Starting phenix.real_space_refine on Sun Jul 5 07:55:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xnr_33324/07_2026/7xnr_33324.map" } resolution = 3.49 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.071 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16860 2.51 5 N 4329 2.21 5 O 5154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26460 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "B" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1095, 8554 Classifications: {'peptide': 1095} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 58, 'TRANS': 1036} Chain breaks: 2 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 5.79, per 1000 atoms: 0.22 Number of scatterers: 26460 At special positions: 0 Unit cell: (156.22, 149.8, 184.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5154 8.00 N 4329 7.00 C 16860 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.02 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " 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-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 603 " " NAG A1303 " - " ASN A 616 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A1074 " " NAG A1306 " - " ASN A 122 " " NAG A1307 " - " ASN A 234 " " NAG A1308 " - " ASN A 282 " " NAG A1309 " - " ASN A 331 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 603 " " NAG B1303 " - " ASN B 616 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B1074 " " NAG B1306 " - " ASN B 122 " " NAG B1307 " - " ASN B 234 " " NAG B1308 " - " ASN B 282 " " NAG B1309 " - " ASN B 331 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 603 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C1074 " " NAG C1306 " - " ASN C 122 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 282 " " NAG C1309 " - " ASN C 331 " " NAG D 1 " - " ASN A 709 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 709 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B1098 " " NAG M 1 " - " ASN B1134 " " NAG N 1 " - " ASN C 709 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG Q 1 " - " ASN C1098 " " NAG R 1 " - " ASN C1134 " Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6144 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 51 sheets defined 24.5% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.998A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.567A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.186A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 5.405A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 421 removed outlier: 4.058A pdb=" N ALA A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 618 through 624 removed outlier: 4.376A pdb=" N VAL A 622 " --> pdb=" O THR A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.737A pdb=" N GLY A 757 " --> pdb=" O LEU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.697A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR A 768 " --> pdb=" O LYS A 764 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ILE A 770 " --> pdb=" O ALA A 766 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 771 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL A 772 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.581A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 854 removed outlier: 3.987A pdb=" N LYS A 854 " --> pdb=" O ILE A 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 850 through 854' Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.532A pdb=" N GLY A 885 " --> pdb=" O THR A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.363A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY A 891 " --> pdb=" O THR A 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 886 through 891' Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.769A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 941 removed outlier: 6.692A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 949 through 965 Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.931A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N THR A 998 " --> pdb=" O ASP A 994 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N GLY A 999 " --> pdb=" O ARG A 995 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG A1000 " --> pdb=" O LEU A 996 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1150 removed outlier: 3.827A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.868A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.829A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 removed outlier: 3.549A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.313A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP B 389 " --> pdb=" O LYS B 386 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 5.276A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 618 through 624 removed outlier: 4.134A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.858A pdb=" N GLY B 757 " --> pdb=" O LEU B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.531A pdb=" N THR B 768 " --> pdb=" O LYS B 764 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 769 " --> pdb=" O ARG B 765 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE B 770 " --> pdb=" O ALA B 766 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ALA B 771 " --> pdb=" O LEU B 767 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.554A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 850 through 854 removed outlier: 3.769A pdb=" N LYS B 854 " --> pdb=" O ILE B 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 850 through 854' Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.605A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 914 No H-bonds generated for 'chain 'B' and resid 912 through 914' Processing helix chain 'B' and resid 915 through 941 removed outlier: 5.902A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR B 