 Angle : 0.527 10.330 35267 Z= 0.263 Chirality : 0.043 0.261 4147 Planarity : 0.004 0.045 4459 Dihedral : 5.388 53.520 4588 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.21 % Allowed : 10.39 % Favored : 88.40 % 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 aren not related in a simple way. whole: 0.43 (0.15), residues: 3060 helix: 2.06 (0.20), residues: 693 sheet: 0.28 (0.20), residues: 646 loop : -0.43 (0.14), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.014 0.001 TYR A1067 PHE 0.023 0.001 PHE B 374 TRP 0.032 0.002 TRP C 353 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00254 (25717) covalent geometry : angle 0.50524 (35003) SS BOND : bond 0.00145 ( 42) SS BOND : angle 0.55954 ( 84) hydrogen bonds : bond 0.04001 ( 924) hydrogen bonds : angle 5.32176 ( 2571) link_BETA1-4 : bond 0.00310 ( 18) link_BETA1-4 : angle 1.03134 ( 54) link_NAG-ASN : bond 0.00558 ( 42) link_NAG-ASN : angle 2.50310 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 103 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8182 (tp) cc_final: 0.7910 (tt) REVERT: A 570 ASP cc_start: 0.8482 (m-30) cc_final: 0.7924 (p0) REVERT: A 1002 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.8411 (tm-30) REVERT: B 108 THR cc_start: 0.4953 (OUTLIER) cc_final: 0.4500 (m) REVERT: B 189 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (tm) REVERT: B 201 PHE cc_start: 0.8865 (t80) cc_final: 0.8424 (t80) REVERT: B 238 PHE cc_start: 0.6376 (p90) cc_final: 0.6018 (p90) REVERT: B 239 GLN cc_start: 0.8031 (tt0) cc_final: 0.7767 (tp40) REVERT: B 245 HIS cc_start: 0.2272 (OUTLIER) cc_final: 0.1618 (m90) REVERT: B 950 ASP cc_start: 0.9029 (m-30) cc_final: 0.8734 (m-30) REVERT: C 440 ASN cc_start: 0.7299 (p0) cc_final: 0.6866 (m110) REVERT: C 441 LEU cc_start: 0.8494 (mt) cc_final: 0.7917 (tm) REVERT: C 1050 MET cc_start: 0.9275 (ptp) cc_final: 0.9067 (ptp) outliers start: 33 outliers final: 11 residues processed: 130 average time/residue: 0.4861 time to fit residues: 77.0272 Evaluate side-chains 105 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 158 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 246 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 288 optimal weight: 2.9990 chunk 245 optimal weight: 6.9990 chunk 252 optimal weight: 9.9990 chunk 13 optimal weight: 3.9990 chunk 260 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 762 GLN B 907 ASN B1002 GLN C 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.115489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.070621 restraints weight = 69981.655| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 3.81 r_work: 0.3068 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 25819 Z= 0.280 Angle : 0.619 10.337 35267 Z= 0.307 Chirality : 0.046 0.257 4147 Planarity : 0.004 0.047 4459 Dihedral : 5.518 53.809 4588 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.40 % Allowed : 10.58 % Favored : 88.03 % 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 aren not related in a simple way. whole: 0.25 (0.15), residues: 3060 helix: 1.97 (0.20), residues: 679 sheet: 0.03 (0.20), residues: 646 loop : -0.50 (0.14), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 357 TYR 0.026 0.002 TYR C 453 PHE 0.027 0.002 PHE B 374 TRP 0.038 0.002 TRP C 353 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00636 (25717) covalent geometry : angle 0.59688 (35003) SS BOND : bond 0.00259 ( 42) SS BOND : angle 0.71260 ( 84) hydrogen bonds : bond 0.04631 ( 924) hydrogen bonds : angle 5.51964 ( 2571) link_BETA1-4 : bond 0.00247 ( 18) link_BETA1-4 : angle 1.31310 ( 54) link_NAG-ASN : bond 0.00690 ( 42) link_NAG-ASN : angle 2.65570 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 94 time to evaluate : 0.669 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.9033 (OUTLIER) cc_final: 0.8446 (tm-30) REVERT: B 108 THR cc_start: 0.5041 (OUTLIER) cc_final: 0.4566 (m) REVERT: B 189 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8230 (tm) REVERT: B 201 PHE cc_start: 0.8902 (t80) cc_final: 0.8468 (t80) REVERT: B 237 ARG cc_start: 0.7516 (OUTLIER) cc_final: 0.7155 (mtm-85) REVERT: B 238 PHE cc_start: 0.6219 (p90) cc_final: 0.5883 (p90) REVERT: B 239 GLN cc_start: 0.7982 (tt0) cc_final: 0.7633 (tp40) REVERT: B 240 THR cc_start: 0.7674 (OUTLIER) cc_final: 0.7059 (t) REVERT: B 245 HIS cc_start: 0.2483 (OUTLIER) cc_final: 0.1920 (m90) REVERT: B 950 ASP cc_start: 0.9052 (m-30) cc_final: 0.8762 (m-30) REVERT: C 324 