Starting phenix.real_space_refine on Sat May 24 10:16:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dli_27502/05_2025/8dli_27502.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dli_27502/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8dli_27502/05_2025/8dli_27502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dli_27502/05_2025/8dli_27502.map" model { file = "/net/cci-nas-00/data/ceres_data/8dli_27502/05_2025/8dli_27502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dli_27502/05_2025/8dli_27502.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 15.26, per 1000 atoms: 0.61 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: 6.79 Conformation dependent library (CDL) restraints added in 3.4 seconds 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: 3.63 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: 11.01 Time building geometry restraints manager: 7.87 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 1147 or resid 1301 thr \ ough 1308)) selection = (chain 'B' and (resid 14 through 552 or resid 554 through 1147 or resid 1301 thr \ ough 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: 0.020 Extract box with map and model: 0.860 Check model and map are aligned: 0.160 Set scattering table: 0.200 Process input model: 57.560 Find NCS groups from input model: 1.370 Set up NCS constraints: 0.160 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:13.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.850 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.028 0.002 TRP A 886 HIS 0.006 0.001 HIS B1118 PHE 0.031 0.002 PHE C 275 TYR 0.029 0.002 TYR A1067 ARG 0.009 0.001 ARG B 995 Details of bonding type rmsd link_NAG-ASN : bond 0.00721 ( 42) link_NAG-ASN : angle 3.43602 ( 126) link_BETA1-4 : bond 0.00622 ( 18) link_BETA1-4 : angle 1.33503 ( 54) hydrogen bonds : bond 0.11675 ( 924) hydrogen bonds : angle 6.95635 ( 2571) SS BOND : bond 0.00291 ( 42) SS BOND : angle 1.26814 ( 84) covalent geometry : bond 0.00497 (25717) covalent geometry : angle 0.82840 (35003) *********************** 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 : 2.496 Fit side-chains 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: 0.8299 (t80) REVERT: B 239 GLN cc_start: 0.8316 (tt0) cc_final: 0.7788 (tp40) REVERT: B 387 LEU cc_start: 0.8247 (mt) cc_final: 0.7753 (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: 0.5653 (p90) outliers start: 2 outliers final: 1 residues processed: 252 average time/residue: 1.3231 time to fit residues: 388.4428 Evaluate side-chains 104 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 260 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 129 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 157 optimal weight: 0.0020 chunk 125 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 chunk 147 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 chunk 280 optimal weight: 5.9990 overall best weight: 0.9570 ------------------------------------------------------------------------------- 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 913 GLN C 960 ASN C1010 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.120025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.075012 restraints weight = 70131.401| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 3.79 r_work: 0.3172 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25819 Z= 0.135 Angle : 0.562 10.907 35267 Z= 0.283 Chirality : 0.044 0.248 4147 Planarity : 0.005 0.059 4459 Dihedral : 6.616 59.104 4590 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.32 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3060 helix: 1.89 (0.20), residues: 680 sheet: 0.89 (0.20), residues: 663 loop : -0.62 (0.14), residues: 1717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 353 HIS 0.003 0.001 HIS C1118 PHE 0.022 0.001 PHE B 342 TYR 0.015 0.001 TYR A1067 ARG 0.009 0.001 ARG C 102 Details of bonding type rmsd link_NAG-ASN : bond 0.00551 ( 42) link_NAG-ASN : angle 2.74975 ( 126) link_BETA1-4 : bond 0.00229 ( 18) link_BETA1-4 : angle 1.09096 ( 54) hydrogen bonds : bond 0.04223 ( 924) hydrogen bonds : angle 5.77947 ( 2571) SS BOND : bond 0.00194 ( 42) SS BOND : angle 0.67130 ( 84) covalent geometry : bond 0.00297 (25717) covalent geometry : angle 0.53649 (35003) *********************** 