941 " --> pdb=" O SER B 937 " (cutoff:3.500A) Processing helix chain 'B' and resid 949 through 965 Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.996A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR B 998 " --> pdb=" O ASP B 994 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY B 999 " --> pdb=" O ARG B 995 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B1021 " --> pdb=" O GLU B1017 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1150 removed outlier: 3.936A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU B1150 " --> pdb=" O ASP B1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 removed outlier: 3.991A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.706A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 371 Processing helix chain 'C' and resid 383 through 387 removed outlier: 3.527A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.445A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 502 through 505 removed outlier: 3.613A pdb=" N HIS C 505 " --> pdb=" O GLY C 502 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 502 through 505' Processing helix chain 'C' and resid 618 through 624 removed outlier: 4.492A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 757 removed outlier: 3.803A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.703A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N THR C 768 " --> pdb=" O LYS C 764 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY C 769 " --> pdb=" O ARG C 765 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA C 771 " --> pdb=" O LEU C 767 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 772 " --> pdb=" O THR C 768 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.516A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 850 through 854 removed outlier: 3.527A pdb=" N LYS C 854 " --> pdb=" O ILE C 850 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 850 through 854' Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.787A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 941 removed outlier: 6.786A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 949 through 965 Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.900A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 998 " --> pdb=" O ASP C 994 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N GLY C 999 " --> pdb=" O ARG C 995 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ARG C1000 " --> pdb=" O LEU C 996 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER C1021 " --> pdb=" O GLU C1017 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 4.027A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.541A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.788A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 63 through 64 removed outlier: 3.721A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 126 through 131 removed outlier: 3.606A pdb=" N LEU A 118 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.131A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.888A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 378 through 379 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 453 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 542 through 543 removed outlier: 3.809A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.789A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N THR A 573 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ASP A 568 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.519A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 702 removed outlier: 7.588A pdb=" N ALA A 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 712 through 714 Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 719 Processing sheet with id=AB8, first strand: chain 'A' and resid 718 through 719 removed outlier: 3.666A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 733 through 735 removed outlier: 4.671A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 787 through 788 removed outlier: 3.546A pdb=" N ILE A 788 " --> pdb=" O ALA B 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC3, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AC4, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.751A pdb=" N THR B 29 " --> pdb=" O VAL B 62 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.844A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.972A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 126 through 131 removed outlier: 3.789A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.234A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 324 through 326 removed outlier: 7.769A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE B 543 " --> pdb=" O LEU B 546 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.583A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 551 through 554 removed outlier: 5.628A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.634A pdb=" N GLU B 654 " --> pdb=" O ILE B 692 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 694 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.402A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 712 through 719 removed outlier: 6.402A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD7, first strand: chain 'B' and resid 787 through 788 removed outlier: 3.616A pdb=" N ILE B 788 " --> pdb=" O ALA C 701 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD9, first strand: chain 'B' and resid 1094 through 1096 Processing sheet with id=AE1, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.950A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 63 through 64 removed outlier: 3.612A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 126 through 131 removed outlier: 6.127A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.286A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.555A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.550A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE9, first strand: chain 'C' and resid 542 through 543 removed outlier: 3.871A pdb=" N PHE C 543 " --> pdb=" O LEU C 546 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 551 through 554 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 660 removed outlier: 5.294A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 712 through 728 removed outlier: 5.956A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA C1056 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.601A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AF6, first strand: chain 'C' and resid 1094 through 1096 874 hydrogen bonds defined for protein. 