Starting phenix.real_space_refine on Fri Mar 6 09:33:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k8s_22729/03_2026/7k8s_22729_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k8s_22729/03_2026/7k8s_22729.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/7k8s_22729/03_2026/7k8s_22729.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k8s_22729/03_2026/7k8s_22729.map" model { file = "/net/cci-nas-00/data/ceres_data/7k8s_22729/03_2026/7k8s_22729_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k8s_22729/03_2026/7k8s_22729_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= 0.017 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 123 5.16 5 C 18837 2.51 5 N 4875 2.21 5 O 5814 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.03s 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: 29649 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 7 Chain: "B" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 7 Chain: "C" Number of atoms: 7845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1004, 7845 Classifications: {'peptide': 1004} Link IDs: {'PTRANS': 49, 'TRANS': 954} Chain breaks: 7 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: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 6.97, per 1000 atoms: 0.24 Number of scatterers: 29649 At special positions: 0 Unit cell: (137.104, 139.612, 205.656, 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 123 16.00 O 5814 8.00 N 4875 7.00 C 18837 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, 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=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 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=2.02 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=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.02 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 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=2.04 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=2.04 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=2.04 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 603 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 657 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B1074 " " NAG B1309 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 122 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 603 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " 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: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 56 sheets defined 22.5% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.791A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.909A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.581A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.582A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 756 removed outlier: 3.546A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.575A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.677A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.379A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.602A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR A 941 " --> pdb=" O SER A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.596A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.742A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.801A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1129 removed outlier: 3.808A pdb=" N VAL A1128 " --> pdb=" O ASN A1125 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 3.979A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.516A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.893A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.556A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.145A pdb=" N ASN B 388 " --> 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 422 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 756 removed outlier: 3.598A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.508A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.502A pdb=" N LEU B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.377A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.629A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.600A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.805A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 5.095A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1129 removed outlier: 3.793A pdb=" N VAL B1128 " --> pdb=" O ASN B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 4.113A 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 removed outlier: 3.895A pdb=" N VAL C 341 " --> pdb=" O PRO C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 353 removed outlier: 3.939A pdb=" N TRP C 353 " --> pdb=" O VAL C 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.771A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.976A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 408 removed outlier: 4.361A pdb=" N ARG C 408 " --> pdb=" O GLY C 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 404 through 408' Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.774A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.506A pdb=" N LEU C 767 " --> pdb=" O LEU C 763 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.595A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.574A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.542A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.627A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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: 3.560A pdb=" N LEU C 984 " --> pdb=" O ILE C 980 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.795A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.055A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'M' and resid 28 through 32 Processing helix chain 'M' and resid 83 through 87 Processing helix chain 'O' and resid 28 through 32 Processing helix chain 'O' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 4.289A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 94 " --> pdb=" O ARG A 190 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 208 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 4.047A 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: 6.933A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.887A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.164A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 326 removed outlier: 4.379A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.101A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.333A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.681A pdb=" N LYS C 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 713 Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.936A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.757A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1123 removed outlier: 3.861A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.227A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 4.227A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 48 through 55 removed outlier: 4.027A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.868A pdb=" N LEU B 141 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.951A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 311 through 317 removed outlier: 5.164A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.162A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 324 through 326 removed outlier: 6.666A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.639A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR B 508 " --> pdb=" O ILE B 402 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 361 through 362 removed outlier: 3.664A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 