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 : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 988 GLU cc_start: 0.9387 (mp0) cc_final: 0.9011 (mp0) REVERT: A 1029 MET cc_start: 0.9594 (tpp) cc_final: 0.9271 (tpp) REVERT: B 201 PHE cc_start: 0.8703 (t80) cc_final: 0.8276 (t80) REVERT: B 237 ARG cc_start: 0.7052 (OUTLIER) cc_final: 0.6688 (mtm-85) REVERT: B 239 GLN cc_start: 0.7963 (tt0) cc_final: 0.7747 (tp40) REVERT: B 387 LEU cc_start: 0.7895 (mt) cc_final: 0.7257 (mp) REVERT: B 950 ASP cc_start: 0.9013 (m-30) cc_final: 0.8773 (m-30) REVERT: B 1029 MET cc_start: 0.9652 (tpp) cc_final: 0.9149 (tpp) REVERT: C 421 TYR cc_start: 0.8449 (m-10) cc_final: 0.8103 (m-10) outliers start: 25 outliers final: 10 residues processed: 135 average time/residue: 1.2268 time to fit residues: 197.7536 Evaluate side-chains 105 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 2.755 ------------------------------------------------------------------------------- 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 993 ILE 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 64 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 283 optimal weight: 0.8980 chunk 50 optimal weight: 10.0000 chunk 207 optimal weight: 0.3980 chunk 27 optimal weight: 0.6980 chunk 32 optimal weight: 30.0000 chunk 144 optimal weight: 0.4980 chunk 30 optimal weight: 20.0000 chunk 54 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 207 HIS C 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.119584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.074659 restraints weight = 69485.052| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.78 r_work: 0.3170 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 25819 Z= 0.123 Angle : 0.525 10.519 35267 Z= 0.261 Chirality : 0.043 0.264 4147 Planarity : 0.004 0.046 4459 Dihedral : 5.881 59.916 4588 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.95 % Allowed : 8.70 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.15), residues: 3060 helix: 2.05 (0.20), residues: 685 sheet: 0.67 (0.20), residues: 636 loop : -0.45 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 104 HIS 0.002 0.001 HIS C1088 PHE 0.026 0.001 PHE B 392 TYR 0.027 0.001 TYR C 453 ARG 0.007 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00552 ( 42) link_NAG-ASN : angle 2.55965 ( 126) link_BETA1-4 : bond 0.00349 ( 18) link_BETA1-4 : angle 1.05237 ( 54) hydrogen bonds : bond 0.03991 ( 924) hydrogen bonds : angle 5.45112 ( 2571) SS BOND : bond 0.00145 ( 42) SS BOND : angle 0.55523 ( 84) covalent geometry : bond 0.00267 (25717) covalent geometry : angle 0.50134 (35003) *********************** 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 136 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 2.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.7277 (p0) cc_final: 0.6973 (p0) REVERT: B 81 ASN cc_start: 0.8289 (OUTLIER) cc_final: 0.7940 (t0) REVERT: B 201 PHE cc_start: 0.8786 (t80) cc_final: 0.8329 (t80) REVERT: B 239 GLN cc_start: 0.7959 (tt0) cc_final: 0.7510 (tp40) REVERT: B 387 LEU cc_start: 0.7928 (mt) cc_final: 0.7365 (mp) REVERT: B 950 ASP cc_start: 0.9004 (m-30) cc_final: 0.8704 (m-30) REVERT: B 1029 MET cc_start: 0.9632 (tpp) cc_final: 0.9290 (tpp) REVERT: C 133 PHE cc_start: 0.7547 (m-80) cc_final: 0.7126 (m-80) REVERT: C 229 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7908 (tm) outliers start: 26 outliers final: 6 residues processed: 131 average time/residue: 1.1306 time to fit residues: 179.7233 Evaluate side-chains 102 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET 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 1141 LEU Chi-restraints excluded: chain C residue 229 LEU 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 138 optimal weight: 6.9990 chunk 34 optimal weight: 30.0000 chunk 139 optimal weight: 0.0570 chunk 213 optimal weight: 8.9990 chunk 279 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 chunk 261 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 253 optimal weight: 8.9990 overall best weight: 1.3700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 487 ASN A 755 GLN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 824 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN B 957 GLN B1002 GLN C 824 