2319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.65 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 6717 1.33 - 1.45: 5919 1.45 - 1.58: 14303 1.58 - 1.70: 1 1.70 - 1.82: 150 Bond restraints: 27090 Sorted by residual: bond pdb=" CB PRO B 491 " pdb=" CG PRO B 491 " ideal model delta sigma weight residual 1.492 1.626 -0.134 5.00e-02 4.00e+02 7.19e+00 bond pdb=" C1 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.89e+00 bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.443 -0.037 2.00e-02 2.50e+03 3.38e+00 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.441 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" CG PRO B 491 " pdb=" CD PRO B 491 " ideal model delta sigma weight residual 1.503 1.445 0.058 3.40e-02 8.65e+02 2.88e+00 ... (remaining 27085 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 36024 1.85 - 3.71: 774 3.71 - 5.56: 73 5.56 - 7.42: 18 7.42 - 9.27: 2 Bond angle restraints: 36891 Sorted by residual: angle pdb=" CA PRO B 491 " pdb=" N PRO B 491 " pdb=" CD PRO B 491 " ideal model delta sigma weight residual 112.00 102.73 9.27 1.40e+00 5.10e-01 4.39e+01 angle pdb=" N PRO B 491 " pdb=" CD PRO B 491 " pdb=" CG PRO B 491 " ideal model delta sigma weight residual 103.20 96.71 6.49 1.50e+00 4.44e-01 1.87e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 110.29 115.02 -4.73 1.28e+00 6.10e-01 1.36e+01 angle pdb=" C ILE C 197 " pdb=" N ASP C 198 " pdb=" CA ASP C 198 " ideal model delta sigma weight residual 121.54 128.12 -6.58 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ALA B 570 " pdb=" N ASP B 571 " pdb=" CA ASP B 571 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 ... (remaining 36886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 14240 17.88 - 35.75: 1162 35.75 - 53.63: 184 53.63 - 71.51: 27 71.51 - 89.39: 29 Dihedral angle restraints: 15642 sinusoidal: 6075 harmonic: 9567 Sorted by residual: dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual -86.00 2.92 -88.92 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 6.74 86.26 1 1.00e+01 1.00e-02 8.97e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 10.92 82.08 1 1.00e+01 1.00e-02 8.28e+01 ... (remaining 15639 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 3561 0.060 - 0.119: 675 0.119 - 0.179: 74 0.179 - 0.239: 4 0.239 - 0.299: 3 Chirality restraints: 4317 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C1 NAG C1301 " pdb=" ND2 ASN C 61 " pdb=" C2 NAG C1301 " pdb=" O5 NAG C1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C1 NAG A1301 " pdb=" ND2 ASN A 61 " pdb=" C2 NAG A1301 " pdb=" O5 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.57e+00 ... (remaining 4314 not shown) Planarity restraints: 4752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE B 490 " 0.088 5.00e-02 4.00e+02 1.27e-01 2.59e+01 pdb=" N PRO B 491 " -0.220 5.00e-02 4.00e+02 pdb=" CA PRO B 491 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO B 491 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 294 " -0.037 5.00e-02 4.00e+02 5.53e-02 4.90e+00 pdb=" N PRO C 295 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 295 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 295 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 906 " -0.015 2.00e-02 2.50e+03 1.40e-02 3.41e+00 pdb=" CG PHE B 906 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 PHE B 906 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE B 906 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE B 906 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 906 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE B 906 " -0.001 2.00e-02 2.50e+03 ... (remaining 4749 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 363 2.65 - 3.21: 24370 3.21 - 3.77: 37328 3.77 - 4.34: 50951 4.34 - 4.90: 84413 Nonbonded interactions: 197425 Sorted by model distance: nonbonded pdb=" OD1 ASP A 568 " pdb=" OG1 THR A 572 " model vdw 2.085 3.040 nonbonded pdb=" OD1 ASP B 568 " pdb=" OG1 THR B 572 " model vdw 2.105 3.040 nonbonded pdb=" OG1 THR C1116 " pdb=" OD1 ASP C1118 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP C 568 " pdb=" OG1 THR C 572 " model vdw 2.165 3.040 nonbonded pdb=" OE2 GLU A 725 " pdb=" NE2 HIS A1064 " model vdw 2.166 3.120 ... (remaining 197420 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' 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' } 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: 2.