Starting phenix.real_space_refine on Fri Mar 6 09:00:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8t_22730/03_2026/7k8t_22730_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8t_22730/03_2026/7k8t_22730.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7k8t_22730/03_2026/7k8t_22730.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8t_22730/03_2026/7k8t_22730.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8t_22730/03_2026/7k8t_22730_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8t_22730/03_2026/7k8t_22730_neut.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 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 120 5.16 5 C 18783 2.51 5 N 4856 2.21 5 O 5817 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 192 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29576 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7810 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 7801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7801 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 7809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1001, 7809 Classifications: {'peptide': 1001} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 49, 'TRANS': 951} Chain breaks: 9 Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "H" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "L" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "M" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "N" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "O" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 959 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "P" Number of atoms: 813 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 813 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 6.22, per 1000 atoms: 0.21 Number of scatterers: 29576 At special positions: 0 Unit cell: (136.268, 157.168, 227.392, 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 120 16.00 O 5817 8.00 N 4856 7.00 C 18783 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=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.02 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.01 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " 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=2.04 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=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 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 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 92 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 92 " distance=2.03 Simple disulfide: pdb=" SG CYS P 23 " - pdb=" SG CYS P 88 " 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 I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 343 " " NAG A1305 " - " ASN A 603 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 657 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1305 " - " ASN B 603 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 657 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1305 " - " ASN C 603 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 657 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 165 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG I 1 " - " ASN A1134 " " NAG J 1 " - " ASN B 234 " " NAG K 1 " - " ASN B 717 " " NAG Q 1 " - " ASN B 801 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN C 234 " " NAG U 1 " - " ASN C 717 " " NAG V 1 " - " ASN C 801 " " NAG W 1 " - " ASN C1098 " " NAG X 1 " - " ASN C1134 " Time building additional restraints: 2.14 Conformation dependent library (CDL) restraints added in 1.3 seconds 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6904 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 53 sheets defined 23.4% alpha, 27.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.31 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.519A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.570A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.902A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.970A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 3.823A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.960A pdb=" N GLN A 409 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 4.109A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.596A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.503A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.539A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.648A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.593A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.588A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.743A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 5.138A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.868A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.066A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.544A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 4.177A pdb=" N ASN B 388 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 455 through 459 Processing helix chain 'B' and resid 501 through 501 No H-bonds generated for 'chain 'B' and resid 501 through 501' Processing helix chain 'B' and resid 503 through 506 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.503A pdb=" N TYR B 741 " --> pdb=" O ASP B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.744A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.566A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.573A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.593A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.541A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 968 removed outlier: 3.854A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 968 " --> pdb=" O LYS B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.704A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.853A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.579A 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 Processing helix chain 'C' and resid 405 through 410 removed outlier: 3.925A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 455 through 459 removed outlier: 3.831A pdb=" N LYS C 458 " --> pdb=" O LEU C 455 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 501 No H-bonds generated for 'chain 'C' and resid 501 through 501' Processing helix chain 'C' and resid 503 through 505 No H-bonds generated for 'chain 'C' and resid 503 through 505' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.660A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.514A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.549A pdb=" N LEU C 822 " --> pdb=" O ILE C 818 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.626A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR C 873 " --> pdb=" O MET C 869 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.642A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.668A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASN C 960 " --> pdb=" O ALA C 956 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 3.557A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.910A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 3.896A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.821A pdb=" N ILE H 31 " --> pdb=" O THR H 28 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.699A pdb=" N LYS H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.606A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 32 removed outlier: 3.978A pdb=" N ILE M 31 " --> pdb=" O THR M 28 " (cutoff:3.500A) Processing helix chain 'M' and resid 61 through 64 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.797A pdb=" N PHE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 32 removed outlier: 3.530A pdb=" N ILE O 31 " --> pdb=" O THR O 28 " (cutoff:3.500A) Processing helix chain 'O' and resid 61 through 64 Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.651A pdb=" N PHE P 83 " --> pdb=" O PRO P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 8.160A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN A 188 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.594A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.554A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.884A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.095A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 132 through 134 removed outlier: 4.994A pdb=" N PHE A 133 " --> pdb=" O SER A 112 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 237 through 244 current: chain 'A' and resid 169 through 171 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.302A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.744A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ASN A 437 " --> pdb=" O PHE A 374 " (cutoff:3.500A) removed outlier: 8.246A pdb=" N PHE A 374 " --> pdb=" O ASN A 437 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 565 through 566 removed outlier: 7.145A pdb=" N PHE A 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.336A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 713 removed outlier: 3.572A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.807A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.557A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.147A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.562A pdb=" N ARG B 273 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.706A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 85 removed outlier: 7.033A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.097A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 324 through 325 removed outlier: 6.386A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.746A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.300A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.503A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.801A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.128A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AC8, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AC9, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.689A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU C 96 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN C 188 " --> pdb=" O GLU C 96 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.378A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.839A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.538A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.139A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 311 through 319 removed outlier: 6.962A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 324 through 326 removed outlier: 4.141A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.706A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N THR C 430 " --> pdb=" O PHE C 515 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AD8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.135A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 711 through 713 removed outlier: 3.638A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.894A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE3, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'H' and resid 10 through 12 removed outlier: 5.900A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.915A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.499A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AE9, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.136A pdb=" N GLY M 10 " --> pdb=" O THR M 110 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.601A pdb=" N ASP N 70 " --> pdb=" O SER N 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLN N 37 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LEU N 46 " --> pdb=" O GLN N 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 10 through 13 removed outlier: 6.299A pdb=" N LEU N 11 " --> pdb=" O GLU N 105 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.730A pdb=" N TYR O 79 " --> pdb=" O SER O 70 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER O 70 " --> pdb=" O TYR O 79 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.002A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 4 through 7 removed outlier: 3.571A pdb=" N ASP P 70 " --> pdb=" O SER P 67 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR P 72 " --> pdb=" O SER P 65 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER P 65 " --> pdb=" O THR P 72 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.537A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N GLN P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N LEU P 46 " --> pdb=" O GLN P 37 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.537A pdb=" N LEU P 11 " --> pdb=" O GLU P 105 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) 1147 hydrogen bonds defined for protein. 3099 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.92 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4784 1.25 - 1.40: 7548 1.40 - 1.54: 17692 1.54 - 1.69: 35 1.69 - 1.83: 151 Bond restraints: 30210 Sorted by residual: bond pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta sigma weight residual 1.469 1.701 -0.232 1.28e-02 6.10e+03 3.30e+02 bond pdb=" N PRO C 85 " pdb=" CA PRO C 85 " ideal model delta sigma weight residual 1.469 1.697 -0.229 1.28e-02 6.10e+03 3.19e+02 bond pdb=" CG PRO B 579 " pdb=" CD PRO B 579 " ideal model delta sigma weight residual 1.503 1.110 0.393 3.40e-02 8.65e+02 1.34e+02 bond pdb=" C LEU A 84 " pdb=" N PRO A 85 " ideal model delta sigma weight residual 1.334 1.454 -0.120 2.34e-02 1.83e+03 2.63e+01 bond pdb=" C LEU C 84 " pdb=" N PRO C 85 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.34e-02 1.83e+03 2.48e+01 ... (remaining 30205 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 40882 4.30 - 8.61: 188 8.61 - 12.91: 7 12.91 - 17.22: 2 17.22 - 21.52: 3 Bond angle restraints: 41082 Sorted by residual: angle pdb=" C LEU A 84 " pdb=" N PRO A 85 " pdb=" CA PRO A 85 " ideal model delta sigma weight residual 119.84 139.24 -19.40 1.25e+00 6.40e-01 2.41e+02 angle pdb=" C LEU C 84 " pdb=" N PRO C 85 " pdb=" CA PRO C 85 " ideal model delta sigma weight residual 119.84 139.19 -19.35 1.25e+00 6.40e-01 2.40e+02 angle pdb=" N PRO B 579 " pdb=" CD PRO B 579 " pdb=" CG PRO B 579 " ideal model delta sigma weight residual 103.20 81.68 21.52 1.50e+00 4.44e-01 2.06e+02 angle pdb=" CA PRO C 85 " pdb=" N PRO C 85 " pdb=" CD PRO C 85 " ideal model delta sigma weight residual 112.00 99.77 12.23 1.40e+00 5.10e-01 7.63e+01 angle pdb=" CA PRO A 85 " pdb=" N PRO A 85 " pdb=" CD PRO A 85 " ideal model delta sigma weight residual 112.00 100.20 11.80 1.40e+00 5.10e-01 7.11e+01 ... (remaining 41077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 17141 17.93 - 35.85: 1265 35.85 - 53.78: 227 53.78 - 71.70: 62 71.70 - 89.63: 27 Dihedral angle restraints: 18722 sinusoidal: 7984 harmonic: 10738 Sorted by residual: dihedral pdb=" CA GLN A 474 " pdb=" C GLN A 474 " pdb=" N ALA A 475 " pdb=" CA