Starting phenix.real_space_refine on Fri Mar 6 07:53:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kne_22943/03_2026/7kne_22943.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kne_22943/03_2026/7kne_22943.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kne_22943/03_2026/7kne_22943.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kne_22943/03_2026/7kne_22943.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kne_22943/03_2026/7kne_22943.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kne_22943/03_2026/7kne_22943.map" } resolution = 3.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.019 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 136 5.16 5 C 18597 2.51 5 N 4776 2.21 5 O 5682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 155 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: 29191 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 7771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7771 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 7771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1006, 7771 Classifications: {'peptide': 1006} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 49, 'TRANS': 956} Chain breaks: 8 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 4, 'ARG:plan': 1, 'GLN:plan1': 2, 'PHE:plan': 2, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 66 Chain: "B" Number of atoms: 8003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1029, 8003 Classifications: {'peptide': 1029} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 977} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 6.28, per 1000 atoms: 0.22 Number of scatterers: 29191 At special positions: 0 Unit cell: (139.656, 157.642, 238.05, 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 136 16.00 O 5682 8.00 N 4776 7.00 C 18597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.04 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 616 " " NAG A1306 " - " ASN A 801 " " NAG A1307 " - " ASN A 709 " " NAG A1308 " - " ASN A1074 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 603 " " NAG A1311 " - " ASN A 165 " " NAG A1312 " - " ASN A 657 " " NAG B1301 " - " ASN B 331 " " NAG B1302 " - " ASN B1134 " " NAG B1303 " - " ASN B1098 " " NAG B1304 " - " ASN B 282 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 801 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG B1314 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 657 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG D 703 " - " ASN D 103 " " NAG D 704 " - " ASN D 90 " " NAG D 705 " - " ASN D 53 " " NAG E 1 " - " ASN C 717 " " NAG F 1 " - " ASN C 343 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 343 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN D 546 " Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 43 sheets defined 30.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.547A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N CYS C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 365 through 372 removed outlier: 3.655A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ALA C 372 " --> pdb=" O TYR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 3.892A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 5.735A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 737 through 742 removed outlier: 3.614A pdb=" N ILE C 742 " --> pdb=" O CYS C 738 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.657A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.563A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU C 780 " --> pdb=" O LYS C 776 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.509A pdb=" N ILE C 870 " --> pdb=" O THR C 866 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.786A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.916A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.831A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.596A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.203A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (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: 4.467A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1032 removed outlier: 4.023A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1116 through 1120 Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.607A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.906A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LEU A 303 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.605A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.859A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 370' Processing helix chain 'A' and resid 385 through 390 removed outlier: 4.153A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 407 No H-bonds generated for 'chain 'A' and resid 405 through 407' Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.762A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.004A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 removed outlier: 3.645A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 883 removed outlier: 3.542A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.709A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.702A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 964 removed outlier: 4.422A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 963 " --> pdb=" O LEU A 959 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS A 964 " --> pdb=" O ASN A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 Processing helix chain 'A' and resid 976 through 983 removed outlier: 3.890A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.158A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLN A1002 " --> pdb=" O THR A 998 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER A1003 " --> pdb=" O GLY A 999 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A1018 " --> pdb=" O ARG A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.731A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.725A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 365 through 370' Processing helix chain 'B' and resid 385 through 390 removed outlier: 4.230A pdb=" N ASP B 389 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 385 through 390' Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.953A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.597A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.581A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 780 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.932A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 4.121A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.541A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.909A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 946 through 965 removed outlier: 4.274A pdb=" N ASP B 950 " --> pdb=" O GLY B 946 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.995A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 3.957A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.635A pdb=" N LYS D 26 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 42 " --> pdb=" O ASP D 38 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 3.885A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.513A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 3.507A pdb=" N LYS D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.152A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.671A pdb=" N ARG D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU D 166 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.678A pdb=" N GLN D 175 " --> pdb=" O VAL D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 176 through 187 removed outlier: 3.772A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL D 185 " --> pdb=" O GLU D 181 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS D 187 " --> pdb=" O TYR D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 removed outlier: 3.617A pdb=" N ALA D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.564A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 245 removed outlier: 3.648A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 234 " --> pdb=" O PHE D 230 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.973A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.706A