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.118317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 102)---------------| | r_work = 0.3489 r_free = 0.3489 target = 0.072621 restraints weight = 70287.442| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 4.13 r_work: 0.3125 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 25819 Z= 0.156 Angle : 0.533 10.441 35267 Z= 0.265 Chirality : 0.044 0.262 4147 Planarity : 0.004 0.047 4459 Dihedral : 5.335 57.780 4588 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.25 % Allowed : 9.07 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.15), residues: 3060 helix: 2.02 (0.20), residues: 692 sheet: 0.53 (0.20), residues: 623 loop : -0.39 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 104 HIS 0.003 0.001 HIS C1088 PHE 0.020 0.001 PHE C 392 TYR 0.020 0.001 TYR C 265 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00556 ( 42) link_NAG-ASN : angle 2.51497 ( 126) link_BETA1-4 : bond 0.00311 ( 18) link_BETA1-4 : angle 1.10166 ( 54) hydrogen bonds : bond 0.04037 ( 924) hydrogen bonds : angle 5.32665 ( 2571) SS BOND : bond 0.00157 ( 42) SS BOND : angle 0.50211 ( 84) covalent geometry : bond 0.00348 (25717) covalent geometry : angle 0.51046 (35003) *********************** 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 144 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 110 time to evaluate : 2.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 985 ASP cc_start: 0.7331 (p0) cc_final: 0.7011 (p0) REVERT: B 81 ASN cc_start: 0.8459 (OUTLIER) cc_final: 0.8184 (t0) REVERT: B 108 THR cc_start: 0.4494 (OUTLIER) cc_final: 0.3589 (m) REVERT: B 201 PHE cc_start: 0.8855 (t80) cc_final: 0.8406 (t80) REVERT: B 237 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.6923 (mtm-85) REVERT: B 239 GLN cc_start: 0.7977 (tt0) cc_final: 0.7663 (tt0) REVERT: B 314 GLN cc_start: 0.9199 (tt0) cc_final: 0.8658 (tm-30) REVERT: B 950 ASP cc_start: 0.9031 (m-30) cc_final: 0.8729 (m-30) REVERT: C 133 PHE cc_start: 0.7651 (m-80) cc_final: 0.7231 (m-80) REVERT: C 229 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8015 (tm) outliers start: 34 outliers final: 12 residues processed: 137 average time/residue: 1.1012 time to fit residues: 184.4337 Evaluate side-chains 110 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 2.669 ------------------------------------------------------------------------------- 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 1145 LEU Chi-restraints excluded: chain B residue 81 ASN 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 237 ARG Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 979 ASP Chi-restraints excluded: chain B residue 1145 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU 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 39 optimal weight: 20.0000 chunk 294 optimal weight: 2.9990 chunk 269 optimal weight: 0.6980 chunk 305 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 177 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 190 optimal weight: 2.9990 chunk 103 optimal weight: 20.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.117080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.071459 restraints weight = 69959.363| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.97 r_work: 0.3104 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25819 Z= 0.219 Angle : 0.570 10.381 35267 Z= 0.283 Chirality : 0.045 0.259 4147 Planarity : 0.004 0.046 4459 Dihedral : 5.257 55.876 4588 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.03 % Allowed : 10.25 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.15), residues: 3060 helix: 1.94 (0.20), residues: 705 sheet: 0.31 (0.21), residues: 596 loop : -0.44 (0.14), residues: 1759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 353 HIS 0.003 0.001 HIS C1088 PHE 0.022 0.001 PHE C 392 TYR 0.025 0.001 TYR C 453 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00601 ( 42) link_NAG-ASN : angle 2.56378 ( 126) link_BETA1-4 : bond 0.00296 ( 18) link_BETA1-4 : angle 1.12972 ( 54) hydrogen bonds : bond 0.04301 ( 924) hydrogen bonds : angle 5.37715 ( 2571) SS BOND : bond 0.00204 ( 42) SS BOND : angle 0.52333 ( 84) covalent geometry : bond 0.00493 (25717) covalent geometry : angle 0.54822 (35003) *********************** 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 125 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 2.