ALA A 475 " ideal model delta harmonic sigma weight residual -180.00 -130.07 -49.93 0 5.00e+00 4.00e-02 9.97e+01 dihedral pdb=" CB CYS C1032 " pdb=" SG CYS C1032 " pdb=" SG CYS C1043 " pdb=" CB CYS C1043 " ideal model delta sinusoidal sigma weight residual 93.00 -177.37 -89.63 1 1.00e+01 1.00e-02 9.54e+01 dihedral pdb=" CA GLU B 471 " pdb=" C GLU B 471 " pdb=" N ILE B 472 " pdb=" CA ILE B 472 " ideal model delta harmonic sigma weight residual -180.00 -133.51 -46.49 0 5.00e+00 4.00e-02 8.65e+01 ... (remaining 18719 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.168: 4787 0.168 - 0.336: 43 0.336 - 0.505: 6 0.505 - 0.673: 2 0.673 - 0.841: 1 Chirality restraints: 4839 Sorted by residual: chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -1.56 -0.84 2.00e-01 2.50e+01 1.77e+01 chirality pdb=" CA PRO C 85 " pdb=" N PRO C 85 " pdb=" C PRO C 85 " pdb=" CB PRO C 85 " both_signs ideal model delta sigma weight residual False 2.72 3.27 -0.55 2.00e-01 2.50e+01 7.61e+00 chirality pdb=" C1 NAG B1305 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1305 " pdb=" O5 NAG B1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.87 -0.53 2.00e-01 2.50e+01 7.06e+00 ... (remaining 4836 not shown) Planarity restraints: 5268 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 84 " -0.026 2.00e-02 2.50e+03 4.90e-02 2.41e+01 pdb=" C LEU C 84 " 0.085 2.00e-02 2.50e+03 pdb=" O LEU C 84 " -0.032 2.00e-02 2.50e+03 pdb=" N PRO C 85 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL P 58 " -0.065 5.00e-02 4.00e+02 9.37e-02 1.40e+01 pdb=" N PRO P 59 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO P 59 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO P 59 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 578 " -0.060 5.00e-02 4.00e+02 8.39e-02 1.13e+01 pdb=" N PRO B 579 " 0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 579 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO B 579 " -0.044 5.00e-02 4.00e+02 ... (remaining 5265 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 99 2.36 - 3.00: 17659 3.00 - 3.63: 43274 3.63 - 4.27: 67555 4.27 - 4.90: 111624 Nonbonded interactions: 240211 Sorted by model distance: nonbonded pdb=" CG PRO M 98 " pdb=" CD1 ILE M 100A" model vdw 1.726 3.860 nonbonded pdb=" O PHE C 490 " pdb=" NH2 ARG H 97 " model vdw 1.813 3.120 nonbonded pdb=" CG PRO M 98 " pdb=" CG1 ILE M 100A" model vdw 1.903 3.840 nonbonded pdb=" CZ TYR A 489 " pdb=" O VAL O 100C" model vdw 1.960 3.260 nonbonded pdb=" OE1 GLN C 804 " pdb=" NE2 GLN C 935 " model vdw 2.042 3.120 ... (remaining 240206 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 524 or (re \ sid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 1310)) selection = (chain 'B' and (resid 27 through 335 or (resid 336 and (name N or name CA or nam \ e C or name O )) or resid 337 through 1310)) selection = (chain 'C' and (resid 27 through 329 or (resid 330 and (name N or name CA or nam \ e C or name O or name CB )) or resid 331 through 335 or (resid 336 and (name N o \ r name CA or name C or name O )) or resid 337 through 378 or (resid 379 and (nam \ e N or name CA or name C or name O or name CB )) or resid 380 through 524 or (re \ sid 525 and (name N or name CA or name C or name O or name CB )) or resid 526 th \ rough 527 or (resid 528 and (name N or name CA or name C or name O or name CB )) \ or resid 529 through 1310)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'H' selection = chain 'M' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'N' selection = chain 'P' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.490 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 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 : 0.010 0.393 30304 Z= 0.451 Angle : 0.976 21.520 41326 Z= 0.551 Chirality : 0.059 0.841 4839 Planarity : 0.005 0.094 5225 Dihedral : 13.076 88.395 11713 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.37 % Favored : 93.41 % Rotamer: Outliers : 0.22 % Allowed : 0.63 % Favored : 99.15 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.13), residues: 3627 helix: 0.24 (0.19), residues: 643 sheet: 0.28 (0.16), residues: 957 loop : -1.16 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG B 346 TYR 0.038 0.003 TYR B 489 PHE 0.044 0.003 PHE B 464 TRP 0.048 0.003 TRP C 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00980 (30210) covalent geometry : angle 0.94863 (41082) SS BOND : bond 0.00557 ( 36) SS BOND : angle 2.04712 ( 70) hydrogen bonds : bond 0.25363 ( 1133) hydrogen bonds : angle 10.01849 ( 3099) link_BETA1-4 : bond 0.00455 ( 15) link_BETA1-4 : angle 1.69310 ( 45) link_NAG-ASN : bond 0.00993 ( 43) link_NAG-ASN : angle 3.90490 ( 129) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 306 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8400 (tm-30) REVERT: A 370 ASN cc_start: 0.8537 (m110) cc_final: 0.8313 (m110) REVERT: A 405 ASP cc_start: 0.8409 (t0) cc_final: 0.8137 (t70) REVERT: A 408 ARG cc_start: 0.9133 (ptm-80) cc_final: 0.8889 (ppt170) REVERT: A 421 TYR cc_start: 0.8750 (m-80) cc_final: 0.8287 (m-80) REVERT: A 855 PHE cc_start: 0.6581 (m-80) cc_final: 0.6371 (m-80) REVERT: B 81 ASN cc_start: 0.8125 (p0) cc_final: 0.7775 (p0) REVERT: B 104 TRP cc_start: 0.8542 (m-90) cc_final: 0.8169 (m-90) REVERT: B 346 ARG cc_start: 0.9028 (mtp-110) cc_final: 0.8442 (tmm-80) REVERT: B 370 ASN cc_start: 0.9008 (m-40) cc_final: 0.8291 (p0) REVERT: B 386 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9091 (ttpp) REVERT: C 104 TRP cc_start: 0.7886 (m-90) cc_final: 0.7627 (m-90) REVERT: C 378 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8316 (ttmm) REVERT: C 406 GLU cc_start: 0.8735 (mp0) cc_final: 0.8209 (mp0) REVERT: H 4 LEU cc_start: 0.7634 (mt) cc_final: 0.7186 (mt) REVERT: H 19 ARG cc_start: 0.8620 (ttp-170) cc_final: 0.8358 (ttp80) REVERT: H 79 TYR cc_start: 0.8777 (m-80) cc_final: 0.8259 (m-80) REVERT: H 91 TYR cc_start: 0.7702 (m-80) cc_final: 0.7029 (m-80) REVERT: H 101 ASP cc_start: 0.4153 (p0) cc_final: 0.3946 (p0) REVERT: H 103 TRP cc_start: 0.8249 (m100) cc_final: 0.7666 (m-10) REVERT: L 18 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8252 (ttm-80) REVERT: L 21 ILE cc_start: 0.8669 (mp) cc_final: 0.8058 (mp) REVERT: L 34 ASN cc_start: 0.8662 (m-40) cc_final: 0.8019 (m-40) REVERT: L 35 TRP cc_start: 0.8604 (m100) cc_final: 0.8116 (m100) REVERT: L 37 GLN cc_start: 0.8315 (tt0) cc_final: 0.7603 (tt0) REVERT: N 32 TYR cc_start: 0.6078 (m-80) cc_final: 0.5802 (m-80) REVERT: N 105 GLU cc_start: 0.6768 (mt-10) cc_final: 0.6412 (tt0) REVERT: O 4 LEU cc_start: 0.7564 (mt) cc_final: 0.6943 (mt) REVERT: O 19 ARG cc_start: 0.7292 (ttp-170) cc_final: 0.6580 (tpt170) REVERT: O 34 MET cc_start: 0.7664 (mmp) cc_final: 0.6174 (mmm) REVERT: O 79 TYR cc_start: 0.7205 (m-80) cc_final: 0.6943 (m-80) REVERT: P 82 ASP cc_start: 0.3679 (m-30) cc_final: 0.2417 (m-30) REVERT: P 92 TYR cc_start: 0.7765 (t80) cc_final: 0.7537 (t80) outliers start: 7 outliers final: 1 residues processed: 311 average time/residue: 0.2033 time to fit residues: 98.0359 Evaluate side-chains 202 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 0.6980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 321 GLN A 394 ASN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 955 ASN A1002 GLN B 49 HIS B 69 HIS B 87 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN B 935 GLN B1088 HIS C 81 ASN O 56 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.110730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.073459 restraints weight = 76240.686| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.88 r_work: 0.3147 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30304 Z= 0.174 Angle : 0.734 18.887 41326 Z= 0.382 Chirality : 0.050 0.563 4839 Planarity : 0.005 0.056 5225 Dihedral : 7.109 57.219 5225 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.21 % Favored : 94.68 % Rotamer: Outliers : 0.66 % Allowed : 5.57 % Favored : 93.