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: C 441 LEU cc_start: 0.8539 (mt) cc_final: 0.8183 (tm) outliers start: 38 outliers final: 15 residues processed: 130 average time/residue: 0.5236 time to fit residues: 81.3087 Evaluate side-chains 109 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 570 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 175 optimal weight: 0.0370 chunk 264 optimal weight: 5.9990 chunk 25 optimal weight: 0.0470 chunk 220 optimal weight: 20.0000 chunk 116 optimal weight: 30.0000 chunk 41 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 39 optimal weight: 30.0000 chunk 168 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN B 907 ASN B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.119527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.075594 restraints weight = 68868.051| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.64 r_work: 0.3125 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 25819 Z= 0.113 Angle : 0.530 10.197 35267 Z= 0.264 Chirality : 0.043 0.263 4147 Planarity : 0.004 0.050 4459 Dihedral : 5.145 53.753 4588 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.88 % Allowed : 11.60 % Favored : 87.51 % 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 aren not related in a simple way. whole: 0.42 (0.15), residues: 3060 helix: 2.22 (0.20), residues: 679 sheet: 0.17 (0.20), residues: 643 loop : -0.45 (0.14), residues: 1738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.013 0.001 TYR B1067 PHE 0.019 0.001 PHE B 374 TRP 0.037 0.002 TRP C 353 HIS 0.005 0.001 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00244 (25717) covalent geometry : angle 0.50914 (35003) SS BOND : bond 0.00158 ( 42) SS BOND : angle 0.59506 ( 84) hydrogen bonds : bond 0.03906 ( 924) hydrogen bonds : angle 5.26204 ( 2571) link_BETA1-4 : bond 0.00360 ( 18) link_BETA1-4 : angle 0.99273 ( 54) link_NAG-ASN : bond 0.00536 ( 42) link_NAG-ASN : angle 2.41366 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 101 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 570 ASP cc_start: 0.8507 (m-30) cc_final: 0.8004 (p0) REVERT: A 1002 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8398 (tm-30) REVERT: B 108 THR cc_start: 0.4907 (OUTLIER) cc_final: 0.4440 (m) REVERT: B 189 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8185 (tm) REVERT: B 201 PHE cc_start: 0.8865 (t80) cc_final: 0.8478 (t80) REVERT: B 238 PHE cc_start: 0.6205 (p90) cc_final: 0.5779 (p90) REVERT: B 239 GLN cc_start: 0.7983 (tt0) cc_final: 0.7620 (tp40) REVERT: B 240 THR cc_start: 0.7490 (OUTLIER) cc_final: 0.6819 (t) REVERT: B 245 HIS cc_start: 0.2295 (OUTLIER) cc_final: 0.1795 (m90) REVERT: B 950 ASP cc_start: 0.9034 (m-30) cc_final: 0.8737 (m-30) REVERT: C 324 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8172 (pm20) REVERT: C 392 PHE cc_start: 0.7165 (m-10) cc_final: 0.6635 (m-10) REVERT: C 441 LEU cc_start: 0.8545 (mt) cc_final: 0.8176 (tm) outliers start: 24 outliers final: 10 residues processed: 122 average time/residue: 0.4666 time to fit residues: 68.9402 Evaluate side-chains 109 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 203 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 229 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS B 957 GLN B1002 GLN C 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.118564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.074569 restraints weight = 69065.531| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.60 r_work: 0.3102 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 25819 Z= 0.188 Angle : 0.554 10.262 35267 Z= 0.275 Chirality : 0.044 0.257 4147 Planarity : 0.004 0.054 4459 Dihedral : 5.095 53.271 4588 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.95 % Allowed : 11.83 % Favored : 87.22 % 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 aren not related in a simple way. whole: 0.39 (0.15), residues: 3060 helix: 2.19 (0.20), residues: 679 sheet: 0.10 (0.20), residues: 648 loop : -0.44 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 357 TYR 0.030 0.001 TYR C 453 PHE 0.018 0.001 PHE C 192 TRP 0.040 0.002 TRP C 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00425 (25717) covalent geometry : angle 0.53370 (35003) SS BOND : bond 0.00196 ( 42) SS BOND : angle 0.60307 ( 84) hydrogen bonds : bond 0.04129 ( 924) hydrogen bonds : angle 5.29898 ( 2571) link_BETA1-4 : bond 0.00280 ( 18) link_BETA1-4 : angle 1.10766 ( 54) link_NAG-ASN : bond 0.00574 ( 42) link_NAG-ASN : angle 2.45872 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.8988 (OUTLIER) cc_final: 0.8415 (tm-30) REVERT: B 108 THR cc_start: 0.5040 (OUTLIER) cc_final: 0.4564 (m) REVERT: B 189 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8213 (tm) REVERT: B 201 PHE cc_start: 0.8926 (t80) cc_final: 0.8482 (t80) REVERT: B 238 PHE cc_start: 0.6313 (p90) cc_final: 0.5831 (p90) REVERT: B 239 GLN cc_start: 0.8003 (tt0) cc_final: 0.7612 (tp40) REVERT: B 240 THR cc_start: 0.7517 (OUTLIER) cc_final: 0.6856 (t) REVERT: B 245 HIS cc_start: 0.2426 (OUTLIER) cc_final: 0.1876 (m90) REVERT: B 950 ASP cc_start: 0.9045 (m-30) cc_final: 0.8753 (m-30) REVERT: C 66 HIS cc_start: 0.5476 (m90) cc_final: 0.5112 (m-70) REVERT: C 218 GLN cc_start: 0.8717 (tt0) cc_final: 0.8511 (mm-40) REVERT: C 324 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8195 (pm20) REVERT: C 441 LEU cc_start: 0.8548 (mt) cc_final: 0.8174 (tm) outliers start: 26 outliers final: 12 residues processed: 122 average time/residue: 0.5019 time to fit residues: 74.2851 Evaluate side-chains 108 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 570 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 101 optimal weight: 2.9990 chunk 249 optimal weight: 20.0000 chunk 168 optimal weight: 1.9990 chunk 108 optimal weight: 20.0000 chunk 286 optimal weight: 0.5980 chunk 202 optimal weight: 0.9990 chunk 165 optimal weight: 3.9990 chunk 302 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 232 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN C 856 ASN C1010 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.118375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074345 restraints weight = 69214.303| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.59 r_work: 0.3083 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25819 Z= 0.215 Angle : 0.576 10.357 35267 Z= 0.286 Chirality : 0.045 0.257 4147 Planarity : 0.004 0.054 4459 Dihedral : 5.174 53.058 4588 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.99 % Allowed : 12.08 % Favored : 86.93 % 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 aren not related in a simple way. whole: 0.35 (0.15), residues: 3060 helix: 2.11 (0.20), residues: 685 sheet: 0.01 (0.20), residues: 655 loop : -0.43 (0.14), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 357 TYR 0.022 0.001 TYR B 170 PHE 0.023 0.001 PHE B 392 TRP 0.044 0.002 TRP C 353 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00485 (25717) covalent geometry : angle 0.55619 (35003) SS BOND : bond 0.00224 ( 42) SS BOND : angle 0.65276 ( 84) hydrogen bonds : bond 0.04228 ( 924) hydrogen bonds : angle 5.33899 ( 2571) link_BETA1-4 : bond 0.00288 ( 18) link_BETA1-4 : angle 1.13305 ( 54) link_NAG-ASN : bond 0.00592 ( 42) link_NAG-ASN : angle 2.48421 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 1002 GLN cc_start: 0.9001 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: B 108 THR cc_start: 0.5036 (OUTLIER) cc_final: 0.4566 (m) REVERT: B 191 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7533 (mm-30) REVERT: B 201 PHE cc_start: 0.8901 (t80) cc_final: 0.8524 (t80) REVERT: B 238 PHE cc_start: 0.6261 (p90) cc_final: 0.5791 (p90) REVERT: B 239 GLN cc_start: 0.7960 (tt0) cc_final: 0.7575 (tp40) REVERT: B 240 THR cc_start: 0.7523 (OUTLIER) cc_final: 0.6855 (t) REVERT: B 245 HIS cc_start: 0.2429 (OUTLIER) cc_final: 0.1868 (m90) REVERT: B 950 ASP cc_start: 0.9044 (m-30) cc_final: 0.8736 (m-30) REVERT: C 66 HIS cc_start: 0.5592 (m90) cc_final: 0.5201 (m-70) REVERT: C 218 GLN cc_start: 0.8742 (tt0) cc_final: 0.8440 (mm110) REVERT: C 324 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8224 (pm20) REVERT: C 441 LEU cc_start: 0.8567 (mt) cc_final: 0.8181 (tm) outliers start: 27 outliers final: 13 residues processed: 119 average time/residue: 0.4821 time to fit residues: 69.9117 Evaluate side-chains 111 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 191 GLU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 570 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 183 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 chunk 164 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 123 optimal weight: 7.9990 chunk 157 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 200 optimal weight: 1.