448 through 452 removed outlier: 5.795A pdb=" N TYR B 449 " --> pdb=" O PHE B 497 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N PHE B 497 " --> pdb=" O TYR B 449 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N TYR B 451 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.328A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.624A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.021A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'B' and resid 788 through 790 removed outlier: 5.651A pdb=" N ILE B 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1123 removed outlier: 3.725A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.518A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 52 removed outlier: 3.993A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.688A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 7.023A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.239A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.610A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE C 358 " --> pdb=" O VAL C 395 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE3, first strand: chain 'C' and resid 538 through 540 removed outlier: 4.992A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.040A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 715 Processing sheet with id=AE6, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.919A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1123 removed outlier: 3.647A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF1, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.253A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 5 through 7 Processing sheet with id=AF3, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.609A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.857A pdb=" N MET M 34 " --> pdb=" O VAL M 50 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'N' and resid 4 through 7 Processing sheet with id=AF7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.577A pdb=" N LEU N 33 " --> pdb=" O TYR N 49 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N TYR N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AF9, first strand: chain 'O' and resid 10 through 12 removed outlier: 6.809A pdb=" N MET O 34 " --> pdb=" O VAL O 50 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL O 50 " --> pdb=" O MET O 34 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 5 through 7 Processing sheet with id=AG2, first strand: chain 'P' and resid 10 through 13 removed outlier: 6.682A pdb=" N LEU P 33 " --> pdb=" O TYR P 49 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR P 49 " --> pdb=" O LEU P 33 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP P 35 " --> pdb=" O LEU P 47 " (cutoff:3.500A) 1155 hydrogen bonds defined for protein. 3126 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: 7.68 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 9273 1.34 - 1.46: 7817 1.46 - 1.59: 13051 1.59 - 1.72: 0 1.72 - 1.85: 153 Bond restraints: 30294 Sorted by residual: bond pdb=" C ALA B 67 " pdb=" N ILE B 68 " ideal model delta sigma weight residual 1.331 1.424 -0.092 1.20e-02 6.94e+03 5.91e+01 bond pdb=" N ILE A 472 " pdb=" CA ILE A 472 " ideal model delta sigma weight residual 1.459 1.508 -0.049 1.25e-02 6.40e+03 1.54e+01 bond pdb=" N ILE C 472 " pdb=" CA ILE C 472 " ideal model delta sigma weight residual 1.459 1.503 -0.044 1.25e-02 6.40e+03 1.23e+01 bond pdb=" N VAL C 445 " pdb=" CA VAL C 445 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.25e-02 6.40e+03 1.20e+01 bond pdb=" N ILE B 68 " pdb=" CA ILE B 68 " ideal model delta sigma weight residual 1.455 1.495 -0.039 1.18e-02 7.18e+03 1.10e+01 ... (remaining 30289 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 39268 1.93 - 3.86: 1664 3.86 - 5.79: 211 5.79 - 7.73: 41 7.73 - 9.66: 9 Bond angle restraints: 41193 Sorted by residual: angle pdb=" CA GLY C 548 " pdb=" C GLY C 548 " pdb=" O GLY C 548 " ideal model delta sigma weight residual 122.23 118.28 3.95 6.90e-01 2.10e+00 3.28e+01 angle pdb=" CA GLU A 471 " pdb=" C GLU A 471 " pdb=" O GLU A 471 " ideal model delta sigma weight residual 120.82 114.96 5.86 1.05e+00 9.07e-01 3.11e+01 angle pdb=" CA GLY B 548 " pdb=" C GLY B 548 " pdb=" O GLY B 548 " ideal model delta sigma weight residual 122.37 118.34 4.03 7.30e-01 1.88e+00 3.04e+01 angle pdb=" CA GLY A 548 " pdb=" C GLY A 548 " pdb=" O GLY A 548 " ideal model delta sigma weight residual 122.37 118.42 3.95 7.30e-01 1.88e+00 2.93e+01 angle pdb=" CA LYS C 444 " pdb=" C LYS C 444 " pdb=" O LYS C 444 " ideal model delta sigma weight residual 120.82 115.39 5.43 1.05e+00 9.07e-01 2.67e+01 ... (remaining 41188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 17140 17.97 - 35.93: 1270 35.93 - 53.90: 248 53.90 - 71.87: 64 71.87 - 89.84: 28 Dihedral angle restraints: 18750 sinusoidal: 7989 harmonic: 10761 Sorted by residual: dihedral pdb=" CA ILE H 100A" pdb=" C ILE H 100A" pdb=" N VAL H 100B" pdb=" CA VAL H 100B" ideal model delta harmonic sigma weight residual 180.00 128.27 51.73 0 5.00e+00 4.00e-02 1.07e+02 dihedral pdb=" CA ILE M 100A" pdb=" C ILE M 100A" pdb=" N VAL M 100B" pdb=" CA VAL M 100B" ideal model delta harmonic sigma weight residual 180.00 131.83 48.17 0 5.00e+00 4.00e-02 9.28e+01 dihedral pdb=" CB CYS A1032 " pdb=" SG CYS A1032 " pdb=" SG CYS A1043 " pdb=" CB CYS A1043 " ideal model delta sinusoidal sigma weight residual 93.00 179.83 -86.83 1 1.00e+01 1.00e-02 9.07e+01 ... (remaining 18747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.126: 4723 0.126 - 0.252: 102 0.252 - 0.379: 5 0.379 - 0.505: 4 0.505 - 0.631: 2 Chirality restraints: 4836 Sorted by residual: chirality pdb=" CB VAL C 445 " pdb=" CA VAL C 445 " pdb=" CG1 VAL C 445 " pdb=" CG2 VAL C 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.63 2.00e-01 2.50e+01 9.95e+00 chirality pdb=" CB VAL A 445 " pdb=" CA VAL A 445 " pdb=" CG1 VAL A 445 " pdb=" CG2 VAL A 445 " both_signs ideal model delta sigma weight residual False -2.63 -2.09 -0.54 2.00e-01 2.50e+01 7.40e+00 chirality pdb=" CA THR C 547 " pdb=" N THR C 547 " pdb=" C THR C 547 " pdb=" CB THR C 547 " both_signs ideal model delta sigma weight residual False 2.53 2.04 0.49 2.00e-01 2.50e+01 6.01e+00 ... (remaining 4833 not shown) Planarity restraints: 5286 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.009 2.00e-02 2.50e+03 5.17e-02 3.34e+01 pdb=" CG ASN B 234 " 0.066 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.061 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.053 2.00e-02 2.50e+03 pdb=" C1 NAG J 1 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 478 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO C 479 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 479 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO C 479 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 442 " -0.018 2.00e-02 2.50e+03 3.57e-02 1.27e+01 pdb=" C ASP B 442 " 0.062 2.00e-02 2.50e+03 pdb=" O ASP B 442 " -0.024 2.00e-02 2.50e+03 pdb=" N SER B 443 " -0.020 2.00e-02 2.50e+03 ... (remaining 5283 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 188 2.45 - 3.06: 21498 3.06 - 3.68: 44042 3.68 - 4.29: 65411 4.29 - 4.90: 107136 Nonbonded interactions: 238275 Sorted by model distance: nonbonded pdb=" CB HIS C 66 " pdb=" CE2 PHE C 79 " model vdw 1.841 3.740 nonbonded pdb=" NE2 GLN B 804 " pdb=" OE1 GLN B 935 " model vdw 1.970 3.120 nonbonded pdb=" OD1 ASP C 389 " pdb=" NZ LYS C 528 " model vdw 2.010 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.013 3.120 nonbonded pdb=" OG1 THR C 108 " pdb=" O ASN C 234 " model vdw 2.022 3.040 ... (remaining 238270 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain '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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.170 