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 23.740 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 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 : 0.004 0.134 27183 Z= 0.201 Angle : 0.655 12.971 37134 Z= 0.333 Chirality : 0.047 0.299 4317 Planarity : 0.004 0.127 4710 Dihedral : 13.400 89.386 9390 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.28 (0.15), residues: 3267 helix: 1.60 (0.22), residues: 612 sheet: -0.62 (0.20), residues: 672 loop : -1.83 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 403 TYR 0.017 0.001 TYR A 756 PHE 0.033 0.001 PHE B 906 TRP 0.011 0.001 TRP B 886 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (27090) covalent geometry : angle 0.63499 / 0.33 (36891) SS BOND : bond 0.00236 / 0.16 ( 36) SS BOND : angle 1.06498 / 0.68 ( 72) hydrogen bonds : bond 0.16228 / 10.19 ( 867) hydrogen bonds : angle 6.53129 / 4.71 ( 2319) link_BETA1-4 : bond 0.00426 / 0.25 ( 15) link_BETA1-4 : angle 0.99327 / 0.62 ( 45) link_NAG-ASN : bond 0.00492 / 0.27 ( 42) link_NAG-ASN : angle 2.70673 / 1.63 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 418 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.3059 (mmp) cc_final: 0.2573 (mmp) REVERT: A 341 VAL cc_start: 0.8466 (t) cc_final: 0.8068 (p) REVERT: A 578 ASP cc_start: 0.6394 (t70) cc_final: 0.5081 (t70) REVERT: A 731 MET cc_start: 0.8960 (ptm) cc_final: 0.8688 (ptt) REVERT: B 353 TRP cc_start: 0.5672 (p-90) cc_final: 0.5163 (p-90) REVERT: C 78 ARG cc_start: 0.2455 (mtt180) cc_final: 0.2001 (mpt180) REVERT: C 585 LEU cc_start: 0.6251 (mt) cc_final: 0.5953 (mp) REVERT: C 780 GLU cc_start: 0.7435 (tt0) cc_final: 0.7221 (mt-10) REVERT: C 976 VAL cc_start: 0.9146 (t) cc_final: 0.8898 (m) outliers start: 0 outliers final: 0 residues processed: 418 average time/residue: 0.1783 time to fit residues: 116.8968 Evaluate side-chains 219 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 219 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 360 ASN A 394 ASN A 417 ASN A 437 ASN A 856 ASN B 173 GLN B 544 ASN B 613 GLN B 955 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 613 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1071 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.185383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.133862 restraints weight = 43469.247| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.83 r_work: 0.3389 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.090 27183 Z= 0.241 Angle : 0.742 12.580 37134 Z= 0.376 Chirality : 0.053 0.538 4317 Planarity : 0.005 0.065 4710 Dihedral : 4.688 26.912 3528 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 1.51 % Allowed : 8.33 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.14), residues: 3267 helix: 1.18 (0.21), residues: 597 sheet: -0.67 (0.19), residues: 723 loop : -2.05 (0.13), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 237 TYR 0.033 0.002 TYR C 265 PHE 0.034 0.002 PHE A 906 TRP 0.021 0.002 TRP A 64 HIS 0.007 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00572 / 0.24 (27090) covalent geometry : angle 0.72308 / 0.37 (36891) SS BOND : bond 0.00481 / 0.32 ( 36) SS BOND : angle 1.27905 / 0.79 ( 72) hydrogen bonds : bond 0.06510 / 4.31 ( 867) hydrogen bonds : angle 5.76476 / 4.03 ( 2319) link_BETA1-4 : bond 0.00260 / 0.16 ( 15) link_BETA1-4 : angle 1.74296 / 1.23 ( 45) link_NAG-ASN : bond 0.00751 / 0.53 ( 42) link_NAG-ASN : angle 2.70851 / 1.67 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 225 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4559 (mmp) cc_final: 0.4186 (mmp) REVERT: A 394 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.6952 (p0) REVERT: A 731 MET cc_start: 0.9050 (ptm) cc_final: 0.8824 (ptt) REVERT: A 980 ILE cc_start: 0.8565 (mm) cc_final: 0.8352 (mt) REVERT: B 104 TRP cc_start: 0.5922 (m-90) cc_final: 0.5488 (m-90) REVERT: B 153 MET cc_start: 0.3074 (tpp) cc_final: 0.2789 (tpt) REVERT: B 394 ASN cc_start: 0.8191 (p0) cc_final: 0.7807 (p0) REVERT: B 565 PHE cc_start: 0.7858 (m-10) cc_final: 0.7630 (m-10) REVERT: C 191 GLU cc_start: 0.7994 (mp0) cc_final: 0.7718 (mp0) outliers start: 43 outliers final: 30 residues processed: 258 average time/residue: 0.1595 time to fit residues: 68.0950 Evaluate side-chains 221 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 422 ASN Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 217 optimal weight: 2.9990 chunk 124 optimal weight: 0.7980 chunk 159 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN B 188 ASN B 544 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN C1106 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.182873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.131402 restraints weight = 43401.150| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.85 r_work: 0.3338 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 27183 Z= 0.242 Angle : 0.682 12.216 37134 Z= 0.350 Chirality : 0.049 0.370 4317 Planarity : 0.005 0.055 4710 Dihedral : 4.594 22.053 3528 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.28 % Allowed : 11.41 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.14), residues: 3267 helix: 1.02 (0.21), residues: 615 sheet: -0.60 (0.20), residues: 663 loop : -2.06 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 905 TYR 0.024 0.002 TYR C 265 PHE 0.030 0.002 PHE A 906 TRP 0.014 0.002 TRP B 436 HIS 0.005 0.001 HIS C1058 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.24 (27090) covalent geometry : angle 0.66215 / 0.35 (36891) SS BOND : bond 0.00720 / 0.37 ( 36) SS BOND : angle 1.68232 / 1.28 ( 72) hydrogen bonds : bond 0.06572 / 4.34 ( 867) hydrogen bonds : angle 5.58311 / 3.90 ( 2319) link_BETA1-4 : bond 0.00349 / 0.19 ( 15) link_BETA1-4 : angle 1.14236 / 0.75 ( 45) link_NAG-ASN : bond 0.00689 / 0.49 ( 42) link_NAG-ASN : angle 2.59502 / 1.59 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4433 (mmp) cc_final: 0.3961 (mmp) REVERT: A 421 TYR cc_start: 0.7864 (m-80) cc_final: 0.7405 (m-80) REVERT: A 878 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8678 (tt) REVERT: B 104 TRP cc_start: 0.5903 (m-90) cc_final: 0.5622 (m-90) REVERT: B 878 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8496 (tt) REVERT: C 191 GLU cc_start: 0.7977 (mp0) cc_final: 0.7720 (mp0) outliers start: 65 outliers final: 35 residues processed: 239 average time/residue: 0.1385 time to fit residues: 56.6248 Evaluate side-chains 205 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 394 