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 755 GLN B1002 GLN C 856 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.122050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.077091 restraints weight = 66228.652| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.92 r_work: 0.3113 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 25819 Z= 0.125 Angle : 0.542 10.816 35267 Z= 0.269 Chirality : 0.044 0.260 4147 Planarity : 0.004 0.055 4459 Dihedral : 4.970 53.539 4588 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.92 % Allowed : 12.05 % Favored : 87.04 % 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 aren not related in a simple way. whole: 0.49 (0.15), residues: 3060 helix: 2.33 (0.20), residues: 673 sheet: 0.03 (0.20), residues: 659 loop : -0.33 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.032 0.001 TYR C 453 PHE 0.027 0.001 PHE C 392 TRP 0.045 0.002 TRP B 353 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00279 (25717) covalent geometry : angle 0.52247 (35003) SS BOND : bond 0.00151 ( 42) SS BOND : angle 0.61200 ( 84) hydrogen bonds : bond 0.03866 ( 924) hydrogen bonds : angle 5.18412 ( 2571) link_BETA1-4 : bond 0.00323 ( 18) link_BETA1-4 : angle 1.00736 ( 54) link_NAG-ASN : bond 0.00514 ( 42) link_NAG-ASN : angle 2.35901 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6120 Ramachandran restraints generated. 3060 Oldfield, 0 Emsley, 3060 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 755 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8637 (mm110) REVERT: A 1002 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8414 (tm-30) REVERT: B 108 THR cc_start: 0.5076 (OUTLIER) cc_final: 0.4599 (m) REVERT: B 238 PHE cc_start: 0.6354 (p90) cc_final: 0.5834 (p90) REVERT: B 239 GLN cc_start: 0.8074 (tt0) cc_final: 0.7669 (tp40) REVERT: B 240 THR cc_start: 0.7573 (OUTLIER) cc_final: 0.6953 (t) REVERT: B 245 HIS cc_start: 0.2462 (OUTLIER) cc_final: 0.1873 (m90) REVERT: B 731 MET cc_start: 0.9518 (ptm) cc_final: 0.9304 (ptm) REVERT: B 950 ASP cc_start: 0.9046 (m-30) cc_final: 0.8738 (m-30) REVERT: C 66 HIS cc_start: 0.5537 (m90) cc_final: 0.5138 (m-70) REVERT: C 304 LYS cc_start: 0.9452 (mmmm) cc_final: 0.9099 (mmmm) REVERT: C 324 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8238 (pm20) REVERT: C 441 LEU cc_start: 0.8559 (mt) cc_final: 0.8169 (tm) outliers start: 25 outliers final: 10 residues processed: 115 average time/residue: 0.5102 time to fit residues: 70.4549 Evaluate side-chains 109 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 755 GLN Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 240 THR Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 324 GLU Chi-restraints excluded: chain C residue 382 VAL Chi-restraints excluded: chain C residue 515 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 84 optimal weight: 2.9990 chunk 164 optimal weight: 0.0270 chunk 31 optimal weight: 8.9990 chunk 252 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 260 optimal weight: 7.9990 chunk 7 optimal weight: 5.9990 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 6.9990 overall best weight: 2.7244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS B1002 GLN ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.128387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.082916 restraints weight = 69206.315| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 4.03 r_work: 0.3113 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.222 25819 Z= 0.216 Angle : 0.679 59.184 35267 Z= 0.371 Chirality : 0.046 0.632 4147 Planarity : 0.004 0.056 4459 Dihedral : 4.969 53.582 4588 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.70 % Allowed : 12.38 % Favored : 86.93 % Cbeta Deviations : 0.03 % 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 aren not related in a simple way. whole: 0.49 (0.15), residues: 3060 helix: 2.31 (0.20), residues: 673 sheet: 0.04 (0.20), residues: 659 loop : -0.33 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 357 TYR 0.018 0.001 TYR C 453 PHE 0.031 0.001 PHE C 32 TRP 0.080 0.003 TRP A 104 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00452 (25717) covalent geometry : angle 0.66537 (35003) SS BOND : bond 0.00230 ( 42) SS BOND : angle 0.61359 ( 84) hydrogen bonds : bond 0.03911 ( 924) hydrogen bonds : angle 5.18270 ( 2571) link_BETA1-4 : bond 0.00403 ( 18) link_BETA1-4 : angle 1.01889 ( 54) link_NAG-ASN : bond 0.00511 ( 42) link_NAG-ASN : angle 2.35396 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11701.65 seconds wall clock time: 199 minutes 17.81 seconds (11957.81 seconds total)