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 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 : 0.009 0.092 30390 Z= 0.397 Angle : 0.916 14.091 41442 Z= 0.515 Chirality : 0.056 0.631 4836 Planarity : 0.005 0.109 5244 Dihedral : 13.330 89.836 11721 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.69 % Favored : 93.01 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.97 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.34 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 3648 helix: 0.14 (0.19), residues: 665 sheet: -0.50 (0.16), residues: 903 loop : -1.46 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 466 TYR 0.029 0.002 TYR C 904 PHE 0.043 0.003 PHE A 906 TRP 0.050 0.003 TRP C 64 HIS 0.009 0.001 HIS C 66 Details of bonding type rmsd covalent geometry : bond 0.00855 (30294) covalent geometry : angle 0.89765 (41193) SS BOND : bond 0.00612 ( 39) SS BOND : angle 1.77704 ( 78) hydrogen bonds : bond 0.25549 ( 1138) hydrogen bonds : angle 9.97966 ( 3126) link_BETA1-4 : bond 0.00596 ( 15) link_BETA1-4 : angle 1.80248 ( 45) link_NAG-ASN : bond 0.00858 ( 42) link_NAG-ASN : angle 3.08345 ( 126) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 349 time to evaluate : 1.107 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 265 TYR cc_start: 0.8974 (p90) cc_final: 0.8724 (p90) REVERT: A 895 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7247 (pp30) REVERT: B 197 ILE cc_start: 0.9092 (tp) cc_final: 0.8890 (tp) REVERT: B 198 ASP cc_start: 0.8210 (p0) cc_final: 0.7878 (p0) REVERT: B 342 PHE cc_start: 0.8871 (m-80) cc_final: 0.8431 (m-80) REVERT: B 740 MET cc_start: 0.8372 (tpp) cc_final: 0.8084 (tpp) REVERT: B 1092 GLU cc_start: 0.8229 (mm-30) cc_final: 0.7989 (mm-30) REVERT: C 242 LEU cc_start: 0.8723 (mm) cc_final: 0.8419 (mm) REVERT: C 406 GLU cc_start: 0.9293 (mm-30) cc_final: 0.8943 (mp0) REVERT: C 529 LYS cc_start: 0.8929 (pptt) cc_final: 0.8587 (mmmt) REVERT: C 1072 GLU cc_start: 0.9095 (pm20) cc_final: 0.8756 (pm20) REVERT: C 1094 VAL cc_start: 0.8986 (t) cc_final: 0.8764 (m) REVERT: H 36 TRP cc_start: 0.7203 (m100) cc_final: 0.6896 (m100) REVERT: L 3 GLN cc_start: 0.8963 (mm110) cc_final: 0.8388 (mp10) REVERT: L 35 TRP cc_start: 0.9051 (m100) cc_final: 0.8497 (m100) REVERT: L 75 ILE cc_start: 0.8862 (mm) cc_final: 0.7972 (tp) REVERT: L 82 ASP cc_start: 0.7819 (m-30) cc_final: 0.7395 (m-30) REVERT: L 85 THR cc_start: 0.8823 (m) cc_final: 0.8549 (t) REVERT: L 96 ARG cc_start: 0.6090 (ptp-110) cc_final: 0.5811 (mmt90) REVERT: L 103 LYS cc_start: 0.9048 (ttpt) cc_final: 0.8617 (mtmm) REVERT: M 67 PHE cc_start: 0.8806 (m-10) cc_final: 0.8372 (m-10) REVERT: M 75 LYS cc_start: 0.9162 (tppt) cc_final: 0.8791 (tppt) REVERT: M 79 TYR cc_start: 0.7995 (m-80) cc_final: 0.7461 (m-80) REVERT: N 62 PHE cc_start: 0.8941 (m-80) cc_final: 0.8726 (m-80) REVERT: O 80 LEU cc_start: 0.4348 (tp) cc_final: 0.4137 (tp) REVERT: O 82 MET cc_start: 0.5950 (mpp) cc_final: 0.4949 (mpp) REVERT: O 100 PHE cc_start: 0.5527 (m-10) cc_final: 0.5228 (m-80) REVERT: P 35 TRP cc_start: 0.1662 (m100) cc_final: 0.1382 (m100) REVERT: P 97 THR cc_start: 0.5068 (m) cc_final: 0.4785 (p) outliers start: 11 outliers final: 1 residues processed: 359 average time/residue: 0.2163 time to fit residues: 120.7743 Evaluate side-chains 211 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 209 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 895 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.3980 chunk 298 optimal weight: 8.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 498 GLN A 675 GLN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 935 GLN A1036 GLN B 87 ASN B 474 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 804 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 955 ASN H 76 ASN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 39 GLN N 37 GLN N 38 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.105835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.062321 restraints weight = 74080.415| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 4.17 r_work: 0.2857 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 30390 Z= 0.174 Angle : 0.716 8.744 41442 Z= 0.379 Chirality : 0.048 0.229 4836 Planarity : 0.005 0.068 5244 Dihedral : 7.740 59.536 5183 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.65 % Favored : 94.24 % Rotamer: Outliers : 0.87 % Allowed : 6.99 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.85 (0.13), residues: 3648 helix: 1.57 (0.19), residues: 632 sheet: -0.43 (0.16), residues: 941 loop : -1.35 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG O 38 TYR 0.021 0.002 TYR O 102 PHE 0.021 0.002 PHE A 906 TRP 0.019 0.002 TRP M 103 HIS 0.010 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00379 (30294) covalent geometry : angle 0.70557 (41193) SS BOND : bond 0.00613 ( 39) SS BOND : angle 1.26526 ( 78) hydrogen bonds : bond 0.05430 ( 1138) hydrogen bonds : angle 6.79077 ( 3126) link_BETA1-4 : bond 0.00400 ( 15) link_BETA1-4 : angle 1.11211 ( 45) link_NAG-ASN : bond 0.00406 ( 42) link_NAG-ASN : angle 2.08983 ( 126) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 299 time to evaluate : 1.094 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 92 PHE cc_start: 0.8875 (t80) cc_final: 0.8649 (t80) REVERT: A 104 TRP cc_start: 0.8611 (m-90) cc_final: 0.8087 (m-90) REVERT: A 135 PHE cc_start: 0.6617 (m-80) cc_final: 0.6152 (m-80) REVERT: A 265 TYR cc_start: 0.8585 (p90) cc_final: 0.8196 (p90) REVERT: A 895 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.7520 (pp30) REVERT: A 950 ASP cc_start: 0.9146 (t70) cc_final: 0.8847 (t0) REVERT: B 101 ILE cc_start: 0.9020 (mt) cc_final: 0.8805 (tp) REVERT: B 197 ILE cc_start: 0.9304 (tp) cc_final: 0.9085 (tp) REVERT: B 342 PHE cc_start: 0.8905 (m-80) cc_final: 0.8411 (m-80) REVERT: B 508 TYR cc_start: 0.6848 (m-80) cc_final: 0.6600 (m-80) REVERT: B 568 ASP cc_start: 0.8622 (t0) cc_final: 0.8277 (t0) REVERT: B 855 PHE cc_start: 0.7349 (m-80) cc_final: 0.6936 (m-80) REVERT: B 1029 MET cc_start: 0.9006 (tpp) cc_final: 0.8474 (tpt) REVERT: B 1092 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8425 (mm-30) REVERT: C 95 THR cc_start: 0.9297 (p) cc_final: 0.9065 (t) REVERT: C 378 LYS cc_start: 0.8687 (mttt) cc_final: 0.8453 (tttt) REVERT: C 406 GLU cc_start: 0.9352 (mm-30) cc_final: 0.8852 (mp0) REVERT: C 529 LYS cc_start: 0.9027 (pptt) cc_final: 0.8599 (mmmt) REVERT: C 995 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8459 (mpp80) REVERT: C 1072 GLU cc_start: 0.9250 (pm20) cc_final: 0.8957 (pm20) REVERT: H 66 ARG cc_start: 0.7775 (ptp-110) cc_final: 0.7160 (ptt180) REVERT: H 67 PHE cc_start: 0.6625 (m-10) cc_final: 0.6050 (m-80) REVERT: H 82 MET cc_start: 0.8533 (mtm) cc_final: 0.7537 (ptp) REVERT: H 94 LYS cc_start: 0.8638 (tttm) cc_final: 0.8270 (tttm) REVERT: H 100 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8312 (tt) REVERT: L 3 GLN cc_start: 0.9079 (mm110) cc_final: 0.8636 (mp10) REVERT: L 35 TRP cc_start: 0.9180 (m100) cc_final: 0.8450 (m100) REVERT: L 45 LYS cc_start: 0.8931 (mmmm) cc_final: 0.8717 (mtmm) REVERT: L 70 ASP cc_start: 0.9331 (p0) cc_final: 0.9013 (m-30) REVERT: L 75 ILE cc_start: 0.8779 (mm) cc_final: 0.7905 (tp) REVERT: L 85 THR cc_start: 0.8524 (m) cc_final: 0.8322 (t) REVERT: M 46 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7486 (tm-30) REVERT: M 82 MET cc_start: 0.8393 (mtm) cc_final: 0.7863 (mtm) REVERT: M 82 LEU cc_start: 0.8851 (mt) cc_final: 0.8476 (mt) REVERT: N 73 LEU cc_start: 0.8871 (tt) cc_final: 0.8350 (mt) REVERT: N 75 ILE cc_start: 0.7935 (mp) cc_final: 0.7668 (mp) REVERT: N 103 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8398 (tppt) REVERT: O 38 ARG cc_start: 0.7198 (ptm160) cc_final: 0.6610 (ttt180) REVERT: O 80 LEU cc_start: 0.3997 (tp) cc_final: 0.3657 (tp) REVERT: O 82 MET cc_start: 0.5499 (mpp) cc_final: 0.4880 (mpp) REVERT: O 100 PHE cc_start: 0.5749 (m-10) cc_final: 0.5067 (m-10) outliers start: 28 outliers final: 13 residues processed: 318 average time/residue: 0.2070 time to fit residues: 103.6892 Evaluate side-chains 254 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 895 GLN Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain P residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 94 optimal weight: 5.9990 chunk 158 optimal weight: 7.9990 chunk 5 optimal weight: 7.9990 chunk 333 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 358 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 231 optimal weight: 0.9990 chunk 342 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN A 774 GLN A 895 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 690 GLN B 901 GLN B 913 GLN B 992 GLN C 196 ASN C 207 HIS C 498 GLN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.112363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.069707 restraints weight = 75747.256| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.12 r_work: 0.2787 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 30390 Z= 0.295 Angle : 0.733 8.284 41442 Z= 0.382 Chirality : 0.048 0.237 4836 Planarity : 0.005 0.074 5244 Dihedral : 7.286 59.590 5181 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.66 % Favored : 93.26 % Rotamer: Outliers : 1.86 % Allowed : 10.34 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.92 (0.13), residues: 3648 helix: 1.60 (0.20), residues: 639 sheet: -0.54 (0.16), residues: 975 loop : -1.40 (0.13), residues: 2034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 66 TYR 0.027 0.002 TYR N 32 PHE 0.019 0.002 PHE C 906 TRP 0.014 0.002 TRP H 36 HIS 0.008 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00683 (30294) covalent geometry : angle 0.72134 (41193) SS BOND : bond 0.00501 ( 39) SS BOND : angle 1.33333 ( 78) hydrogen bonds : bond 0.05052 ( 1138) hydrogen bonds : angle 6.28984 ( 3126) link_BETA1-4 : bond 0.00322 ( 15) link_BETA1-4 : angle 1.36370 ( 45) link_NAG-ASN : bond 0.00582 ( 42) link_NAG-ASN : angle 2.17777 ( 126) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 252 time to evaluate : 1.012 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 92 PHE cc_start: 0.8912 (t80) cc_final: 0.8603 (t80) REVERT: A 104 TRP cc_start: 0.8603 (m-90) cc_final: 0.8085 (m-90) REVERT: A 265 TYR cc_start: 0.8571 (p90) cc_final: 0.8327 (p90) REVERT: A 950 ASP cc_start: 0.9183 (t70) cc_final: 0.8882 (t0) REVERT: B 342 PHE cc_start: 0.8904 (m-80) cc_final: 0.8393 (m-80) REVERT: B 508 TYR cc_start: 0.6982 (m-80) cc_final: 0.6717 (m-80) REVERT: B 568 ASP cc_start: 0.8726 (t0) cc_final: 0.8366 (t0) REVERT: B 661 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8208 (tm-30) REVERT: B 740 MET cc_start: 0.9094 (mmm) cc_final: 0.8753 (tpp) REVERT: C 95 THR cc_start: 0.9272 (p) cc_final: 0.8982 (t) REVERT: C 196 ASN cc_start: 0.8837 (OUTLIER) cc_final: 0.8509 (t0) REVERT: C 406 GLU cc_start: 0.9403 (mm-30) cc_final: 0.8840 (mp0) REVERT: C 995 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8464 (mpp80) REVERT: C 1072 GLU cc_start: 0.9381 (pm20) cc_final: 0.9089 (pm20) REVERT: H 66 ARG cc_start: 0.8372 (ptp-110) cc_final: 0.7611 (ptt180) REVERT: H 67 PHE cc_start: 0.6521 (m-10) cc_final: 0.5779 (m-80) REVERT: L 3 GLN cc_start: 0.9019 (mm110) cc_final: 0.8466 (mp10) REVERT: L 35 TRP cc_start: 0.9125 (m100) cc_final: 0.8401 (m100) REVERT: L 73 LEU cc_start: 0.8839 (tp) cc_final: 0.8510 (mt) REVERT: L 75 ILE cc_start: 0.8758 (mm) cc_final: 0.7852 (tp) REVERT: L 85 THR cc_start: 0.8556 (m) cc_final: 0.8340 (t) REVERT: N 37 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8157 (tm-30) REVERT: N 39 LYS cc_start: 0.9083 (mmmt) cc_final: 0.8803 (mptt) REVERT: N 62 PHE cc_start: 0.8407 (m-80) cc_final: 0.8103 (m-80) REVERT: N 73 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8454 (mt) REVERT: O 38 ARG cc_start: 0.7528 (ptm160) cc_final: 0.6989 (ttt180) REVERT: O 80 LEU cc_start: 0.3988 (tp) cc_final: 0.3727 (tp) REVERT: O 82 MET cc_start: 0.5318 (mpp) cc_final: 0.5037 (mpp) outliers start: 60 outliers final: 27 residues processed: 301 average time/residue: 0.2110 time to fit residues: 99.4345 Evaluate side-chains 249 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 882 ILE Chi-restraints excluded: chain C residue 196 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 141 optimal weight: 10.0000 chunk 188 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 330 optimal weight: 7.9990 chunk 295 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 221 optimal weight: 0.8980 chunk 263 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 344 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN B 99 ASN B 370 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 ASN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN L 38 GLN ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82AASN M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 55 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.117149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.075757 restraints weight = 74653.537| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 4.12 r_work: 0.2871 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 30390 Z= 0.142 Angle : 0.633 8.409 41442 Z= 0.330 Chirality : 0.045 0.304 4836 Planarity : 0.004 0.057 5244 Dihedral : 6.784 59.444 5178 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.78 % Favored : 94.13 % Rotamer: Outliers : 1.89 % Allowed : 12.08 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: -0.69 (0.14), residues: 3648 helix: 1.95 (0.20), residues: 640 sheet: -0.52 (0.15), residues: 1012 loop : -1.26 (0.13), residues: 1996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.029 0.001 TYR M 102 PHE 0.030 0.001 PHE M 67 TRP 0.012 0.001 TRP O 103 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00321 (30294) covalent geometry : angle 0.62389 (41193) SS BOND : bond 0.00507 ( 39) SS BOND : angle 1.14802 ( 78) hydrogen bonds : bond 0.04216 ( 1138) hydrogen bonds : angle 5.87554 ( 3126) link_BETA1-4 : bond 0.00376 ( 15) link_BETA1-4 : angle 1.14336 ( 45) link_NAG-ASN : bond 0.00321 ( 42) link_NAG-ASN : angle 1.81908 ( 126) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 267 time to evaluate : 1.248 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 104 TRP cc_start: 0.8463 (m-90) cc_final: 0.8249 (m-90) REVERT: A 265 TYR cc_start: 0.8203 (p90) cc_final: 0.7923 (p90) REVERT: A 290 ASP cc_start: 0.8043 (t0) cc_final: 0.7762 (t70) REVERT: A 370 ASN cc_start: 0.9095 (m110) cc_final: 0.8715 (m-40) REVERT: A 950 ASP cc_start: 0.9046 (t70) cc_final: 0.8733 (t0) REVERT: B 342 PHE cc_start: 0.8936 (m-80) cc_final: 0.8437 (m-80) REVERT: B 508 TYR cc_start: 0.7131 (m-80) cc_final: 0.6745 (m-10) REVERT: B 568 ASP cc_start: 0.8686 (t0) cc_final: 0.8374 (t0) REVERT: B 661 GLU cc_start: 0.8402 (tm-30) cc_final: 0.8042 (tm-30) REVERT: B 740 MET cc_start: 0.8985 (mmm) cc_final: 0.8688 (tpp) REVERT: C 95 THR cc_start: 0.9282 (p) cc_final: 0.9010 (t) REVERT: C 387 LEU cc_start: 0.9163 (mp) cc_final: 0.8956 (mp) REVERT: C 406 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8799 (mp0) REVERT: C 957 GLN cc_start: 0.8477 (tm-30) cc_final: 0.8233 (tm-30) REVERT: C 995 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8439 (mpp80) REVERT: C 1072 GLU cc_start: 0.9283 (pm20) cc_final: 0.9013 (pm20) REVERT: H 66 ARG cc_start: 0.8914 (ptp-110) cc_final: 0.8552 (ptt180) REVERT: H 67 PHE cc_start: 0.6140 (m-10) cc_final: 0.5471 (m-80) REVERT: H 75 LYS cc_start: 0.9219 (tppt) cc_final: 0.8969 (tptp) REVERT: H 