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.14), residues: 3627 helix: 1.44 (0.20), residues: 678 sheet: 0.24 (0.16), residues: 955 loop : -1.04 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG P 24 TYR 0.036 0.002 TYR C 489 PHE 0.026 0.002 PHE A 400 TRP 0.023 0.002 TRP C 64 HIS 0.005 0.001 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00385 (30210) covalent geometry : angle 0.70627 (41082) SS BOND : bond 0.00546 ( 36) SS BOND : angle 1.90615 ( 70) hydrogen bonds : bond 0.05420 ( 1133) hydrogen bonds : angle 6.62584 ( 3099) link_BETA1-4 : bond 0.00483 ( 15) link_BETA1-4 : angle 1.07121 ( 45) link_NAG-ASN : bond 0.00670 ( 43) link_NAG-ASN : angle 3.36053 ( 129) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 264 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.8078 (p90) cc_final: 0.7787 (p90) REVERT: A 408 ARG cc_start: 0.9205 (ptm-80) cc_final: 0.8991 (ptm-80) REVERT: A 855 PHE cc_start: 0.6906 (m-80) cc_final: 0.6576 (m-80) REVERT: A 1017 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8598 (tm-30) REVERT: B 81 ASN cc_start: 0.8549 (p0) cc_final: 0.8116 (p0) REVERT: B 346 ARG cc_start: 0.9152 (mtp-110) cc_final: 0.8570 (tmm-80) REVERT: B 386 LYS cc_start: 0.9397 (mmtt) cc_final: 0.9053 (ttpp) REVERT: B 483 VAL cc_start: 0.5521 (OUTLIER) cc_final: 0.4946 (p) REVERT: C 104 TRP cc_start: 0.8233 (m-90) cc_final: 0.7770 (m-90) REVERT: C 200 TYR cc_start: 0.7733 (m-80) cc_final: 0.7422 (t80) REVERT: C 406 GLU cc_start: 0.8869 (mp0) cc_final: 0.8259 (mp0) REVERT: H 19 ARG cc_start: 0.8573 (ttp-170) cc_final: 0.8282 (ttt90) REVERT: H 59 TYR cc_start: 0.7305 (m-80) cc_final: 0.6819 (m-80) REVERT: H 75 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8697 (mtmm) REVERT: H 79 TYR cc_start: 0.8974 (m-80) cc_final: 0.8760 (m-10) REVERT: H 91 TYR cc_start: 0.7575 (m-80) cc_final: 0.7114 (m-10) REVERT: H 101 ASP cc_start: 0.4681 (p0) cc_final: 0.4181 (p0) REVERT: H 103 TRP cc_start: 0.8157 (m100) cc_final: 0.7560 (m-10) REVERT: L 34 ASN cc_start: 0.8280 (m-40) cc_final: 0.7766 (m-40) REVERT: L 37 GLN cc_start: 0.8198 (tt0) cc_final: 0.7576 (tt0) REVERT: M 77 THR cc_start: 0.7260 (p) cc_final: 0.7060 (t) REVERT: M 100 VAL cc_start: 0.7137 (OUTLIER) cc_final: 0.6707 (p) REVERT: N 105 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6332 (tt0) REVERT: O 19 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6618 (tpt170) REVERT: O 76 ASN cc_start: 0.8164 (m-40) cc_final: 0.7927 (t0) REVERT: P 71 PHE cc_start: 0.5854 (m-80) cc_final: 0.5641 (m-80) outliers start: 21 outliers final: 7 residues processed: 276 average time/residue: 0.2041 time to fit residues: 88.1717 Evaluate side-chains 213 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 204 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 236 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 57 optimal weight: 0.0980 chunk 292 optimal weight: 1.9990 chunk 363 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 225 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN ** A 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 207 HIS C1010 GLN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.110907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.072234 restraints weight = 76816.457| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 3.47 r_work: 0.3176 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 30304 Z= 0.137 Angle : 0.657 18.894 41326 Z= 0.338 Chirality : 0.047 0.533 4839 Planarity : 0.004 0.052 5225 Dihedral : 6.376 59.910 5225 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.73 % Favored : 94.18 % Rotamer: Outliers : 0.88 % Allowed : 8.89 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3627 helix: 1.85 (0.20), residues: 675 sheet: 0.20 (0.16), residues: 973 loop : -1.03 (0.14), residues: 1979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 403 TYR 0.037 0.002 TYR C 489 PHE 0.021 0.001 PHE C 347 TRP 0.031 0.002 TRP H 36 HIS 0.005 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00302 (30210) covalent geometry : angle 0.62955 (41082) SS BOND : bond 0.00514 ( 36) SS BOND : angle 1.81730 ( 70) hydrogen bonds : bond 0.04478 ( 1133) hydrogen bonds : angle 5.95830 ( 3099) link_BETA1-4 : bond 0.00433 ( 15) link_BETA1-4 : angle 1.12756 ( 45) link_NAG-ASN : bond 0.00617 ( 43) link_NAG-ASN : angle 3.12815 ( 129) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 265 TYR cc_start: 0.7930 (p90) cc_final: 0.7624 (p90) REVERT: A 421 TYR cc_start: 0.8554 (m-80) cc_final: 0.8235 (m-80) REVERT: A 855 PHE cc_start: 0.6963 (m-80) cc_final: 0.6586 (m-80) REVERT: A 900 MET cc_start: 0.8827 (mtt) cc_final: 0.8598 (mtt) REVERT: A 1017 GLU cc_start: 0.9007 (tm-30) cc_final: 0.8613 (tm-30) REVERT: B 81 ASN cc_start: 0.8497 (p0) cc_final: 0.8030 (p0) REVERT: B 346 ARG cc_start: 0.9172 (mtp-110) cc_final: 0.8594 (tmm-80) REVERT: B 386 LYS cc_start: 0.9397 (mmtt) cc_final: 0.9051 (ttpp) REVERT: B 483 VAL cc_start: 0.5406 (OUTLIER) cc_final: 0.5024 (p) REVERT: C 104 TRP cc_start: 0.8297 (m-90) cc_final: 0.7880 (m-90) REVERT: C 200 TYR cc_start: 0.7845 (m-80) cc_final: 0.7503 (t80) REVERT: C 406 GLU cc_start: 0.8867 (mp0) cc_final: 0.8255 (mp0) REVERT: C 547 THR cc_start: 0.9036 (OUTLIER) cc_final: 0.8634 (p) REVERT: H 19 ARG cc_start: 0.8636 (ttp-170) cc_final: 0.8335 (ttt90) REVERT: H 59 TYR cc_start: 0.6950 (m-80) cc_final: 0.6714 (m-80) REVERT: H 75 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8699 (mtmm) REVERT: H 76 ASN cc_start: 0.9166 (m-40) cc_final: 0.8922 (t0) REVERT: H 79 TYR cc_start: 0.8950 (m-80) cc_final: 0.8732 (m-10) REVERT: H 101 ASP cc_start: 0.4362 (p0) cc_final: 0.3953 (p0) REVERT: H 103 TRP cc_start: 0.8102 (m100) cc_final: 0.7438 (m-10) REVERT: L 3 GLN cc_start: 0.8078 (tp40) cc_final: 0.7832 (mp10) REVERT: L 34 ASN cc_start: 0.8138 (m-40) cc_final: 0.7698 (m110) REVERT: L 37 GLN cc_start: 0.8084 (tt0) cc_final: 0.7417 (tt0) REVERT: L 92 TYR cc_start: 0.8304 (t80) cc_final: 0.7892 (t80) REVERT: M 45 LEU cc_start: 0.7166 (OUTLIER) cc_final: 0.6801 (mm) REVERT: N 32 TYR cc_start: 0.6672 (m-80) cc_final: 0.6309 (m-80) REVERT: N 35 TRP cc_start: 0.4201 (m100) cc_final: 0.3480 (m100) REVERT: N 39 LYS cc_start: 0.7043 (mmpt) cc_final: 0.6166 (tmtt) REVERT: N 105 GLU cc_start: 0.6639 (mt-10) cc_final: 0.6401 (tt0) REVERT: O 19 ARG cc_start: 0.7452 (ttp-170) cc_final: 0.6667 (tpt170) REVERT: O 32 TYR cc_start: 0.6001 (m-80) cc_final: 0.5565 (m-10) REVERT: O 34 MET cc_start: 0.8011 (mmp) cc_final: 0.7365 (mmm) REVERT: P 32 TYR cc_start: 0.4714 (m-80) cc_final: 0.4423 (m-80) outliers start: 28 outliers final: 11 residues processed: 248 average time/residue: 0.1979 time to fit residues: 77.6788 Evaluate side-chains 214 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 200 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain B residue 335 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain P residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 101 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 355 optimal weight: 30.0000 chunk 191 