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 THR cc_start: 0.4485 (OUTLIER) cc_final: 0.3678 (m) REVERT: B 189 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8149 (tm) REVERT: B 201 PHE cc_start: 0.8885 (t80) cc_final: 0.8444 (t80) REVERT: B 237 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6814 (mtm-85) REVERT: B 239 GLN cc_start: 0.7918 (tt0) cc_final: 0.7692 (tp40) REVERT: B 314 GLN cc_start: 0.9179 (tt0) cc_final: 0.8596 (tm-30) REVERT: B 342 PHE cc_start: 0.7037 (m-80) cc_final: 0.6827 (t80) REVERT: B 950 ASP cc_start: 0.9049 (m-30) cc_final: 0.8759 (m-30) REVERT: C 133 PHE cc_start: 0.7654 (m-80) cc_final: 0.7214 (m-80) REVERT: C 229 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8134 (tm) outliers start: 28 outliers final: 11 residues processed: 119 average time/residue: 1.1113 time to fit residues: 160.6035 Evaluate side-chains 104 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET 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 237 ARG Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 277 LEU 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 147 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 205 optimal weight: 0.9990 chunk 188 optimal weight: 3.9990 chunk 240 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 138 optimal weight: 20.0000 chunk 233 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 282 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN ** A 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 901 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 = 0.4190 r_free = 0.4190 target = 0.117334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.072286 restraints weight = 69692.181| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.81 r_work: 0.3100 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25819 Z= 0.167 Angle : 0.537 10.238 35267 Z= 0.267 Chirality : 0.044 0.257 4147 Planarity : 0.003 0.045 4459 Dihedral : 5.044 54.067 4588 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.07 % Allowed : 10.47 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.15), residues: 3060 helix: 2.11 (0.20), residues: 691 sheet: 0.23 (0.21), residues: 601 loop : -0.38 (0.14), residues: 1768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 353 HIS 0.003 0.001 HIS C1088 PHE 0.018 0.001 PHE A 898 TYR 0.020 0.001 TYR C 265 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00555 ( 42) link_NAG-ASN : angle 2.47714 ( 126) link_BETA1-4 : bond 0.00317 ( 18) link_BETA1-4 : angle 1.03441 ( 54) hydrogen bonds : bond 0.04022 ( 924) hydrogen bonds : angle 5.28848 ( 2571) SS BOND : bond 0.00179 ( 42) SS BOND : angle 0.49048 ( 84) covalent geometry : bond 0.00373 (25717) covalent geometry : angle 0.51588 (35003) *********************** 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 126 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 97 time to evaluate : 2.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8218 (tp) cc_final: 0.7942 (tt) REVERT: B 108 THR cc_start: 0.4711 (OUTLIER) cc_final: 0.4194 (m) REVERT: B 189 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8211 (tm) REVERT: B 201 PHE cc_start: 0.8862 (t80) cc_final: 0.8449 (t80) REVERT: B 238 PHE cc_start: 0.6375 (p90) cc_final: 0.6172 (p90) REVERT: B 239 GLN cc_start: 0.8029 (tt0) cc_final: 0.7818 (tp40) REVERT: B 314 GLN cc_start: 0.9136 (tt0) cc_final: 0.8561 (tm-30) REVERT: B 950 ASP cc_start: 0.9054 (m-30) cc_final: 0.8754 (m-30) REVERT: C 133 PHE cc_start: 0.7656 (m-80) cc_final: 0.7256 (m-80) REVERT: C 229 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8155 (tm) outliers start: 29 outliers final: 12 residues processed: 119 average time/residue: 1.0651 time to fit residues: 153.4613 Evaluate side-chains 107 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET 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 120 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 565 PHE Chi-restraints excluded: chain B residue 697 MET Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 382 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 309 random chunks: chunk 247 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 177 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 175 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 92 optimal weight: 0.9980 chunk 221 optimal weight: 8.