83 ARG cc_start: 0.6543 (OUTLIER) cc_final: 0.6081 (ptp90) REVERT: H 90 TYR cc_start: 0.6959 (m-10) cc_final: 0.6744 (m-10) REVERT: H 94 LYS cc_start: 0.8274 (tttm) cc_final: 0.7752 (tttp) REVERT: L 3 GLN cc_start: 0.9046 (mm110) cc_final: 0.8628 (mp10) REVERT: L 35 TRP cc_start: 0.9077 (m100) cc_final: 0.8443 (m100) REVERT: L 73 LEU cc_start: 0.8863 (tp) cc_final: 0.8541 (mt) REVERT: L 75 ILE cc_start: 0.8765 (mm) cc_final: 0.7855 (tp) REVERT: L 85 THR cc_start: 0.8468 (m) cc_final: 0.8267 (t) REVERT: N 62 PHE cc_start: 0.8470 (m-80) cc_final: 0.8223 (m-80) REVERT: N 73 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8473 (mt) REVERT: O 38 ARG cc_start: 0.7550 (ptm160) cc_final: 0.7134 (ttt180) REVERT: O 80 LEU cc_start: 0.3909 (tp) cc_final: 0.3659 (tp) REVERT: O 82 MET cc_start: 0.5408 (mpp) cc_final: 0.5137 (mpp) REVERT: O 100 PHE cc_start: 0.5814 (m-10) cc_final: 0.4993 (m-10) outliers start: 61 outliers final: 32 residues processed: 314 average time/residue: 0.1994 time to fit residues: 99.4912 Evaluate side-chains 270 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain N residue 32 TYR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 60 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 0.6980 chunk 270 optimal weight: 1.9990 chunk 341 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 321 optimal weight: 0.0570 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1036 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 90 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 = 0.3810 r_free = 0.3810 target = 0.109937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.067601 restraints weight = 73206.937| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 4.18 r_work: 0.2857 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 30390 Z= 0.158 Angle : 0.629 11.085 41442 Z= 0.326 Chirality : 0.045 0.281 4836 Planarity : 0.004 0.049 5244 Dihedral : 6.427 58.368 5178 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.86 % Rotamer: Outliers : 2.30 % Allowed : 13.48 % Favored : 84.22 % 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: -0.58 (0.14), residues: 3648 helix: 2.16 (0.20), residues: 632 sheet: -0.53 (0.15), residues: 1029 loop : -1.16 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 16 TYR 0.025 0.001 TYR M 102 PHE 0.018 0.001 PHE H 67 TRP 0.011 0.001 TRP O 103 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00361 (30294) covalent geometry : angle 0.61933 (41193) SS BOND : bond 0.00473 ( 39) SS BOND : angle 1.21699 ( 78) hydrogen bonds : bond 0.03999 ( 1138) hydrogen bonds : angle 5.62921 ( 3126) link_BETA1-4 : bond 0.00308 ( 15) link_BETA1-4 : angle 1.13258 ( 45) link_NAG-ASN : bond 0.00319 ( 42) link_NAG-ASN : angle 1.82477 ( 126) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 255 time to evaluate : 1.109 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 265 TYR cc_start: 0.8254 (p90) cc_final: 0.8047 (p90) REVERT: A 290 ASP cc_start: 0.8023 (t0) cc_final: 0.7754 (t70) REVERT: A 950 ASP cc_start: 0.9032 (t70) cc_final: 0.8712 (t0) REVERT: B 33 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8780 (m) REVERT: B 342 PHE cc_start: 0.8907 (m-80) cc_final: 0.8490 (m-80) REVERT: B 508 TYR cc_start: 0.7189 (m-80) cc_final: 0.6724 (m-10) REVERT: B 568 ASP cc_start: 0.8637 (t0) cc_final: 0.8329 (t0) REVERT: B 661 GLU cc_start: 0.8420 (tm-30) cc_final: 0.8027 (tm-30) REVERT: B 784 GLN cc_start: 0.8856 (OUTLIER) cc_final: 0.8634 (mt0) REVERT: C 95 THR cc_start: 0.9264 (p) cc_final: 0.8967 (t) REVERT: C 212 LEU cc_start: 0.8841 (tp) cc_final: 0.8596 (tt) REVERT: C 378 LYS cc_start: 0.8663 (mttt) cc_final: 0.8372 (tttt) REVERT: C 387 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8913 (mp) REVERT: C 957 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8255 (tm-30) REVERT: C 995 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8371 (mpp80) REVERT: C 1072 GLU cc_start: 0.9334 (pm20) cc_final: 0.9064 (pm20) REVERT: H 16 ARG cc_start: 0.9297 (ptp-170) cc_final: 0.9096 (ptp90) REVERT: H 75 LYS cc_start: 0.9229 (tppt) cc_final: 0.8974 (tptp) REVERT: H 83 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.6104 (ptp90) REVERT: H 90 TYR cc_start: 0.7054 (m-10) cc_final: 0.6671 (m-10) REVERT: H 94 LYS cc_start: 0.8135 (tttm) cc_final: 0.7660 (tttp) REVERT: L 3 GLN cc_start: 0.9049 (mm110) cc_final: 0.8646 (mp10) REVERT: L 35 TRP cc_start: 0.9051 (m100) cc_final: 0.8597 (m100) REVERT: L 73 LEU cc_start: 0.8834 (tp) cc_final: 0.8582 (mp) REVERT: L 75 ILE cc_start: 0.8756 (mm) cc_final: 0.7843 (tp) REVERT: L 85 THR cc_start: 0.8417 (m) cc_final: 0.8190 (t) REVERT: M 34 MET cc_start: 0.8390 (mmm) cc_final: 0.8144 (mmm) REVERT: M 67 PHE cc_start: 0.6562 (OUTLIER) cc_final: 0.5125 (m-80) REVERT: N 48 ILE cc_start: 0.9153 (mm) cc_final: 0.8927 (mp) REVERT: N 62 PHE cc_start: 0.8495 (m-80) cc_final: 0.8139 (m-80) REVERT: N 73 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8275 (mt) REVERT: O 38 ARG cc_start: 0.7576 (ptm160) cc_final: 0.7353 (ttm-80) REVERT: O 80 LEU cc_start: 0.3833 (tp) cc_final: 0.3629 (tp) outliers start: 74 outliers final: 37 residues processed: 309 average time/residue: 0.1968 time to fit residues: 97.3592 Evaluate side-chains 286 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 242 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 990 GLU Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 251 optimal weight: 0.8980 chunk 323 optimal weight: 20.0000 chunk 229 optimal weight: 5.9990 chunk 186 optimal weight: 2.9990 chunk 100 optimal weight: 10.0000 chunk 305 optimal weight: 8.9990 chunk 259 optimal weight: 4.9990 chunk 236 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 165 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3786 r_free = 0.3786 target = 0.107870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065753 restraints weight = 73941.358| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 4.12 r_work: 0.2825 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 30390 Z= 0.213 Angle : 0.653 9.101 41442 Z= 0.337 Chirality : 0.045 0.251 4836 Planarity : 0.004 0.047 5244 Dihedral : 6.209 57.623 5178 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.92 % Favored : 93.97 % Rotamer: Outliers : 2.67 % Allowed : 13.67 % Favored : 83.66 % 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: -0.56 (0.14), residues: 3648 helix: 2.13 (0.20), residues: 632 sheet: -0.54 (0.16), residues: 1031 loop : -1.12 (0.14), residues: 1985 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 83 TYR 0.024 0.001 TYR M 102 PHE 0.031 0.002 PHE M 27 TRP 0.012 0.001 TRP H 103 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00491 (30294) covalent geometry : angle 0.64264 (41193) SS BOND : bond 0.00557 ( 39) SS BOND : angle 1.41400 ( 78) hydrogen bonds : bond 0.04092 ( 1138) hydrogen bonds : angle 5.54884 ( 3126) link_BETA1-4 : bond 0.00301 ( 15) link_BETA1-4 : angle 1.15681 ( 45) link_NAG-ASN : bond 0.00403 ( 42) link_NAG-ASN : angle 1.87737 ( 126) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 246 time to evaluate : 1.191 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: 0.8323 (p90) cc_final: 0.8120 (p90) REVERT: A 290 ASP cc_start: 0.7975 (t0) cc_final: 0.7764 (t70) REVERT: A 370 ASN cc_start: 0.9148 (m110) cc_final: 0.8708 (m110) REVERT: A 950 ASP cc_start: 0.9044 (t70) cc_final: 0.8723 (t0) REVERT: B 33 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8770 (m) REVERT: B 342 PHE cc_start: 0.8900 (m-80) cc_final: 0.8514 (m-80) REVERT: B 508 TYR cc_start: 0.7307 (m-80) cc_final: 0.6776 (m-10) REVERT: B 568 ASP cc_start: 0.8618 (t0) cc_final: 0.8299 (t0) REVERT: B 661 GLU cc_start: 0.8467 (tm-30) cc_final: 0.8097 (tm-30) REVERT: C 95 THR cc_start: 0.9276 (p) cc_final: 0.8970 (t) REVERT: C 