ASN Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 902 MET Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 102 optimal weight: 0.0570 chunk 10 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 95 optimal weight: 0.5980 chunk 275 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 263 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 287 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 62 optimal weight: 0.5980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 66 HIS ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 901 GLN C 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.186097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134592 restraints weight = 43227.945| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.77 r_work: 0.3423 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3276 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 27183 Z= 0.111 Angle : 0.591 12.411 37134 Z= 0.296 Chirality : 0.046 0.350 4317 Planarity : 0.004 0.046 4710 Dihedral : 4.223 22.200 3528 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.14 % Allowed : 13.24 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.32 (0.14), residues: 3267 helix: 1.58 (0.22), residues: 612 sheet: -0.49 (0.19), residues: 699 loop : -1.94 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 493 TYR 0.022 0.001 TYR C 265 PHE 0.037 0.001 PHE A 342 TRP 0.008 0.001 TRP B 436 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (27090) covalent geometry : angle 0.57052 / 0.29 (36891) SS BOND : bond 0.00341 / 0.18 ( 36) SS BOND : angle 1.58104 / 0.93 ( 72) hydrogen bonds : bond 0.04738 / 3.14 ( 867) hydrogen bonds : angle 5.16700 / 3.61 ( 2319) link_BETA1-4 : bond 0.00378 / 0.22 ( 15) link_BETA1-4 : angle 0.83443 / 0.53 ( 45) link_NAG-ASN : bond 0.00624 / 0.43 ( 42) link_NAG-ASN : angle 2.44871 / 1.50 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 192 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 177 MET cc_start: 0.4453 (mmp) cc_final: 0.4031 (mmp) REVERT: A 239 GLN cc_start: 0.7684 (mt0) cc_final: 0.7097 (mm110) REVERT: A 265 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.6264 (t80) REVERT: A 421 TYR cc_start: 0.7948 (m-80) cc_final: 0.7559 (m-80) REVERT: A 424 LYS cc_start: 0.7712 (ttmt) cc_final: 0.7490 (mttm) REVERT: A 452 MET cc_start: 0.7069 (mpp) cc_final: 0.6695 (mmp) REVERT: A 878 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8694 (tt) REVERT: A 980 ILE cc_start: 0.8421 (mm) cc_final: 0.8193 (mt) REVERT: B 104 TRP cc_start: 0.5962 (m-90) cc_final: 0.5689 (m-90) REVERT: B 153 MET cc_start: 0.3211 (tpp) cc_final: 0.2876 (tpt) REVERT: B 177 MET cc_start: 0.2522 (mmp) cc_final: 0.2313 (mmp) REVERT: B 353 TRP cc_start: 0.6234 (p-90) cc_final: 0.5030 (p-90) REVERT: B 394 ASN cc_start: 0.8216 (p0) cc_final: 0.7909 (p0) REVERT: B 740 MET cc_start: 0.8719 (tpp) cc_final: 0.8480 (tpp) REVERT: B 878 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8470 (tt) REVERT: C 191 GLU cc_start: 0.8075 (mp0) cc_final: 0.7873 (mp0) REVERT: C 242 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.6923 (mp) outliers start: 61 outliers final: 27 residues processed: 241 average time/residue: 0.1406 time to fit residues: 58.4419 Evaluate side-chains 208 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 533 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain B residue 286 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 945 LEU Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 270 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 222 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 271 optimal weight: 0.4980 chunk 244 optimal weight: 5.9990 chunk 257 optimal weight: 40.0000 chunk 123 optimal weight: 7.9990 chunk 241 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 394 ASN A1048 HIS B 26 GLN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 787 GLN B1083 HIS C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.178368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.127118 restraints weight = 43226.167| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.88 r_work: 0.3256 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.099 27183 Z= 0.419 Angle : 0.853 12.002 37134 Z= 0.437 Chirality : 0.055 0.381 4317 Planarity : 0.006 0.055 4710 Dihedral : 5.054 23.067 3528 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.20 % Favored : 91.77 % Rotamer: Outliers : 3.01 % Allowed : 14.50 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.14), residues: 3267 helix: 0.31 (0.20), residues: 651 sheet: -0.72 (0.20), residues: 621 loop : -2.20 (0.12), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 905 TYR 0.027 0.002 TYR A 508 PHE 0.043 0.003 PHE B 927 TRP 0.010 0.002 TRP A 436 HIS 0.007 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.01042 / 0.42 (27090) covalent geometry : angle 0.83426 / 0.43 (36891) SS BOND : bond 0.00506 / 0.35 ( 36) SS BOND : angle 2.00872 / 1.22 ( 72) hydrogen bonds : bond 0.08415 / 5.56 ( 867) hydrogen bonds : angle 5.86601 / 4.09 ( 2319) link_BETA1-4 : bond 0.00300 / 0.20 ( 15) link_BETA1-4 : angle 1.47619 / 0.94 ( 45) link_NAG-ASN : bond 0.00747 / 0.52 ( 42) link_NAG-ASN : angle 2.77875 / 1.73 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 183 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4647 (mmp) cc_final: 0.4197 (mmp) REVERT: A 265 TYR cc_start: 0.7365 (OUTLIER) cc_final: 0.6580 (t80) REVERT: A 421 TYR cc_start: 0.8153 (m-80) cc_final: 0.7691 (m-80) REVERT: A 429 PHE cc_start: 0.8228 (t80) cc_final: 0.7946 (t80) REVERT: A 452 MET cc_start: 0.6938 (mpp) cc_final: 0.6579 (mmp) REVERT: A 878 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8679 (tt) REVERT: B 153 MET cc_start: 0.3111 (tpp) cc_final: 0.2723 (tpt) REVERT: B 394 ASN cc_start: 0.8142 (p0) cc_final: 0.7911 (p0) REVERT: B 902 MET cc_start: 