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 162 optimal weight: 0.9990 chunk 347 optimal weight: 10.0000 chunk 99 optimal weight: 1.9990 chunk 350 optimal weight: 30.0000 chunk 136 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 321 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN B 992 GLN B1088 HIS C 69 HIS C 81 ASN C 87 ASN C 196 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 935 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.106183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.068109 restraints weight = 77727.406| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 3.85 r_work: 0.3049 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 30304 Z= 0.314 Angle : 0.763 19.969 41326 Z= 0.391 Chirality : 0.050 0.527 4839 Planarity : 0.005 0.046 5225 Dihedral : 6.455 58.879 5225 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.84 % Favored : 93.11 % Rotamer: Outliers : 1.56 % Allowed : 10.95 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.14), residues: 3627 helix: 1.37 (0.20), residues: 682 sheet: 0.07 (0.16), residues: 928 loop : -1.16 (0.14), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 905 TYR 0.026 0.002 TYR A1067 PHE 0.026 0.002 PHE C 347 TRP 0.022 0.002 TRP M 103 HIS 0.006 0.001 HIS A1058 Details of bonding type rmsd covalent geometry : bond 0.00729 (30210) covalent geometry : angle 0.73490 (41082) SS BOND : bond 0.00696 ( 36) SS BOND : angle 2.26458 ( 70) hydrogen bonds : bond 0.04893 ( 1133) hydrogen bonds : angle 6.02350 ( 3099) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.28062 ( 45) link_NAG-ASN : bond 0.00734 ( 43) link_NAG-ASN : angle 3.30941 ( 129) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8768 (m-80) cc_final: 0.8496 (m-80) REVERT: A 855 PHE cc_start: 0.7202 (m-80) cc_final: 0.6593 (m-80) REVERT: B 346 ARG cc_start: 0.9175 (mtp-110) cc_final: 0.8759 (tmm-80) REVERT: B 386 LYS cc_start: 0.9375 (mmtt) cc_final: 0.9038 (ttpp) REVERT: B 979 ASP cc_start: 0.8775 (m-30) cc_final: 0.8562 (p0) REVERT: C 406 GLU cc_start: 0.9035 (mp0) cc_final: 0.8462 (mp0) REVERT: C 740 MET cc_start: 0.8858 (mmm) cc_final: 0.8070 (tmm) REVERT: H 34 MET cc_start: 0.6967 (mmm) cc_final: 0.6714 (mmm) REVERT: H 64 LYS cc_start: 0.8514 (mttp) cc_final: 0.8187 (tptp) REVERT: H 75 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8683 (mtmm) REVERT: H 76 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8956 (t0) REVERT: H 79 TYR cc_start: 0.9070 (m-80) cc_final: 0.8725 (m-10) REVERT: H 91 TYR cc_start: 0.7218 (m-10) cc_final: 0.6766 (m-10) REVERT: H 101 ASP cc_start: 0.4302 (p0) cc_final: 0.3664 (p0) REVERT: L 3 GLN cc_start: 0.8142 (tp40) cc_final: 0.7839 (mp10) REVERT: L 34 ASN cc_start: 0.8399 (m-40) cc_final: 0.7943 (m110) REVERT: L 37 GLN cc_start: 0.8007 (tt0) cc_final: 0.7736 (tt0) REVERT: L 47 LEU cc_start: 0.8418 (mt) cc_final: 0.7983 (mt) REVERT: L 61 ARG cc_start: 0.7426 (ptt-90) cc_final: 0.7196 (ptt-90) REVERT: L 92 TYR cc_start: 0.8385 (t80) cc_final: 0.7989 (t80) REVERT: M 102 TYR cc_start: 0.8473 (t80) cc_final: 0.8183 (t80) REVERT: N 35 TRP cc_start: 0.4405 (m100) cc_final: 0.3696 (m100) REVERT: N 39 LYS cc_start: 0.7098 (mmpt) cc_final: 0.6344 (tmtt) REVERT: N 105 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6487 (tt0) REVERT: O 19 ARG cc_start: 0.7370 (ttp-170) cc_final: 0.6716 (tpp-160) REVERT: P 32 TYR cc_start: 0.5776 (m-80) cc_final: 0.5173 (m-10) outliers start: 50 outliers final: 25 residues processed: 247 average time/residue: 0.1964 time to fit residues: 76.6918 Evaluate side-chains 214 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 188 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 510 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 76 ASN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 45 LEU Chi-restraints excluded: chain M residue 68 THR Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 31 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 326 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 297 optimal weight: 0.6980 chunk 269 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 277 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 120 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 171 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 481 ASN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.109206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.071746 restraints weight = 76818.406| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 3.94 r_work: 0.3115 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 30304 Z= 0.126 Angle : 0.626 17.809 41326 Z= 0.319 Chirality : 0.046 0.544 4839 Planarity : 0.005 0.178 5225 Dihedral : 5.940 58.119 5223 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.79 % Favored : 94.15 % Rotamer: Outliers : 1.25 % Allowed : 12.46 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.14), residues: 3627 helix: 1.97 (0.20), residues: 673 sheet: 0.12 (0.16), residues: 958 loop : -1.07 (0.14), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 18 TYR 0.031 0.002 TYR B 380 PHE 0.018 0.001 PHE B 392 TRP 0.022 0.002 TRP H 103 HIS 0.005 0.001 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00278 (30210) covalent geometry : angle 0.60082 (41082) SS BOND : bond 0.00536 ( 36) SS BOND : angle 1.65089 ( 70) hydrogen bonds : bond 0.03954 ( 1133) hydrogen bonds : angle 5.54727 ( 3099) link_BETA1-4 : bond 0.00426 ( 15) link_BETA1-4 : angle 1.13650 ( 45) link_NAG-ASN : bond 0.00562 ( 43) link_NAG-ASN : angle 2.93316 ( 129) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8909 (m-80) cc_final: 0.8419 (m-80) REVERT: A 855 PHE cc_start: 0.7095 (m-80) cc_final: 0.6430 (m-80) REVERT: A 1017 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8650 (tm-30) REVERT: B 81 ASN cc_start: 0.8593 (p0) cc_final: 0.8114 (p0) REVERT: B 346 ARG cc_start: 0.9181 (mtp-110) cc_final: 0.8735 (tmm-80) REVERT: B 380 TYR cc_start: 0.7445 (m-10) cc_final: 0.7195 (m-10) REVERT: B 386 LYS cc_start: 0.9344 (mmtt) cc_final: 0.9003 (ttpp) REVERT: B 483 VAL cc_start: 0.5228 (OUTLIER) cc_final: 0.4804 (p) REVERT: C 200 TYR cc_start: 0.7934 (m-80) cc_final: 0.7460 (t80) REVERT: C 406 GLU cc_start: 0.9018 (mp0) cc_final: 0.8411 (mp0) REVERT: C 453 TYR cc_start: 0.8528 (p90) cc_final: 0.7815 (p90) REVERT: C 547 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8613 (p) REVERT: C 740 MET cc_start: 0.8754 (mmm) cc_final: 0.8016 (tmm) REVERT: H 34 MET cc_start: 0.6861 (mmm) cc_final: 0.6428 (mmp) REVERT: H 75 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8666 (mtmm) REVERT: H 76 ASN cc_start: 0.9206 (m-40) cc_final: 0.8980 (t0) REVERT: H 79 TYR cc_start: 0.8978 (m-80) cc_final: 0.8708 (m-80) REVERT: H 91 TYR cc_start: 0.7004 (m-10) cc_final: 0.6729 (m-10) REVERT: H 101 ASP cc_start: 0.4260 (p0) cc_final: 0.3761 (p0) REVERT: L 3 GLN cc_start: 0.8110 (tp40) cc_final: 0.7773 (mp10) REVERT: L 34 ASN cc_start: 0.8097 (m-40) cc_final: 0.7718 (m110) REVERT: L 37 GLN cc_start: 0.7940 (tt0) cc_final: 0.7561 (tt0) REVERT: L 47 LEU cc_start: 0.8376 (mt) cc_final: 0.8146 (pp) REVERT: L 61 ARG cc_start: 0.7279 (ptt-90) cc_final: 0.6716 (ptt-90) REVERT: L 79 GLN cc_start: 0.7206 (mp10) cc_final: 0.6896 (mp10) REVERT: L 92 TYR cc_start: 0.8237 (t80) cc_final: 0.7917 (t80) REVERT: M 91 TYR cc_start: 0.6952 (OUTLIER) cc_final: 0.6636 (m-80) REVERT: N 35 TRP cc_start: 0.3962 (m100) cc_final: 0.3270 (m100) REVERT: N 39 LYS cc_start: 0.7193 (mmpt) cc_final: 0.6469 (tmtt) REVERT: N 105 GLU cc_start: 0.6820 (mt-10) cc_final: 0.6494 (tt0) REVERT: O 19 ARG cc_start: 0.7420 (ttp-170) cc_final: 0.6704 (tpt170) REVERT: O 34 MET cc_start: 0.8052 (mmp) cc_final: 0.7289 (mmm) REVERT: P 32 TYR cc_start: 0.5855 (m-80) cc_final: 0.5071 (m-10) outliers start: 40 outliers final: 23 residues processed: 246 average time/residue: 0.1904 time to fit residues: 75.2612 Evaluate side-chains 216 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 190 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 166 CYS Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 505 TYR Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 207 optimal weight: 0.0370 chunk 232 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 211 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 122 optimal weight: 0.7980 chunk 231 optimal weight: 1.9990 chunk 209 optimal weight: 3.