212 LEU cc_start: 0.8882 (tp) cc_final: 0.8653 (tt) REVERT: C 369 TYR cc_start: 0.7810 (p90) cc_final: 0.7557 (p90) REVERT: C 370 ASN cc_start: 0.8548 (m-40) cc_final: 0.8324 (m110) REVERT: C 387 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8899 (mp) REVERT: C 957 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8151 (tm-30) REVERT: C 995 ARG cc_start: 0.8861 (OUTLIER) cc_final: 0.8448 (mpp80) REVERT: C 1072 GLU cc_start: 0.9340 (pm20) cc_final: 0.9077 (pm20) REVERT: C 1107 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8263 (mtp85) REVERT: C 1142 GLN cc_start: 0.9575 (tp40) cc_final: 0.9241 (tp-100) REVERT: H 16 ARG cc_start: 0.9313 (ptp-170) cc_final: 0.9110 (ptp90) REVERT: H 75 LYS cc_start: 0.9266 (tppt) cc_final: 0.8986 (tptp) REVERT: H 90 TYR cc_start: 0.6947 (m-10) cc_final: 0.6683 (m-10) REVERT: H 94 LYS cc_start: 0.8183 (tttm) cc_final: 0.7693 (tttp) REVERT: L 3 GLN cc_start: 0.8998 (mm110) cc_final: 0.8581 (mp10) REVERT: L 35 TRP cc_start: 0.9077 (m100) cc_final: 0.8616 (m100) REVERT: L 36 TYR cc_start: 0.7428 (m-10) cc_final: 0.6943 (m-10) REVERT: L 73 LEU cc_start: 0.8811 (tp) cc_final: 0.8569 (mp) REVERT: L 75 ILE cc_start: 0.8761 (mm) cc_final: 0.7849 (tp) REVERT: L 85 THR cc_start: 0.8388 (m) cc_final: 0.8146 (t) REVERT: M 67 PHE cc_start: 0.6001 (OUTLIER) cc_final: 0.4753 (m-80) REVERT: M 75 LYS cc_start: 0.8961 (mmmt) cc_final: 0.8669 (tptp) REVERT: M 82 LEU cc_start: 0.8857 (tp) cc_final: 0.8421 (pp) REVERT: N 39 LYS cc_start: 0.9129 (mmmt) cc_final: 0.8864 (mmtt) REVERT: N 62 PHE cc_start: 0.8481 (m-80) cc_final: 0.8099 (m-80) REVERT: N 73 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8517 (mt) REVERT: N 92 TYR cc_start: 0.7478 (t80) cc_final: 0.7274 (t80) REVERT: N 103 LYS cc_start: 0.8410 (mtpp) cc_final: 0.7909 (tppt) REVERT: O 38 ARG cc_start: 0.7452 (ptm160) cc_final: 0.7173 (ttm-80) REVERT: O 100 PHE cc_start: 0.5858 (m-10) cc_final: 0.5106 (m-10) outliers start: 86 outliers final: 54 residues processed: 313 average time/residue: 0.1976 time to fit residues: 99.1855 Evaluate side-chains 292 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 233 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 804 GLN Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 30 SER Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 360 optimal weight: 9.9990 chunk 314 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 336 optimal weight: 5.9990 chunk 203 optimal weight: 1.9990 chunk 281 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 chunk 135 optimal weight: 0.4980 chunk 69 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 302 optimal weight: 0.9980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1106 GLN ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 82AASN ** N 90 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 = 0.3806 r_free = 0.3806 target = 0.109332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067329 restraints weight = 73649.036| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 4.14 r_work: 0.2858 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30390 Z= 0.148 Angle : 0.620 9.156 41442 Z= 0.319 Chirality : 0.045 0.254 4836 Planarity : 0.004 0.053 5244 Dihedral : 5.868 57.596 5178 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.95 % Favored : 93.97 % Rotamer: Outliers : 2.39 % Allowed : 15.04 % Favored : 82.57 % 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: -0.50 (0.14), residues: 3648 helix: 2.19 (0.20), residues: 648 sheet: -0.54 (0.16), residues: 1003 loop : -1.07 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 646 TYR 0.027 0.001 TYR A 873 PHE 0.030 0.001 PHE M 27 TRP 0.013 0.001 TRP O 36 HIS 0.006 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00341 (30294) covalent geometry : angle 0.61149 (41193) SS BOND : bond 0.00529 ( 39) SS BOND : angle 1.26342 ( 78) hydrogen bonds : bond 0.03806 ( 1138) hydrogen bonds : angle 5.37155 ( 3126) link_BETA1-4 : bond 0.00317 ( 15) link_BETA1-4 : angle 1.07772 ( 45) link_NAG-ASN : bond 0.00285 ( 42) link_NAG-ASN : angle 1.70783 ( 126) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 264 time to evaluate : 1.079 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 242 LEU cc_start: 0.9067 (mt) cc_final: 0.8823 (mm) REVERT: A 265 TYR cc_start: 0.8284 (p90) cc_final: 0.8084 (p90) REVERT: A 370 ASN cc_start: 0.9163 (m110) cc_final: 0.8721 (m110) REVERT: A 950 ASP cc_start: 0.9013 (t70) cc_final: 0.8694 (t0) REVERT: B 33 THR cc_start: 0.9023 (OUTLIER) cc_final: 0.8717 (m) REVERT: B 338 PHE cc_start: 0.9279 (m-80) cc_final: 0.9062 (m-80) REVERT: B 342 PHE cc_start: 0.8858 (m-80) cc_final: 0.8579 (m-80) REVERT: B 508 TYR cc_start: 0.7433 (m-80) cc_final: 0.6860 (m-10) REVERT: B 568 ASP cc_start: 0.8610 (t0) cc_final: 0.8297 (t0) REVERT: B 661 GLU cc_start: 0.8430 (tm-30) cc_final: 0.8029 (tm-30) REVERT: B 740 MET cc_start: 0.8895 (tpp) cc_final: 0.8558 (mmm) REVERT: C 95 THR cc_start: 0.9276 (p) cc_final: 0.8979 (t) REVERT: C 212 LEU cc_start: 0.8893 (tp) cc_final: 0.8669 (tt) REVERT: C 369 TYR cc_start: 0.7889 (p90) cc_final: 0.7638 (p90) REVERT: C 378 LYS cc_start: 0.8653 (mttt) cc_final: 0.8342 (tttt) REVERT: C 387 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8926 (mp) REVERT: C 957 GLN cc_start: 0.8452 (tm-30) cc_final: 0.8096 (tm-30) REVERT: C 995 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.8396 (mpp80) REVERT: C 1072 GLU cc_start: 0.9329 (pm20) cc_final: 0.9075 (pm20) REVERT: C 1107 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.7902 (mtt90) REVERT: H 75 LYS cc_start: 0.9271 (tppt) cc_final: 0.8980 (tptp) REVERT: H 90 TYR cc_start: 0.7109 (m-10) cc_final: 0.6766 (m-10) REVERT: H 94 LYS cc_start: 0.8198 (tttm) cc_final: 0.7794 (tttp) REVERT: L 3 GLN cc_start: 0.9026 (mm110) cc_final: 0.8640 (mp10) REVERT: L 35 TRP cc_start: 0.9022 (m100) cc_final: 0.8530 (m100) REVERT: L 45 LYS cc_start: 0.8514 (mtmm) cc_final: 0.8101 (mtmm) REVERT: L 73 LEU cc_start: 0.8817 (tp) cc_final: 0.8585 (mp) REVERT: L 75 ILE cc_start: 0.8761 (mm) cc_final: 0.7840 (tp) REVERT: L 85 THR cc_start: 0.8370 (m) cc_final: 0.8128 (t) REVERT: L 98 PHE cc_start: 0.7263 (m-80) cc_final: 0.6697 (m-10) REVERT: M 67 PHE cc_start: 0.5883 (OUTLIER) cc_final: 0.4909 (m-80) REVERT: M 75 LYS cc_start: 0.8988 (mmmt) cc_final: 0.8661 (tptp) REVERT: N 62 PHE cc_start: 0.8504 (m-80) cc_final: 0.8115 (m-80) REVERT: N 73 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8529 (mt) REVERT: N 92 TYR cc_start: 0.7473 (t80) cc_final: 0.7237 (t80) REVERT: N 103 LYS cc_start: 0.8444 (mtpp) cc_final: 0.7961 (tppt) REVERT: O 38 ARG cc_start: 0.7380 (ptm160) cc_final: 0.6692 (ttm-80) outliers start: 77 outliers final: 50 residues processed: 326 average time/residue: 0.1914 time to fit residues: 99.7753 Evaluate side-chains 301 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 246 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 87 optimal weight: 0.8980 chunk 195 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 338 optimal weight: 0.3980 chunk 312 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 268 optimal weight: 0.1980 chunk 248 optimal weight: 3.9990 chunk 281 optimal weight: 3.9990 chunk 323 optimal weight: 8.9990 chunk 204 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 564 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 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 = 0.3796 r_free = 0.3796 target = 0.108914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.066852 restraints weight = 73676.803| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.15 r_work: 0.2848 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 30390 Z= 0.161 Angle : 0.629 12.854 41442 Z= 0.322 Chirality : 0.045 0.363 4836 Planarity : 0.004 0.049 5244 