0.8780 (tpp) cc_final: 0.8545 (tpt) REVERT: C 191 GLU cc_start: 0.8024 (mp0) cc_final: 0.7335 (mp0) REVERT: C 690 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6880 (mm110) outliers start: 86 outliers final: 60 residues processed: 258 average time/residue: 0.1468 time to fit residues: 64.5630 Evaluate side-chains 224 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 161 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 719 THR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 534 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 963 VAL Chi-restraints excluded: chain B residue 1001 LEU Chi-restraints excluded: chain B residue 1008 VAL Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 595 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 997 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1118 ASP Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 279 optimal weight: 0.9990 chunk 212 optimal weight: 0.7980 chunk 109 optimal weight: 30.0000 chunk 94 optimal weight: 0.8980 chunk 153 optimal weight: 9.9990 chunk 249 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 200 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN B 66 HIS B 690 GLN C 81 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.183094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.131233 restraints weight = 43013.673| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.75 r_work: 0.3379 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27183 Z= 0.133 Angle : 0.613 12.581 37134 Z= 0.308 Chirality : 0.046 0.280 4317 Planarity : 0.004 0.046 4710 Dihedral : 4.468 21.124 3528 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.07 % Allowed : 16.35 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.52 (0.14), residues: 3267 helix: 1.26 (0.21), residues: 618 sheet: -0.71 (0.19), residues: 714 loop : -2.00 (0.13), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 237 TYR 0.017 0.001 TYR B 266 PHE 0.019 0.001 PHE C 823 TRP 0.009 0.001 TRP A 436 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (27090) covalent geometry : angle 0.59416 / 0.30 (36891) SS BOND : bond 0.00249 / 0.17 ( 36) SS BOND : angle 1.47421 / 0.84 ( 72) hydrogen bonds : bond 0.05217 / 3.46 ( 867) hydrogen bonds : angle 5.27676 / 3.69 ( 2319) link_BETA1-4 : bond 0.00372 / 0.22 ( 15) link_BETA1-4 : angle 0.90209 / 0.57 ( 45) link_NAG-ASN : bond 0.00595 / 0.41 ( 42) link_NAG-ASN : angle 2.40654 / 1.49 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 176 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4533 (mmp) cc_final: 0.4212 (mmp) REVERT: A 239 GLN cc_start: 0.7730 (mt0) cc_final: 0.7064 (mm110) REVERT: A 265 TYR cc_start: 0.7330 (OUTLIER) cc_final: 0.6704 (t80) REVERT: A 421 TYR cc_start: 0.8080 (m-80) cc_final: 0.7689 (m-80) REVERT: A 429 PHE cc_start: 0.8282 (t80) cc_final: 0.7994 (t80) REVERT: A 452 MET cc_start: 0.7262 (mpp) cc_final: 0.6971 (mmp) REVERT: A 878 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8741 (tt) REVERT: B 42 VAL cc_start: 0.8707 (p) cc_final: 0.8373 (m) REVERT: B 153 MET cc_start: 0.3158 (tpp) cc_final: 0.2722 (tpt) REVERT: B 170 TYR cc_start: 0.6890 (t80) cc_final: 0.6540 (t80) REVERT: B 394 ASN cc_start: 0.8217 (p0) cc_final: 0.7954 (p0) REVERT: C 177 MET cc_start: 0.4310 (pmm) cc_final: 0.2264 (mmp) REVERT: C 220 PHE cc_start: 0.7329 (t80) cc_final: 0.7001 (t80) REVERT: C 242 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.6991 (mp) REVERT: C 584 ILE cc_start: 0.6769 (OUTLIER) cc_final: 0.6196 (mp) outliers start: 59 outliers final: 38 residues processed: 230 average time/residue: 0.1434 time to fit residues: 56.1472 Evaluate side-chains 209 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 709 ASN Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 81 ASN Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 299 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 261 optimal weight: 9.9990 chunk 260 optimal weight: 20.0000 chunk 214 optimal weight: 0.9980 chunk 232 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 57 optimal weight: 0.6980 chunk 270 optimal weight: 0.4980 chunk 317 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 417 ASN ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.183437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.131075 restraints weight = 42945.993| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.83 r_work: 0.3365 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3213 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 27183 Z= 0.128 Angle : 0.597 12.474 37134 Z= 0.297 Chirality : 0.045 0.272 4317 Planarity : 0.004 0.055 4710 Dihedral : 4.281 20.387 3528 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 1.93 % Allowed : 16.53 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.14), residues: 3267 helix: 1.54 (0.22), residues: 621 sheet: -0.57 (0.20), residues: 684 loop : -1.92 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 577 TYR 0.015 0.001 TYR A 160 PHE 0.020 0.001 PHE B 92 TRP 0.007 0.001 TRP B 436 HIS 0.003 0.000 HIS B 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (27090) covalent geometry : angle 0.57958 / 0.29 (36891) SS BOND : bond 0.00242 / 0.16 ( 36) SS BOND : angle 1.36130 / 0.78 ( 72) hydrogen bonds : bond 0.04928 / 3.26 ( 867) hydrogen bonds : angle 5.09643 / 3.57 ( 2319) link_BETA1-4 : bond 0.00393 / 0.23 ( 15) link_BETA1-4 : angle 0.91926 / 0.58 ( 45) link_NAG-ASN : bond 0.00483 / 0.30 ( 42) link_NAG-ASN : angle 2.28080 / 1.42 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 180 time to evaluate : 0.985 Fit side-chains REVERT: A 177 MET cc_start: 0.4493 (mmp) cc_final: 0.4215 (mmp) REVERT: A 239 GLN cc_start: 0.7762 (mt0) cc_final: 0.7116 (mm110) REVERT: A 265 TYR cc_start: 0.7179 (OUTLIER) cc_final: 0.6533 (t80) REVERT: A 421 TYR cc_start: 0.8083 (m-80) cc_final: 0.7274 (m-80) REVERT: A 429 PHE cc_start: 0.8332 (t80) cc_final: 0.8013 (t80) REVERT: A 452 MET cc_start: 0.7349 (mpp) cc_final: 0.7059 (mmp) REVERT: A 878 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8743 (tt) REVERT: B 42 VAL cc_start: 0.8769 (p) cc_final: 0.8404 (m) REVERT: B 153 MET cc_start: 0.3135 (tpp) cc_final: 0.2741 (tpt) REVERT: B 170 TYR cc_start: 0.6936 (t80) cc_final: 0.6625 (t80) REVERT: B 353 TRP cc_start: 0.6618 (p-90) cc_final: 0.5325 (p-90) REVERT: B 394 ASN cc_start: 0.8231 (p0) cc_final: 0.7984 (p0) REVERT: C 177 MET cc_start: 0.4304 (pmm) cc_final: 0.2437 (mmp) REVERT: C 200 TYR cc_start: 0.7463 (OUTLIER) cc_final: 0.7088 (t80) REVERT: C 220 PHE cc_start: 0.7342 (t80) cc_final: 0.6980 (t80) REVERT: C 242 LEU cc_start: 0.7442 (OUTLIER) cc_final: 0.6917 (mp) outliers start: 55 outliers final: 38 residues processed: 226 average time/residue: 0.1422 time to fit residues: 55.5136 Evaluate side-chains 216 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 174 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 265 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 41 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 58 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 312 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 chunk 267 optimal weight: 20.0000 chunk 43 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 ASN ** C 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.182195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117038 restraints weight = 42917.673| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 4.01 r_work: 0.3276 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 27183 Z= 0.261 Angle : 0.693 12.334 37134 Z= 0.350 Chirality : 0.050 0.554 4317 Planarity : 0.005 0.046 4710 Dihedral : 4.614 20.732 3528 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.07 % Allowed : 17.02 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.14), residues: 3267 helix: 1.05 (0.21), residues: 642 sheet: -0.75 (0.19), residues: 717 loop : -2.02 (0.13), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 237 TYR 0.026 0.002 TYR A 904 PHE 0.026 0.002 PHE B 927 TRP 0.012 0.001 TRP B 64 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00644 / 0.26 (27090) covalent geometry : angle 0.67539 / 0.35 (36891) SS BOND : bond 0.00352 / 0.24 ( 36) SS BOND : angle 1.76949 / 1.06 ( 72) hydrogen bonds : bond 0.06724 / 4.44 ( 867) hydrogen bonds : angle 5.40552 / 3.78 ( 2319) link_BETA1-4 : bond 0.00283 / 0.16 ( 15) link_BETA1-4 : angle 1.13260 / 0.68 ( 45) link_NAG-ASN : bond 0.00465 / 0.28 ( 42) link_NAG-ASN : angle 2.42094 / 1.51 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 172 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.4641 (mmp) cc_final: 0.4344 (mmp) REVERT: A 421 TYR cc_start: 0.8216 (m-80) cc_final: 0.7950 (m-80) REVERT: A 452 MET cc_start: 0.7507 (mpp) cc_final: 0.7211 (mmp) REVERT: A 878 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8688 (tt) REVERT: B 153 MET cc_start: 0.3059 (tpp) cc_final: 0.2707 (tpt) REVERT: B 271 GLN cc_start: 0.8435 (mp10) cc_final: 0.8149 (mp10) REVERT: C 177 MET cc_start: 0.4297 (pmm) cc_final: 0.2435 (mmp) REVERT: C 200 TYR cc_start: 0.7525 (OUTLIER) cc_final: 0.7248 (t80) REVERT: C 220 PHE cc_start: 0.7326 (t80) cc_final: 0.6804 (t80) REVERT: C 242 LEU cc_start: 0.7610 (OUTLIER) cc_final: 0.7069 (mp) REVERT: C 567 ARG cc_start: 0.7252 (mtm110) cc_final: 0.6938 (mtp85) REVERT: C 690 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.6648 (mm110) outliers start: 59 outliers final: 47 residues processed: 221 average time/residue: 0.1437 time to fit residues: 54.4544 Evaluate side-chains 215 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 164 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 267 VAL Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 973 ILE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 67 optimal weight: 0.9980 chunk 169 optimal weight: 8.9990 chunk 303 optimal weight: 0.9990 chunk 272 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 279 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 285 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.186292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.136058 restraints weight = 43059.829| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.63 r_work: 0.3470 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 27183 Z= 0.111 Angle : 0.591 12.592 37134 Z= 0.294 Chirality : 0.045 0.270 4317 Planarity : 0.004 0.048 4710 Dihedral : 4.212 20.035 3528 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.65 % Allowed : 17.33 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3267 helix: 1.58 (0.22), residues: 624 sheet: -0.59 (0.19), residues: 714 loop : -1.90 (0.13), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 577 TYR 0.020 0.001 TYR B 160 PHE 0.020 0.001 PHE B 201 TRP 0.010 0.001 TRP C 104 HIS 0.007 0.001 HIS C 505 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (27090) covalent geometry : angle 0.57374 / 0.29 (36891) SS BOND : bond 0.00220 / 0.14 ( 36) SS BOND : angle 1.40128 / 0.81 ( 72) hydrogen bonds : bond 0.04578 / 3.03 ( 867) hydrogen bonds : angle 5.02376 / 3.52 ( 2319) link_BETA1-4 : bond 0.00421 / 0.25 ( 15) link_BETA1-4 : angle 0.88284 / 0.56 ( 45) link_NAG-ASN : bond 0.00451 / 0.26 ( 42) link_NAG-ASN : angle 2.24755 / 1.42 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 64 TRP cc_start: 0.5756 (m-10) cc_final: 0.5503 (m100) REVERT: A 177 MET cc_start: 0.4309 (mmp) cc_final: 0.4103 (mmp) REVERT: A 239 GLN cc_start: 0.7643 (mt0) cc_final: 0.7012 (mm110) REVERT: A 421 TYR cc_start: 0.8052 (m-80) cc_final: 0.7709 (m-80) REVERT: A 452 MET cc_start: 0.7419 (mpp) cc_final: 0.7134 (mmp) REVERT: A 878 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8696 (tt) REVERT: A 1138 TYR cc_start: 0.7963 (t80) cc_final: 0.7683 (m-10) REVERT: B 42 VAL cc_start: 0.8882 (p) cc_final: 0.8550 (m) REVERT: B 153 MET cc_start: 0.3086 (tpp) cc_final: 0.2626 (tpt) REVERT: B 170 TYR cc_start: 0.6761 (t80) cc_final: 0.6456 (t80) REVERT: B 353 TRP cc_start: 0.6663 (p-90) cc_final: 0.5390 (p-90) REVERT: C 220 PHE cc_start: 0.7090 (t80) cc_final: 0.6736 (t80) REVERT: C 452 MET cc_start: 0.3419 (tmm) cc_final: 0.1254 (ptt) REVERT: C 567 ARG cc_start: 0.7434 (mtm110) cc_final: 0.7077 (mtp85) outliers start: 47 outliers final: 38 residues processed: 215 average time/residue: 0.1538 time to fit residues: 56.6724 Evaluate side-chains 207 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 284 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 195 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.186419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.135916 restraints weight = 42827.013| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.63 r_work: 0.3420 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 27183 Z= 0.166 Angle : 0.622 12.604 37134 Z= 0.312 Chirality : 0.046 0.268 4317 Planarity : 0.004 0.049 4710 Dihedral : 4.287 18.935 3528 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.51 % Allowed : 17.79 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.14), residues: 3267 helix: 1.61 (0.22), residues: 621 sheet: -0.57 (0.19), residues: 714 loop : -1.92 (0.13), residues: 1932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 237 TYR 0.021 0.001 TYR B 160 PHE 0.040 0.001 PHE C 86 TRP 0.010 0.001 TRP B 64 HIS 0.003 0.001 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.17 (27090) covalent geometry : angle 0.60601 / 0.31 (36891) SS BOND : bond 0.00273 / 0.19 ( 36) SS BOND : angle 1.43734 / 0.83 ( 72) hydrogen bonds : bond 0.05386 / 3.56 ( 867) hydrogen bonds : angle 5.08988 / 3.57 ( 2319) link_BETA1-4 : bond 0.00295 / 0.17 ( 15) link_BETA1-4 : angle 0.97690 / 0.60 ( 45) link_NAG-ASN : bond 0.00404 / 0.22 ( 42) link_NAG-ASN : angle 2.26129 / 1.41 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6534 Ramachandran restraints generated. 3267 Oldfield, 0 Emsley, 3267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.050 Fit side-chains revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8125 (m-80) cc_final: 0.7785 (m-80) REVERT: A 452 MET cc_start: 0.7612 (mpp) cc_final: 0.7326 (mmp) REVERT: A 878 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8729 (tt) REVERT: A 934 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8870 (tp) REVERT: A 1138 TYR cc_start: 0.8002 (t80) cc_final: 0.7723 (m-10) REVERT: B 153 MET cc_start: 0.3124 (tpp) cc_final: 0.2659 (tpt) REVERT: B 170 TYR cc_start: 0.6863 (t80) cc_final: 0.6548 (t80) REVERT: B 353 TRP cc_start: 0.6592 (p-90) cc_final: 0.5324 (p-90) REVERT: B 490 PHE cc_start: 0.7072 (t80) cc_final: 0.6857 (t80) REVERT: C 220 PHE cc_start: 0.7201 (t80) cc_final: 0.6766 (t80) REVERT: C 452 MET cc_start: 0.3470 (tmm) cc_final: 0.1345 (ptt) REVERT: C 567 ARG cc_start: 0.7483 (mtm110) cc_final: 0.7097 (mtp85) outliers start: 43 outliers final: 40 residues processed: 201 average time/residue: 0.1479 time to fit residues: 51.3932 Evaluate side-chains 203 residues out of total 2871 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 VAL Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 676 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 949 GLN Chi-restraints excluded: chain A residue 955 ASN Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 671 CYS Chi-restraints excluded: chain B residue 874 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 696 THR Chi-restraints excluded: chain C residue 855 PHE Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 874 THR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 931 ILE Chi-restraints excluded: chain C residue 957 GLN Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1092 GLU Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 159 optimal weight: 20.0000 chunk 61 optimal weight: 0.0070 chunk 14 optimal weight: 20.0000 chunk 181 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 183 optimal weight: 0.4980 chunk 243 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 12 optimal weight: 0.0870 chunk 324 optimal weight: 2.9990 overall best weight: 0.4576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 87 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.187444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.138150 restraints weight = 42926.411| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.66 r_work: 0.3490 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3338 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 27183 Z= 0.104 Angle : 0.577 12.743 37134 Z= 0.286 Chirality : 0.045 0.273 4317 Planarity : 0.004 0.050 4710 Dihedral : 4.006 18.886 3528 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 1.30 % Allowed : 18.07 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.14), residues: 3267 helix: 1.85 (0.22), residues: 624 sheet: -0.32 (0.20), residues: 681 loop : -1.81 (0.13), residues: 1962 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 577 TYR 0.022 0.001 TYR B 160 PHE 0.043 0.001 PHE C 86 TRP 0.012 0.001 TRP B 436 HIS 0.002 0.000 HIS C1088 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 (27090) covalent geometry : angle 0.56202 / 0.28 (36891) SS BOND : bond 0.00200 / 0.13 ( 36) SS BOND : angle 1.22737 / 0.71 ( 72) hydrogen bonds : bond 0.04084 / 2.71 ( 867) hydrogen bonds : angle 4.84637 / 3.40 ( 2319) link_BETA1-4 : bond 0.00427 / 0.26 ( 15) link_BETA1-4 : angle 0.89956 / 0.57 ( 45) link_NAG-ASN : bond 0.00441 / 0.25 ( 42) link_NAG-ASN : angle 2.15703 / 1.37 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6958.87 seconds wall clock time: 135 minutes 30.30 seconds (8130.30 seconds total)