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 907 ASN ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN H 81 GLN ** L 100 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 = 0.3989 r_free = 0.3989 target = 0.108735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071258 restraints weight = 76402.259| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 3.85 r_work: 0.3119 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30304 Z= 0.152 Angle : 0.624 18.299 41326 Z= 0.315 Chirality : 0.046 0.523 4839 Planarity : 0.004 0.061 5225 Dihedral : 5.764 59.908 5223 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.09 % Favored : 93.85 % Rotamer: Outliers : 1.75 % Allowed : 12.77 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3627 helix: 2.11 (0.20), residues: 673 sheet: 0.12 (0.16), residues: 965 loop : -1.03 (0.14), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 403 TYR 0.029 0.002 TYR A 453 PHE 0.020 0.001 PHE P 71 TRP 0.030 0.001 TRP H 47 HIS 0.008 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00347 (30210) covalent geometry : angle 0.59933 (41082) SS BOND : bond 0.00448 ( 36) SS BOND : angle 1.60965 ( 70) hydrogen bonds : bond 0.03864 ( 1133) hydrogen bonds : angle 5.40117 ( 3099) link_BETA1-4 : bond 0.00330 ( 15) link_BETA1-4 : angle 1.10553 ( 45) link_NAG-ASN : bond 0.00553 ( 43) link_NAG-ASN : angle 2.90629 ( 129) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 208 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8910 (m-80) cc_final: 0.8437 (m-80) REVERT: B 81 ASN cc_start: 0.8595 (p0) cc_final: 0.8096 (p0) REVERT: B 346 ARG cc_start: 0.9173 (mtp-110) cc_final: 0.8728 (tmm-80) REVERT: B 370 ASN cc_start: 0.8976 (m-40) cc_final: 0.8256 (p0) REVERT: C 200 TYR cc_start: 0.7956 (m-80) cc_final: 0.7577 (t80) REVERT: C 406 GLU cc_start: 0.9051 (mp0) cc_final: 0.8458 (mp0) REVERT: C 453 TYR cc_start: 0.8528 (p90) cc_final: 0.7739 (p90) REVERT: H 32 TYR cc_start: 0.6764 (m-10) cc_final: 0.6438 (m-10) REVERT: H 34 MET cc_start: 0.6772 (mmm) cc_final: 0.6295 (mmp) REVERT: H 64 LYS cc_start: 0.8582 (mttp) cc_final: 0.8242 (tptp) REVERT: H 75 LYS cc_start: 0.8978 (mtpp) cc_final: 0.8608 (mtmm) REVERT: H 79 TYR cc_start: 0.9037 (m-80) cc_final: 0.8660 (m-80) REVERT: H 91 TYR cc_start: 0.7023 (m-10) cc_final: 0.6675 (m-10) REVERT: H 101 ASP cc_start: 0.4280 (p0) cc_final: 0.3733 (p0) REVERT: L 3 GLN cc_start: 0.8157 (tp40) cc_final: 0.7812 (mp10) REVERT: L 34 ASN cc_start: 0.8130 (m-40) cc_final: 0.7807 (m110) REVERT: L 37 GLN cc_start: 0.7983 (tt0) cc_final: 0.7604 (tt0) REVERT: L 47 LEU cc_start: 0.8414 (mt) cc_final: 0.8211 (pp) REVERT: L 79 GLN cc_start: 0.7361 (mp10) cc_final: 0.7091 (mp10) REVERT: L 96 ARG cc_start: 0.7877 (mmt90) cc_final: 0.6673 (mmm-85) REVERT: M 91 TYR cc_start: 0.6837 (OUTLIER) cc_final: 0.6527 (m-80) REVERT: N 35 TRP cc_start: 0.4017 (m100) cc_final: 0.3505 (m100) REVERT: N 39 LYS cc_start: 0.7297 (mmpt) cc_final: 0.6575 (tmtt) REVERT: N 105 GLU cc_start: 0.6807 (mt-10) cc_final: 0.6493 (tt0) REVERT: O 19 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.6780 (tpp-160) REVERT: O 67 PHE cc_start: 0.0339 (m-80) cc_final: 0.0119 (m-80) REVERT: P 32 TYR cc_start: 0.6067 (m-80) cc_final: 0.5195 (m-10) outliers start: 56 outliers final: 32 residues processed: 256 average time/residue: 0.1915 time to fit residues: 79.2346 Evaluate side-chains 222 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 102 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 332 optimal weight: 0.9990 chunk 243 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 264 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 288 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 907 ASN L 100 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.109721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.071357 restraints weight = 76661.023| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.36 r_work: 0.3156 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.3276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.109 30304 Z= 0.144 Angle : 0.627 17.842 41326 Z= 0.318 Chirality : 0.046 0.523 4839 Planarity : 0.004 0.058 5225 Dihedral : 5.647 59.271 5223 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.90 % Favored : 94.04 % Rotamer: Outliers : 1.53 % Allowed : 13.52 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3627 helix: 2.16 (0.20), residues: 678 sheet: 0.09 (0.16), residues: 976 loop : -1.00 (0.14), residues: 1973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 18 TYR 0.030 0.001 TYR A 453 PHE 0.018 0.001 PHE A 400 TRP 0.038 0.001 TRP H 47 HIS 0.008 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00327 (30210) covalent geometry : angle 0.59951 (41082) SS BOND : bond 0.00588 ( 36) SS BOND : angle 2.39893 ( 70) hydrogen bonds : bond 0.03751 ( 1133) hydrogen bonds : angle 5.32122 ( 3099) link_BETA1-4 : bond 0.00365 ( 15) link_BETA1-4 : angle 1.09647 ( 45) link_NAG-ASN : bond 0.00528 ( 43) link_NAG-ASN : angle 2.80117 ( 129) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 211 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8918 (m-80) cc_final: 0.8449 (m-80) REVERT: A 740 MET cc_start: 0.8679 (OUTLIER) cc_final: 0.8313 (mtt) REVERT: A 760 CYS cc_start: 0.5376 (OUTLIER) cc_final: 0.5119 (t) REVERT: B 81 ASN cc_start: 0.8562 (p0) cc_final: 0.8056 (p0) REVERT: B 346 ARG cc_start: 0.9164 (mtp-110) cc_final: 0.8716 (tmm-80) REVERT: B 370 ASN cc_start: 0.8979 (m-40) cc_final: 0.8271 (p0) REVERT: C 200 TYR cc_start: 0.7937 (m-80) cc_final: 0.7598 (t80) REVERT: C 406 GLU cc_start: 0.9050 (mp0) cc_final: 0.8472 (mp0) REVERT: C 453 TYR cc_start: 0.8518 (p90) cc_final: 0.7697 (p90) REVERT: H 34 MET cc_start: 0.6814 (mmm) cc_final: 0.6318 (mmp) REVERT: H 46 GLU cc_start: 0.7710 (tp30) cc_final: 0.7471 (tt0) REVERT: H 64 LYS cc_start: 0.8578 (mttp) cc_final: 0.8258 (tptp) REVERT: H 75 LYS cc_start: 0.9011 (mtpp) cc_final: 0.8619 (mtmm) REVERT: H 79 TYR cc_start: 0.9008 (m-80) cc_final: 0.8611 (m-80) REVERT: H 101 ASP cc_start: 0.4320 (p0) cc_final: 0.3783 (p0) REVERT: L 3 GLN cc_start: 0.8107 (tp40) cc_final: 0.7778 (mp10) REVERT: L 34 ASN cc_start: 0.8085 (m-40) cc_final: 0.7742 (m110) REVERT: L 37 GLN cc_start: 0.7903 (tt0) cc_final: 0.7577 (tt0) REVERT: L 47 LEU cc_start: 0.8450 (mt) cc_final: 0.8244 (pp) REVERT: L 96 ARG cc_start: 0.7933 (mmt90) cc_final: 0.7075 (mmm-85) REVERT: M 82 MET cc_start: 0.3751 (mmp) cc_final: 0.2563 (tpp) REVERT: M 91 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6515 (m-80) REVERT: N 35 TRP cc_start: 0.3997 (m100) cc_final: 0.3336 (m100) REVERT: N 39 LYS cc_start: 0.7290 (mmpt) cc_final: 0.6572 (tmtt) REVERT: N 105 GLU cc_start: 0.6886 (mt-10) cc_final: 0.6492 (tt0) REVERT: O 3 GLN cc_start: 0.7486 (mp10) cc_final: 0.6752 (pt0) REVERT: O 19 ARG cc_start: 0.7466 (ttp-170) cc_final: 0.6870 (tpp-160) outliers start: 49 outliers final: 35 residues processed: 248 average time/residue: 0.2085 time to fit residues: 81.2773 Evaluate side-chains 227 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 760 CYS Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 102 TYR Chi-restraints excluded: chain P residue 47 LEU Chi-restraints excluded: chain P residue 96 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 54 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 331 optimal weight: 20.0000 chunk 209 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 349 optimal weight: 6.9990 chunk 257 optimal weight: 0.6980 chunk 83 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.4013 r_free = 0.4013 target = 0.109607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071204 restraints weight = 76763.884| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 3.36 r_work: 0.3113 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.3349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 30304 Z= 0.197 Angle : 0.638 18.180 41326 Z= 0.323 Chirality : 0.046 0.514 4839 Planarity : 0.004 0.054 5225 Dihedral : 5.675 58.748 5223 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.26 % Favored : 93.69 % Rotamer: Outliers : 1.66 % Allowed : 14.08 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3627 helix: 2.13 (0.20), residues: 673 sheet: 0.11 (0.16), residues: 971 loop : -1.04 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 18 TYR 0.026 0.001 TYR A 453 PHE 0.020 0.002 PHE A 168 TRP 0.029 0.001 TRP H 47 HIS 0.005 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00458 (30210) covalent geometry : angle 0.61544 (41082) SS BOND : bond 0.00429 ( 36) SS BOND : angle 1.57130 ( 70) hydrogen bonds : bond 0.03915 ( 1133) hydrogen bonds : angle 5.35403 ( 3099) link_BETA1-4 : bond 0.00292 ( 15) link_BETA1-4 : angle 1.10281 ( 45) link_NAG-ASN : bond 0.00546 ( 43) link_NAG-ASN : angle 2.83903 ( 129) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 200 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8948 (m-80) cc_final: 0.8517 (m-80) REVERT: B 81 ASN cc_start: 0.8587 (p0) cc_final: 0.8067 (p0) REVERT: B 346 ARG cc_start: 0.9171 (mtp-110) cc_final: 0.8763 (tmm-80) REVERT: C 200 TYR cc_start: 0.7945 (m-80) cc_final: 0.7578 (t80) REVERT: C 406 GLU cc_start: 0.9043 (mp0) cc_final: 0.8490 (mp0) REVERT: C 453 TYR cc_start: 0.8549 (p90) cc_final: 0.7694 (p90) REVERT: H 34 MET cc_start: 0.6904 (mmm) cc_final: 0.6394 (mmp) REVERT: H 64 LYS cc_start: 0.8575 (mttp) cc_final: 0.8282 (tptp) REVERT: H 79 TYR cc_start: 0.9018 (m-80) cc_final: 0.8602 (m-80) REVERT: H 101 ASP cc_start: 0.4325 (p0) cc_final: 0.3759 (p0) REVERT: L 3 GLN cc_start: 0.8134 (tp40) cc_final: 0.7805 (mp10) REVERT: L 34 ASN cc_start: 0.8198 (m-40) cc_final: 0.7857 (m110) REVERT: L 37 GLN cc_start: 0.7903 (tt0) cc_final: 0.7589 (tt0) REVERT: L 47 LEU cc_start: 0.8465 (mt) cc_final: 0.8216 (pp) REVERT: L 96 ARG cc_start: 0.7978 (mmt90) cc_final: 0.7207 (mmm-85) REVERT: M 91 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.6492 (m-80) REVERT: N 32 TYR cc_start: 0.6339 (m-10) cc_final: 0.6074 (m-10) REVERT: N 35 TRP cc_start: 0.4052 (m100) cc_final: 0.3653 (m100) REVERT: N 39 LYS cc_start: 0.7323 (mmpt) cc_final: 0.6616 (tmtt) REVERT: N 88 CYS cc_start: 0.4229 (OUTLIER) cc_final: 0.3889 (m) REVERT: N 105 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6534 (tt0) REVERT: O 3 GLN cc_start: 0.7393 (mp10) cc_final: 0.6711 (pt0) REVERT: O 19 ARG cc_start: 0.7450 (ttp-170) cc_final: 0.6698 (tpt170) REVERT: O 28 THR cc_start: 0.8392 (p) cc_final: 0.8162 (p) REVERT: O 67 PHE cc_start: 0.0590 (m-80) cc_final: -0.0131 (t80) REVERT: P 3 GLN cc_start: 0.7735 (mm110) cc_final: 0.7435 (mm-40) outliers start: 53 outliers final: 43 residues processed: 244 average time/residue: 0.1962 time to fit residues: 76.8000 Evaluate side-chains 235 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 190 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 442 ASP Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 24 ARG Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain N residue 88 CYS Chi-restraints excluded: chain O residue 102 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 101 optimal weight: 0.7980 chunk 251 optimal weight: 6.9990 chunk 280 optimal weight: 0.7980 chunk 63 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 365 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 242 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 175 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN ** N 34 ASN ** 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 = 0.4024 r_free = 0.4024 target = 0.111940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.072566 restraints weight = 77028.515| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 3.36 r_work: 0.3124 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30304 Z= 0.167 Angle : 0.624 17.807 41326 Z= 0.316 Chirality : 0.046 0.519 4839 Planarity : 0.004 0.067 5225 Dihedral : 5.602 58.486 5223 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.96 % Favored : 93.99 % Rotamer: Outliers : 1.50 % Allowed : 14.43 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3627 helix: 2.14 (0.20), residues: 678 sheet: 0.14 (0.16), residues: 992 loop : -1.01 (0.14), residues: 1957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 18 TYR 0.025 0.001 TYR A 453 PHE 0.016 0.001 PHE A 400 TRP 0.029 0.001 TRP H 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00386 (30210) covalent geometry : angle 0.60073 (41082) SS BOND : bond 0.00459 ( 36) SS BOND : angle 1.69502 ( 70) hydrogen bonds : bond 0.03803 ( 1133) hydrogen bonds : angle 5.29127 ( 3099) link_BETA1-4 : bond 0.00353 ( 15) link_BETA1-4 : angle 1.10058 ( 45) link_NAG-ASN : bond 0.00523 ( 43) link_NAG-ASN : angle 2.77887 ( 129) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 200 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8972 (m-80) cc_final: 0.8548 (m-80) REVERT: B 81 ASN cc_start: 0.8573 (p0) cc_final: 0.8045 (p0) REVERT: B 346 ARG cc_start: 0.9138 (mtp-110) cc_final: 0.8772 (tmm-80) REVERT: B 370 ASN cc_start: 0.8973 (m-40) cc_final: 0.8252 (p0) REVERT: B 380 TYR cc_start: 0.7900 (m-10) cc_final: 0.7481 (m-10) REVERT: B 988 GLU cc_start: 0.8705 (mp0) cc_final: 0.8368 (mp0) REVERT: C 200 TYR cc_start: 0.7945 (m-80) cc_final: 0.7603 (t80) REVERT: C 406 GLU cc_start: 0.9032 (mp0) cc_final: 0.8492 (mp0) REVERT: C 453 TYR cc_start: 0.8549 (p90) cc_final: 0.7767 (p90) REVERT: H 34 MET cc_start: 0.6843 (mmm) cc_final: 0.6322 (mmp) REVERT: H 46 GLU cc_start: 0.7794 (tp30) cc_final: 0.7575 (tt0) REVERT: H 64 LYS cc_start: 0.8591 (mttp) cc_final: 0.8289 (tptp) REVERT: H 79 TYR cc_start: 0.8964 (m-80) cc_final: 0.8487 (m-80) REVERT: H 101 ASP cc_start: 0.4524 (p0) cc_final: 0.3942 (p0) REVERT: L 3 GLN cc_start: 0.8186 (tp40) cc_final: 0.7857 (mp10) REVERT: L 34 ASN cc_start: 0.8217 (m-40) cc_final: 0.7939 (m-40) REVERT: L 37 GLN cc_start: 0.7890 (tt0) cc_final: 0.7553 (tt0) REVERT: M 82 MET cc_start: 0.3819 (mmp) cc_final: 0.2646 (tpp) REVERT: M 91 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.6456 (m-80) REVERT: N 35 TRP cc_start: 0.4049 (m100) cc_final: 0.3457 (m100) REVERT: N 39 