Dihedral : 5.685 57.399 5178 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 2.21 % Allowed : 15.75 % Favored : 82.04 % 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: -0.47 (0.14), residues: 3648 helix: 2.20 (0.20), residues: 648 sheet: -0.45 (0.16), residues: 1002 loop : -1.10 (0.14), residues: 1998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 646 TYR 0.027 0.001 TYR B 421 PHE 0.023 0.001 PHE A 92 TRP 0.018 0.001 TRP A 104 HIS 0.007 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00373 (30294) covalent geometry : angle 0.62045 (41193) SS BOND : bond 0.00533 ( 39) SS BOND : angle 1.34502 ( 78) hydrogen bonds : bond 0.03792 ( 1138) hydrogen bonds : angle 5.31217 ( 3126) link_BETA1-4 : bond 0.00296 ( 15) link_BETA1-4 : angle 1.08518 ( 45) link_NAG-ASN : bond 0.00308 ( 42) link_NAG-ASN : angle 1.70926 ( 126) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 251 time to evaluate : 1.017 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: symmetry clash REVERT: A 242 LEU cc_start: 0.9072 (mt) cc_final: 0.8824 (mm) REVERT: A 950 ASP cc_start: 0.9018 (t70) cc_final: 0.8676 (t0) REVERT: B 33 THR cc_start: 0.9009 (OUTLIER) cc_final: 0.8688 (m) REVERT: B 338 PHE cc_start: 0.9297 (m-80) cc_final: 0.9080 (m-80) REVERT: B 342 PHE cc_start: 0.8846 (m-80) cc_final: 0.8587 (m-80) REVERT: B 508 TYR cc_start: 0.7597 (m-80) cc_final: 0.7083 (m-80) REVERT: B 661 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8008 (tm-30) REVERT: B 740 MET cc_start: 0.8857 (tpp) cc_final: 0.8497 (mmm) REVERT: C 95 THR cc_start: 0.9267 (p) cc_final: 0.8971 (t) REVERT: C 212 LEU cc_start: 0.8916 (tp) cc_final: 0.8696 (tt) REVERT: C 369 TYR cc_start: 0.7905 (p90) cc_final: 0.7582 (p90) REVERT: C 370 ASN cc_start: 0.8512 (m-40) cc_final: 0.8283 (m110) REVERT: C 387 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8881 (mp) REVERT: C 957 GLN cc_start: 0.8446 (tm-30) cc_final: 0.8074 (tm-30) REVERT: C 995 ARG cc_start: 0.8824 (OUTLIER) cc_final: 0.8413 (mpp80) REVERT: C 1072 GLU cc_start: 0.9337 (pm20) cc_final: 0.9081 (pm20) REVERT: C 1107 ARG cc_start: 0.8552 (mtt-85) cc_final: 0.7913 (mtt90) REVERT: H 67 PHE cc_start: 0.4733 (m-80) cc_final: 0.2850 (m-80) REVERT: H 75 LYS cc_start: 0.9307 (tppt) cc_final: 0.9003 (tptp) REVERT: H 90 TYR cc_start: 0.7104 (m-10) cc_final: 0.6677 (m-10) REVERT: H 94 LYS cc_start: 0.8196 (tttm) cc_final: 0.7778 (tttp) REVERT: L 3 GLN cc_start: 0.9043 (mm110) cc_final: 0.8615 (mp10) REVERT: L 35 TRP cc_start: 0.9045 (m100) cc_final: 0.8483 (m100) REVERT: L 36 TYR cc_start: 0.7041 (m-10) cc_final: 0.6780 (m-80) REVERT: L 45 LYS cc_start: 0.8527 (mtmm) cc_final: 0.8105 (mtmm) REVERT: L 73 LEU cc_start: 0.8821 (tp) cc_final: 0.8598 (mp) REVERT: L 75 ILE cc_start: 0.8755 (mm) cc_final: 0.7822 (tp) REVERT: L 85 THR cc_start: 0.8377 (m) cc_final: 0.8127 (t) REVERT: M 67 PHE cc_start: 0.5884 (OUTLIER) cc_final: 0.4467 (m-80) REVERT: M 75 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8641 (tptp) REVERT: N 62 PHE cc_start: 0.8519 (m-80) cc_final: 0.8108 (m-80) REVERT: N 73 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8552 (mt) REVERT: N 92 TYR cc_start: 0.7474 (t80) cc_final: 0.7212 (t80) REVERT: N 103 LYS cc_start: 0.8454 (mtpp) cc_final: 0.7954 (tppt) REVERT: O 38 ARG cc_start: 0.7362 (ptm160) cc_final: 0.7036 (ttm-80) REVERT: O 100 PHE cc_start: 0.5953 (m-10) cc_final: 0.5234 (m-10) outliers start: 71 outliers final: 55 residues processed: 307 average time/residue: 0.1896 time to fit residues: 92.3945 Evaluate side-chains 303 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 961 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 781 VAL Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain C residue 1115 ILE Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 72 THR Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 23 optimal weight: 7.9990 chunk 185 optimal weight: 2.9990 chunk 126 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 0.0270 chunk 211 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 chunk 137 optimal weight: 0.3980 chunk 203 optimal weight: 1.9990 chunk 339 optimal weight: 8.9990 overall best weight: 1.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82AASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.109789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.068001 restraints weight = 73377.452| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.15 r_work: 0.2875 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30390 Z= 0.129 Angle : 0.615 13.748 41442 Z= 0.314 Chirality : 0.045 0.245 4836 Planarity : 0.004 0.050 5244 Dihedral : 5.416 59.864 5178 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer: Outliers : 1.93 % Allowed : 16.25 % Favored : 81.83 % 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: -0.43 (0.14), residues: 3648 helix: 2.32 (0.21), residues: 643 sheet: -0.50 (0.16), residues: 1030 loop : -1.06 (0.14), residues: 1975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 83 TYR 0.030 0.001 TYR B 421 PHE 0.026 0.001 PHE M 27 TRP 0.016 0.001 TRP A 104 HIS 0.006 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00295 (30294) covalent geometry : angle 0.60671 (41193) SS BOND : bond 0.00484 ( 39) SS BOND : angle 1.19768 ( 78) hydrogen bonds : bond 0.03595 ( 1138) hydrogen bonds : angle 5.20375 ( 3126) link_BETA1-4 : bond 0.00332 ( 15) link_BETA1-4 : angle 1.03597 ( 45) link_NAG-ASN : bond 0.00263 ( 42) link_NAG-ASN : angle 1.61979 ( 126) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 263 time to evaluate : 1.150 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: symmetry clash REVERT: A 242 LEU cc_start: 0.9076 (mt) cc_final: 0.8834 (mm) REVERT: A 950 ASP cc_start: 0.8986 (t70) cc_final: 0.8649 (t0) REVERT: B 33 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8672 (m) REVERT: B 338 PHE cc_start: 0.9294 (m-80) cc_final: 0.9081 (m-80) REVERT: B 342 PHE cc_start: 0.8810 (m-80) cc_final: 0.8564 (m-80) REVERT: B 508 TYR cc_start: 0.7695 (m-80) cc_final: 0.7160 (m-80) REVERT: B 661 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8110 (tm-30) REVERT: B 740 MET cc_start: 0.8778 (tpp) cc_final: 0.8393 (mmm) REVERT: B 957 GLN cc_start: 0.8334 (tm-30) cc_final: 0.8133 (tm-30) REVERT: B 1107 ARG cc_start: 0.8483 (ttm170) cc_final: 0.8165 (mpt180) REVERT: C 95 THR cc_start: 0.9267 (p) cc_final: 0.8973 (t) REVERT: C 369 TYR cc_start: 0.7912 (p90) cc_final: 0.7589 (p90) REVERT: C 370 ASN cc_start: 0.8512 (m-40) cc_final: 0.8285 (m110) REVERT: C 378 LYS cc_start: 0.8606 (mttt) cc_final: 0.8352 (mmmt) REVERT: C 387 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8862 (mp) REVERT: C 957 GLN cc_start: 0.8399 (tm-30) cc_final: 0.8057 (tm-30) REVERT: C 995 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.8364 (mpp80) REVERT: C 1072 GLU cc_start: 0.9328 (pm20) cc_final: 0.9086 (pm20) REVERT: H 46 GLU cc_start: 0.7337 (pp20) cc_final: 0.6993 (pp20) REVERT: H 67 PHE cc_start: 0.4351 (m-80) cc_final: 0.2662 (m-80) REVERT: H 75 LYS cc_start: 0.9311 (tppt) cc_final: 0.9001 (tptp) REVERT: H 90 TYR cc_start: 0.7054 (m-10) cc_final: 0.6662 (m-10) REVERT: H 94 LYS cc_start: 0.8068 (tttm) cc_final: 0.7652 (tttp) REVERT: L 3 GLN cc_start: 0.9189 (mm110) cc_final: 0.8709 (mp10) REVERT: L 35 TRP cc_start: 0.9053 (m100) cc_final: 0.8201 (m100) REVERT: L 45 LYS cc_start: 0.8518 (mtmm) cc_final: 0.8068 (mtmm) REVERT: L 46 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8067 (mt) REVERT: L 75 ILE cc_start: 0.8682 (mm) cc_final: 0.7921 (tp) REVERT: L 85 THR cc_start: 0.8368 (m) cc_final: 0.8085 (t) REVERT: L 98 PHE cc_start: 0.7339 (m-80) cc_final: 0.6581 (m-10) REVERT: M 66 ARG cc_start: 0.7925 (mtm110) cc_final: 0.7412 (ptm160) REVERT: M 67 PHE cc_start: 0.5860 (OUTLIER) cc_final: 0.3393 (m-80) REVERT: N 62 PHE cc_start: 0.8521 (m-80) cc_final: 0.8120 (m-80) REVERT: N 73 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8569 (mt) REVERT: N 92 TYR cc_start: 0.7468 (t80) cc_final: 0.7141 (t80) REVERT: N 103 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7956 (tppt) REVERT: O 38 ARG cc_start: 0.7349 (ptm160) cc_final: 0.6604 (ttm-80) REVERT: O 100 PHE cc_start: 0.5992 (m-10) cc_final: 0.5265 (m-10) outliers start: 62 outliers final: 50 residues processed: 311 average time/residue: 0.1910 time to fit residues: 94.1669 Evaluate side-chains 300 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 244 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 781 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 781 VAL Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 326 ILE Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 311 optimal weight: 10.0000 chunk 266 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 159 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 149 optimal weight: 0.0170 chunk 24 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 193 optimal weight: 4.9990 chunk 321 optimal weight: 6.9990 chunk 355 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1010 GLN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 105 GLN ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.109773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.067485 restraints weight = 73385.108| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 4.13 r_work: 0.2906 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30390 Z= 0.111 Angle : 0.607 14.223 41442 Z= 0.308 Chirality : 0.044 0.217 4836 Planarity : 0.004 0.065 5244 Dihedral : 5.151 57.450 5178 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.24 % Favored : 94.68 % Rotamer: Outliers : 1.68 % Allowed : 16.71 % Favored : 81.61 % 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: -0.35 (0.14), residues: 3648 helix: 2.42 (0.21), residues: 644 sheet: -0.45 (0.16), residues: 1033 loop : -1.02 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG O 16 TYR 0.032 0.001 TYR B 421 PHE 0.011 0.001 PHE M 29 TRP 0.015 0.001 TRP M 47 HIS 0.005 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00248 (30294) covalent geometry : angle 0.59981 (41193) SS BOND : bond 0.00383 ( 39) SS BOND : angle 1.02823 ( 78) hydrogen bonds : bond 0.03387 ( 1138) hydrogen bonds : angle 5.09464 ( 3126) link_BETA1-4 : bond 0.00352 ( 15) link_BETA1-4 : angle 1.02511 ( 45) link_NAG-ASN : bond 0.00235 ( 42) link_NAG-ASN : angle 1.54253 ( 126) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7296 Ramachandran restraints generated. 3648 Oldfield, 0 Emsley, 3648 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 270 time to evaluate : 1.152 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 LEU cc_start: 0.9079 (mt) cc_final: 0.8825 (mm) REVERT: A 950 ASP cc_start: 0.8950 (t70) cc_final: 0.8649 (t0) REVERT: B 342 PHE cc_start: 0.8839 (m-80) cc_final: 0.8585 (m-80) REVERT: B 495 TYR cc_start: 0.6551 (m-10) cc_final: 0.5629 (m-10) REVERT: B 508 TYR cc_start: 0.7748 (m-80) cc_final: 0.7229 (m-80) REVERT: B 661 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8047 (tm-30) REVERT: B 1107 ARG cc_start: 0.8373 (ttm170) cc_final: 0.8157 (mpt180) REVERT: C 95 THR cc_start: 0.9244 (p) cc_final: 0.8980 (t) REVERT: C 369 TYR cc_start: 0.7904 (p90) cc_final: 0.7603 (p90) REVERT: C 370 ASN cc_start: 0.8536 (m-40) cc_final: 0.8310 (m110) REVERT: C 462 LYS cc_start: 0.8299 (pttm) cc_final: 0.8073 (mtmt) REVERT: C 995 ARG cc_start: 0.8771 (OUTLIER) cc_final: 0.8342 (mpp80) REVERT: C 1072 GLU cc_start: 0.9331 (pm20) cc_final: 0.9099 (pm20) REVERT: H 67 PHE cc_start: 0.3887 (m-80) cc_final: 0.2479 (m-80) REVERT: H 75 LYS cc_start: 0.9309 (tppt) cc_final: 0.8956 (tptp) REVERT: H 90 TYR cc_start: 0.7106 (m-10) cc_final: 0.6735 (m-10) REVERT: H 94 LYS cc_start: 0.8101 (tttm) cc_final: 0.7669 (tttp) REVERT: L 3 GLN cc_start: 0.9188 (mm110) cc_final: 0.8915 (mm-40) REVERT: L 35 TRP cc_start: 0.8942 (m100) cc_final: 0.8396 (m100) REVERT: L 45 LYS cc_start: 0.8470 (mtmm) cc_final: 0.8027 (mtmm) REVERT: L 46 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8047 (tp) REVERT: L 75 ILE cc_start: 0.8742 (mm) cc_final: 0.7828 (tp) REVERT: L 85 THR cc_start: 0.8367 (m) cc_final: 0.8112 (t) REVERT: M 38 ARG cc_start: 0.7859 (ptt-90) cc_final: 0.7613 (ptt-90) REVERT: M 66 ARG cc_start: 0.7913 (mtm110) cc_final: 0.7438 (ptm160) REVERT: M 67 PHE cc_start: 0.5656 (OUTLIER) cc_final: 0.3281 (m-80) REVERT: N 48 ILE cc_start: 0.9248 (mm) cc_final: 0.8902 (mt) REVERT: N 62 PHE cc_start: 0.8558 (m-80) cc_final: 0.8153 (m-80) REVERT: N 73 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8370 (mt) REVERT: O 38 ARG cc_start: 0.7336 (ptm160) cc_final: 0.7006 (ttm-80) REVERT: O 100 PHE cc_start: 0.5963 (m-10) cc_final: 0.5290 (m-10) outliers start: 54 outliers final: 40 residues processed: 311 average time/residue: 0.1979 time to fit residues: 98.1743 Evaluate side-chains 294 residues out of total 3219 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 250 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain A residue 369 TYR Chi-restraints excluded: chain A residue 432 CYS Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 791 THR Chi-restraints excluded: chain B residue 993 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain C residue 401 VAL Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 437 ASN Chi-restraints excluded: chain C residue 495 TYR Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 995 ARG Chi-restraints excluded: chain H residue 100 ILE Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain L residue 22 THR Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain M residue 67 PHE Chi-restraints excluded: chain N residue 73 LEU Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 51 ILE Chi-restraints excluded: chain O residue 82 MET Chi-restraints excluded: chain P residue 33 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 7 optimal weight: 8.9990 chunk 200 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 282 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 356 optimal weight: 10.0000 chunk 51 optimal weight: 0.5980 chunk 329 optimal weight: 20.0000 chunk 177 optimal weight: 0.7980 chunk 236 optimal weight: 10.0000 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.108859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.066861 restraints weight = 73805.186| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 4.14 r_work: 0.2851 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 30390 Z= 0.172 Angle : 0.638 14.209 41442 Z= 0.324 Chirality : 0.045 0.295 4836 Planarity : 0.004 0.052 5244 Dihedral : 5.153 57.297 5178 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.81 % Favored : 94.11 % Rotamer: Outliers : 1.77 % Allowed : 17.02 % Favored : 81.21 % 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: -0.34 (0.14), residues: 3648 helix: 2.39 (0.21), residues: 644 sheet: -0.40 (0.16), residues: 995 loop : -1.02 (0.14), residues: 2009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG O 16 TYR 0.031 0.001 TYR B 421 PHE 0.031 0.001 PHE M 27 TRP 0.013 0.001 TRP A 104 HIS 0.005 0.001 HIS O 35 Details of bonding type rmsd covalent geometry : bond 0.00401 (30294) covalent geometry : angle 0.62992 (41193) SS BOND : bond 0.00446 ( 39) SS BOND : angle 1.20197 ( 78) hydrogen bonds : bond 0.03660 ( 1138) hydrogen bonds : angle 5.14467 ( 3126) link_BETA1-4 : bond 0.00242 ( 15) link_BETA1-4 : angle 1.06216 ( 45) link_NAG-ASN : bond 0.00285 ( 42) link_NAG-ASN : angle 1.63798 ( 126) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7755.18 seconds wall clock time: 133 minutes 48.01 seconds (8028.01 seconds total)