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN B 762 GLN B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.116827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.072222 restraints weight = 69670.851| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 3.61 r_work: 0.3087 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25819 Z= 0.187 Angle : 0.555 10.871 35267 Z= 0.275 Chirality : 0.044 0.260 4147 Planarity : 0.004 0.048 4459 Dihedral : 5.031 53.364 4588 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.14 % Allowed : 11.05 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.15), residues: 3060 helix: 2.09 (0.20), residues: 691 sheet: 0.27 (0.21), residues: 630 loop : -0.38 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 104 HIS 0.004 0.001 HIS C1088 PHE 0.020 0.001 PHE B 374 TYR 0.026 0.001 TYR C 453 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00586 ( 42) link_NAG-ASN : angle 2.50517 ( 126) link_BETA1-4 : bond 0.00283 ( 18) link_BETA1-4 : angle 1.08483 ( 54) hydrogen bonds : bond 0.04129 ( 924) hydrogen bonds : angle 5.29252 ( 2571) SS BOND : bond 0.00192 ( 42) SS BOND : angle 0.57631 ( 84) covalent geometry : bond 0.00421 (25717) covalent geometry : angle 0.53376 (35003) *********************** 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 126 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 95 time to evaluate : 2.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8276 (tp) cc_final: 0.7973 (tt) REVERT: B 108 THR cc_start: 0.4792 (OUTLIER) cc_final: 0.4048 (m) REVERT: B 189 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8188 (tm) REVERT: B 201 PHE cc_start: 0.8900 (t80) cc_final: 0.8459 (t80) REVERT: B 237 ARG cc_start: 0.7403 (OUTLIER) cc_final: 0.6958 (mtm-85) REVERT: B 239 GLN cc_start: 0.8055 (tt0) cc_final: 0.7805 (tp40) REVERT: B 240 THR cc_start: 0.7502 (OUTLIER) cc_final: 0.6862 (t) REVERT: B 245 HIS cc_start: 0.2270 (OUTLIER) cc_final: 0.1704 (m90) REVERT: B 314 GLN cc_start: 0.9119 (tt0) cc_final: 0.8558 (tm-30) REVERT: B 950 ASP cc_start: 0.9053 (m-30) cc_final: 0.8758 (m-30) REVERT: C 133 PHE cc_start: 0.7642 (m-80) cc_final: 0.7170 (m-80) REVERT: C 229 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8206 (tm) outliers start: 31 outliers final: 12 residues processed: 119 average time/residue: 1.0504 time to fit residues: 152.8737 Evaluate side-chains 112 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 2.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 MET Chi-restraints excluded: chain A residue 197 ILE 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 120 VAL 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 565 PHE Chi-restraints excluded: chain B residue 900 MET Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 229 LEU 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 234 optimal weight: 0.7980 chunk 245 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 294 optimal weight: 1.9990 chunk 121 optimal weight: 0.0050 chunk 115 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 224 optimal weight: 0.9990 chunk 32 optimal weight: 30.0000 chunk 205 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 955 ASN A1011 GLN B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.120741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.077056 restraints weight = 68276.331| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.59 r_work: 0.3143 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25819 Z= 0.111 Angle : 0.515 10.147 35267 Z= 0.256 Chirality : 0.043 0.264 4147 Planarity : 0.003 0.051 4459 Dihedral : 4.796 53.826 4588 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.81 % Allowed : 11.60 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.15), residues: 3060 helix: 2.25 (0.20), residues: 691 sheet: 0.30 (0.21), residues: 636 loop : -0.30 (0.14), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 353 HIS 0.002 0.000 HIS C1088 PHE 0.020 0.001 PHE C 192 TYR 0.018 0.001 TYR C 265 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 42) link_NAG-ASN : angle 2.35799 ( 126) link_BETA1-4 : bond 0.00334 ( 18) link_BETA1-4 : angle 0.94477 ( 54) hydrogen bonds : bond 0.03718 ( 924) hydrogen bonds : angle 5.12840 ( 2571) SS BOND : bond 0.00131 ( 42) SS BOND : angle 0.51646 ( 84) covalent geometry : bond 0.00243 (25717) covalent geometry : angle 0.49512 (35003) *********************** 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 123 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8323 (tp) cc_final: 0.8078 (pp) REVERT: B 108 THR cc_start: 0.4819 (OUTLIER) cc_final: 0.4321 (m) REVERT: B 189 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8273 (tm) REVERT: B 201 PHE cc_start: 0.8923 (t80) cc_final: 0.8436 (t80) REVERT: B 245 HIS cc_start: 0.2320 (OUTLIER) cc_final: 0.1777 (m90) REVERT: B 314 GLN cc_start: 0.9082 (tt0) cc_final: 0.8499 (tm-30) REVERT: B 950 ASP cc_start: 0.9040 (m-30) cc_final: 0.8746 (m-30) REVERT: C 133 PHE cc_start: 0.7560 (m-80) cc_final: 0.7077 (m-80) REVERT: C 229 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.8174 (tm) REVERT: C 304 LYS cc_start: 0.9450 (mmmm) cc_final: 0.9086 (mmmm) outliers start: 22 outliers final: 9 residues processed: 118 average time/residue: 1.1350 time to fit residues: 162.8426 Evaluate side-chains 110 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 2.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU 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 934 ILE Chi-restraints excluded: chain C residue 229 LEU 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 12 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 305 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 292 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 179 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1002 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.124319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.078433 restraints weight = 64813.341| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 4.15 r_work: 0.3138 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 25819 Z= 0.117 Angle : 0.518 10.316 35267 Z= 0.257 Chirality : 0.043 0.262 4147 Planarity : 0.004 0.055 4459 Dihedral : 4.702 53.500 4588 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.66 % Allowed : 11.94 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.15), residues: 3060 helix: 2.26 (0.20), residues: 691 sheet: 0.37 (0.20), residues: 669 loop : -0.30 (0.14), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 353 HIS 0.002 0.000 HIS C1088 PHE 0.022 0.001 PHE B 338 TYR 0.027 0.001 TYR C 453 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00519 ( 42) link_NAG-ASN : angle 2.34366 ( 126) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 0.98046 ( 54) hydrogen bonds : bond 0.03724 ( 924) hydrogen bonds : angle 5.10454 ( 2571) SS BOND : bond 0.00127 ( 42) SS BOND : angle 0.51359 ( 84) covalent geometry : bond 0.00257 (25717) covalent geometry : angle 0.49801 (35003) *********************** 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 115 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 226 LEU cc_start: 0.8289 (tp) cc_final: 0.8072 (pp) REVERT: B 108 THR cc_start: 0.4646 (OUTLIER) cc_final: 0.3915 (m) REVERT: B 189 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8295 (tm) REVERT: B 201 PHE cc_start: 0.8931 (t80) cc_final: 0.8471 (t80) REVERT: B 237 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6870 (mtm-85) REVERT: B 245 HIS cc_start: 0.2347 (OUTLIER) cc_final: 0.1810 (m90) REVERT: B 314 GLN cc_start: 0.9080 (tt0) cc_final: 0.8446 (tm-30) REVERT: B 731 MET cc_start: 0.9497 (ptm) cc_final: 0.9281 (ptm) REVERT: B 950 ASP cc_start: 0.9053 (m-30) cc_final: 0.8745 (m-30) REVERT: C 133 PHE cc_start: 0.7569 (m-80) cc_final: 0.7082 (m-80) REVERT: C 229 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8155 (tm) REVERT: C 304 LYS cc_start: 0.9453 (mmmm) cc_final: 0.9081 (mmmm) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 1.0976 time to fit residues: 148.1580 Evaluate side-chains 111 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 2.