LYS cc_start: 0.7279 (mmpt) cc_final: 0.6575 (tmtt) REVERT: N 105 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6502 (tt0) REVERT: O 3 GLN cc_start: 0.7386 (mp10) cc_final: 0.6715 (pt0) REVERT: O 19 ARG cc_start: 0.7427 (ttp-170) cc_final: 0.6679 (tpt170) REVERT: O 28 THR cc_start: 0.8408 (p) cc_final: 0.8158 (p) REVERT: O 58 TYR cc_start: 0.5896 (t80) cc_final: 0.5584 (t80) REVERT: O 67 PHE cc_start: 0.0742 (m-80) cc_final: -0.0028 (t80) REVERT: P 3 GLN cc_start: 0.7649 (mm110) cc_final: 0.7336 (mm-40) REVERT: P 32 TYR cc_start: 0.5849 (m-10) cc_final: 0.5018 (m-80) outliers start: 48 outliers final: 40 residues processed: 237 average time/residue: 0.1940 time to fit residues: 73.7552 Evaluate side-chains 233 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 192 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain O residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 15 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 chunk 197 optimal weight: 3.9990 chunk 316 optimal weight: 6.9990 chunk 139 optimal weight: 0.6980 chunk 358 optimal weight: 6.9990 chunk 172 optimal weight: 2.9990 chunk 328 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 352 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.4007 r_free = 0.4007 target = 0.110638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.071634 restraints weight = 77094.401| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.40 r_work: 0.3127 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30304 Z= 0.154 Angle : 0.628 17.677 41326 Z= 0.315 Chirality : 0.046 0.516 4839 Planarity : 0.004 0.057 5225 Dihedral : 5.501 57.983 5223 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.15 % Favored : 93.80 % Rotamer: Outliers : 1.50 % Allowed : 14.65 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3627 helix: 2.21 (0.20), residues: 675 sheet: 0.12 (0.16), residues: 1018 loop : -1.01 (0.14), residues: 1934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 18 TYR 0.030 0.001 TYR A 453 PHE 0.021 0.001 PHE A 168 TRP 0.028 0.002 TRP H 47 HIS 0.004 0.001 HIS A1048 Details of bonding type rmsd covalent geometry : bond 0.00353 (30210) covalent geometry : angle 0.60525 (41082) SS BOND : bond 0.00398 ( 36) SS BOND : angle 1.73051 ( 70) hydrogen bonds : bond 0.03700 ( 1133) hydrogen bonds : angle 5.23843 ( 3099) link_BETA1-4 : bond 0.00281 ( 15) link_BETA1-4 : angle 1.09197 ( 45) link_NAG-ASN : bond 0.00511 ( 43) link_NAG-ASN : angle 2.74045 ( 129) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7254 Ramachandran restraints generated. 3627 Oldfield, 0 Emsley, 3627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 196 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 421 TYR cc_start: 0.8957 (m-80) cc_final: 0.8555 (m-80) REVERT: A 988 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8353 (pm20) REVERT: B 81 ASN cc_start: 0.8568 (p0) cc_final: 0.8045 (p0) REVERT: B 346 ARG cc_start: 0.9134 (mtp-110) cc_final: 0.8763 (tmm-80) REVERT: B 370 ASN cc_start: 0.8984 (m-40) cc_final: 0.8269 (p0) REVERT: B 380 TYR cc_start: 0.7870 (m-10) cc_final: 0.7503 (m-10) REVERT: B 988 GLU cc_start: 0.8743 (mp0) cc_final: 0.8418 (mp0) REVERT: C 200 TYR cc_start: 0.7958 (m-80) cc_final: 0.7602 (t80) REVERT: C 406 GLU cc_start: 0.9045 (mp0) cc_final: 0.8502 (mp0) REVERT: C 453 TYR cc_start: 0.8547 (p90) cc_final: 0.7762 (p90) REVERT: H 34 MET cc_start: 0.6810 (mmm) cc_final: 0.6469 (mmm) REVERT: H 46 GLU cc_start: 0.7793 (tp30) cc_final: 0.7577 (tt0) REVERT: H 64 LYS cc_start: 0.8612 (mttp) cc_final: 0.8298 (tptp) REVERT: H 79 TYR cc_start: 0.8973 (m-80) cc_final: 0.8466 (m-80) REVERT: H 101 ASP cc_start: 0.4217 (p0) cc_final: 0.3625 (p0) REVERT: L 3 GLN cc_start: 0.8171 (tp40) cc_final: 0.7836 (mp10) REVERT: L 34 ASN cc_start: 0.8120 (m-40) cc_final: 0.7695 (m110) REVERT: L 37 GLN cc_start: 0.7907 (tt0) cc_final: 0.7582 (tt0) REVERT: L 96 ARG cc_start: 0.8367 (mmt90) cc_final: 0.7381 (mmm-85) REVERT: M 82 MET cc_start: 0.3910 (mmp) cc_final: 0.2757 (tpp) REVERT: M 91 TYR cc_start: 0.6867 (OUTLIER) cc_final: 0.6504 (m-80) REVERT: N 35 TRP cc_start: 0.4082 (m100) cc_final: 0.3428 (m100) REVERT: N 39 LYS cc_start: 0.7281 (OUTLIER) cc_final: 0.6568 (tmtt) REVERT: N 105 GLU cc_start: 0.6921 (mt-10) cc_final: 0.6517 (tt0) REVERT: O 19 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.6706 (tpt170) REVERT: O 28 THR cc_start: 0.8397 (p) cc_final: 0.8090 (p) REVERT: O 34 MET cc_start: 0.7571 (mmp) cc_final: 0.7359 (mmm) REVERT: O 67 PHE cc_start: 0.0569 (m-80) cc_final: -0.0244 (t80) REVERT: P 3 GLN cc_start: 0.7654 (mm110) cc_final: 0.7344 (mm-40) REVERT: P 92 TYR cc_start: 0.7458 (t80) cc_final: 0.7234 (t80) outliers start: 48 outliers final: 40 residues processed: 234 average time/residue: 0.1930 time to fit residues: 72.6133 Evaluate side-chains 232 residues out of total 3216 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 189 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 473 TYR Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 988 GLU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 873 TYR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 304 LYS Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 429 PHE Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 584 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 91 TYR Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain M residue 100 VAL Chi-restraints excluded: chain N residue 39 LYS Chi-restraints excluded: chain N residue 71 PHE Chi-restraints excluded: chain O residue 35 HIS Chi-restraints excluded: chain O residue 102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 270 optimal weight: 0.4980 chunk 313 optimal weight: 2.9990 chunk 280 optimal weight: 1.9990 chunk 220 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 chunk 296 optimal weight: 0.0980 chunk 158 optimal weight: 0.0970 chunk 262 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 125 ASN ** B 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 992 GLN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** 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 = 0.4008 r_free = 0.4008 target = 0.110089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.073341 restraints weight = 76706.292| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.94 r_work: 0.3128 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 30304 Z= 0.107 Angle : 0.598 16.892 41326 Z= 0.302 Chirality : 0.045 0.512 4839 Planarity : 0.004 0.083 5225 Dihedral : 5.231 59.374 5223 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.87 % Favored : 94.07 % Rotamer: Outliers : 1.16 % Allowed : 15.24 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.14), residues: 3627 helix: 2.40 (0.20), residues: 674 sheet: 0.19 (0.16), residues: 975 loop : -0.98 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG B 214 TYR 0.030 0.001 TYR A 453 PHE 0.017 0.001 PHE O 27 TRP 0.024 0.002 TRP H 47 HIS 0.011 0.001 HIS M 35 Details of bonding type rmsd covalent geometry : bond 0.00235 (30210) covalent geometry : angle 0.57797 (41082) SS BOND : bond 0.00329 ( 36) SS BOND : angle 1.38527 ( 70) hydrogen bonds : bond 0.03367 ( 1133) hydrogen bonds : angle 5.00981 ( 3099) link_BETA1-4 : bond 0.00387 ( 15) link_BETA1-4 : angle 1.05977 ( 45) link_NAG-ASN : bond 0.00516 ( 43) link_NAG-ASN : angle 2.60742 ( 129) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7592.58 seconds wall clock time: 130 minutes 56.50 seconds (7856.50 seconds total)