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU 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 237 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain C residue 229 LEU 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 175 optimal weight: 0.8980 chunk 87 optimal weight: 1.9990 chunk 6 optimal weight: 0.0000 chunk 70 optimal weight: 0.8980 chunk 255 optimal weight: 0.0870 chunk 293 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1002 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.128968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.083732 restraints weight = 69097.551| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.98 r_work: 0.3132 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 25819 Z= 0.102 Angle : 0.511 10.256 35267 Z= 0.254 Chirality : 0.043 0.263 4147 Planarity : 0.004 0.054 4459 Dihedral : 4.575 53.480 4588 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.62 % Allowed : 12.08 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 3060 helix: 2.36 (0.20), residues: 686 sheet: 0.39 (0.20), residues: 679 loop : -0.28 (0.14), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A 104 HIS 0.005 0.000 HIS A 245 PHE 0.025 0.001 PHE C 392 TYR 0.017 0.001 TYR C 265 ARG 0.004 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00507 ( 42) link_NAG-ASN : angle 2.30085 ( 126) link_BETA1-4 : bond 0.00316 ( 18) link_BETA1-4 : angle 0.94854 ( 54) hydrogen bonds : bond 0.03606 ( 924) hydrogen bonds : angle 5.04066 ( 2571) SS BOND : bond 0.00110 ( 42) SS BOND : angle 0.47549 ( 84) covalent geometry : bond 0.00223 (25717) covalent geometry : angle 0.49212 (35003) ********************** 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 115 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 98 time to evaluate : 2.621 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 108 THR cc_start: 0.4675 (OUTLIER) cc_final: 0.3862 (m) REVERT: B 189 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8292 (tm) REVERT: B 201 PHE cc_start: 0.8912 (t80) cc_final: 0.8476 (t80) REVERT: B 237 ARG cc_start: 0.7400 (OUTLIER) cc_final: 0.6879 (mtm-85) REVERT: B 245 HIS cc_start: 0.2326 (OUTLIER) cc_final: 0.1780 (m90) REVERT: B 314 GLN cc_start: 0.9057 (tt0) cc_final: 0.8437 (tm-30) REVERT: B 731 MET cc_start: 0.9469 (ptm) cc_final: 0.9263 (ptm) REVERT: B 950 ASP cc_start: 0.9019 (m-30) cc_final: 0.8763 (m-30) REVERT: C 133 PHE cc_start: 0.7558 (m-80) cc_final: 0.7042 (m-80) REVERT: C 304 LYS cc_start: 0.9451 (mmmm) cc_final: 0.9159 (mmmm) outliers start: 17 outliers final: 9 residues processed: 112 average time/residue: 1.1392 time to fit residues: 154.5084 Evaluate side-chains 107 residues out of total 2723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 94 time to evaluate : 2.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1145 LEU 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 237 ARG Chi-restraints excluded: chain B residue 245 HIS Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 934 ILE 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 271 optimal weight: 2.9990 chunk 255 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 202 optimal weight: 0.7980 chunk 149 optimal weight: 7.9990 chunk 157 optimal weight: 9.9990 chunk 26 optimal weight: 0.0010 chunk 264 optimal weight: 4.9990 overall best weight: 2.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 580 GLN C1002 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.119247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.075188 restraints weight = 68696.405| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 3.59 r_work: 0.3088 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 25819 Z= 0.231 Angle : 0.582 10.132 35267 Z= 0.289 Chirality : 0.045 0.267 4147 Planarity : 0.004 0.055 4459 Dihedral : 4.882 53.487 4588 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.66 % Allowed : 12.16 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.15), residues: 3060 helix: 2.20 (0.20), residues: 679 sheet: 0.24 (0.20), residues: 645 loop : -0.36 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP C 353 HIS 0.004 0.001 HIS C1088 PHE 0.036 0.001 PHE C 392 TYR 0.028 0.001 TYR C 453 ARG 0.006 0.000 ARG C 357 Details of bonding type rmsd link_NAG-ASN : bond 0.00597 ( 42) link_NAG-ASN : angle 2.46535 ( 126) link_BETA1-4 : bond 0.00234 ( 18) link_BETA1-4 : angle 1.14508 ( 54) hydrogen bonds : bond 0.04265 ( 924) hydrogen bonds : angle 5.28369 ( 2571) SS BOND : bond 0.00231 ( 42) SS BOND : angle 0.59004 ( 84) covalent geometry : bond 0.00520 (25717) covalent geometry : angle 0.56273 (35003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23738.93 seconds wall clock time: 410 minutes 11.16 seconds (24611.16 seconds total)