pdb=" N LEU D 266 " --> pdb=" O PRO D 263 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU D 267 " --> pdb=" O ALA D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.946A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 319 removed outlier: 3.768A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.538A pdb=" N PHE D 369 " --> pdb=" O THR D 365 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.236A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.611A pdb=" N GLY D 422 " --> pdb=" O LEU D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 3.505A pdb=" N ASN D 437 " --> pdb=" O GLU D 433 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS D 441 " --> pdb=" O ASN D 437 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 removed outlier: 3.537A pdb=" N LEU D 456 " --> pdb=" O PHE D 452 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLU D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET D 462 " --> pdb=" O LYS D 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.899A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 481 " --> pdb=" O TRP D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 512 through 523 removed outlier: 4.119A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 523 through 533 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.679A pdb=" N GLY D 551 " --> pdb=" O SER D 547 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS D 553 " --> pdb=" O GLU D 549 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.513A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 4.291A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASN D 586 " --> pdb=" O ARG D 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 581 through 586' Processing helix chain 'D' and resid 588 through 599 removed outlier: 3.695A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 30 removed outlier: 3.667A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 65 " --> pdb=" O TYR C 265 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR C 208 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.266A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.764A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 51 removed outlier: 3.616A pdb=" N PHE C 275 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 104 through 106 removed outlier: 3.538A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.520A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 376 through 380 removed outlier: 3.569A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE C 434 " --> pdb=" O VAL C 511 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE C 400 " --> pdb=" O VAL C 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.595A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 539 through 543 removed outlier: 3.531A pdb=" N GLY C 548 " --> pdb=" O PHE C 541 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 653 through 655 Processing sheet with id=AB1, first strand: chain 'C' and resid 703 through 704 removed outlier: 6.970A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER C 721 " --> pdb=" O THR C1066 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 787 through 788 Processing sheet with id=AB4, first strand: chain 'C' and resid 1086 through 1088 Processing sheet with id=AB5, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB6, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.608A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU A 226 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER A 205 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.608A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 50 through 51 removed outlier: 3.525A pdb=" N PHE A 275 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS A 278 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 104 through 106 Processing sheet with id=AC1, first strand: chain 'A' and resid 311 through 318 removed outlier: 5.508A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N GLY A 593 " --> pdb=" O PHE A 318 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.725A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA A 397 " --> pdb=" O LYS A 356 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA A 435 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.768A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 539 through 543 removed outlier: 3.736A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 565 through 567 removed outlier: 3.574A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 653 through 655 removed outlier: 3.627A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.003A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 712 through 728 removed outlier: 7.003A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.222A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1086 through 1088 Processing sheet with id=AD2, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.889A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 65 " --> pdb=" O TYR B 265 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 266 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLU B 191 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.609A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR B 279 " --> pdb=" O VAL B 47 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.503A pdb=" N LEU B 118 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS B 129 " --> pdb=" O LEU B 118 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.063A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 354 through 356 removed outlier: 4.032A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.514A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 539 through 542 removed outlier: 3.689A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.517A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.737A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 711 through 719 removed outlier: 7.058A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 711 through 719 removed outlier: 7.058A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 726 through 728 Processing sheet with id=AE4, first strand: chain 'B' and resid 734 through 736 removed outlier: 3.562A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 5.632A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AE7, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.559A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 922 hydrogen bonds defined for protein. 2532 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: 8.11 Time building geometry restraints manager: 3.12 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: 9050 1.34 - 1.46: 6254 1.46 - 1.58: 14367 1.58 - 1.70: 1 1.70 - 1.82: 183 Bond restraints: 29855 Sorted by residual: bond pdb=" N ASP D 303 " pdb=" CA ASP D 303 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.16e-02 7.43e+03 1.13e+01 bond pdb=" N VAL B 524 " pdb=" CA VAL B 524 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.20e-02 6.94e+03 9.15e+00 bond pdb=" N CYS B 525 " pdb=" CA CYS B 525 " ideal model delta sigma weight residual 1.454 1.489 -0.036 1.23e-02 6.61e+03 8.50e+00 bond pdb=" N TRP D 302 " pdb=" CA TRP D 302 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.23e-02 6.61e+03 8.38e+00 bond pdb=" N THR B 523 " pdb=" CA THR B 523 " ideal model delta sigma weight residual 1.453 1.490 -0.038 1.31e-02 5.83e+03 8.31e+00 ... (remaining 29850 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 39730 1.91 - 3.82: 760 3.82 - 5.74: 128 5.74 - 7.65: 10 7.65 - 9.56: 1 Bond angle restraints: 40629 Sorted by residual: angle pdb=" CA ASP D 303 " pdb=" C ASP D 303 " pdb=" O ASP D 303 " ideal model delta sigma weight residual 121.89 117.36 4.53 1.27e+00 6.20e-01 1.27e+01 angle pdb=" N ASP D 499 " pdb=" CA ASP D 499 " pdb=" C ASP D 499 " ideal model delta sigma weight residual 109.81 117.29 -7.48 2.21e+00 2.05e-01 1.15e+01 angle pdb=" CB LYS D 553 " pdb=" CG LYS D 553 " pdb=" CD LYS D 553 " ideal model delta sigma weight residual 111.30 118.88 -7.58 2.30e+00 1.89e-01 1.09e+01 angle pdb=" C ASP D 494 " pdb=" N GLU D 495 " pdb=" CA GLU D 495 " ideal model delta sigma weight residual 121.58 128.00 -6.42 1.95e+00 2.63e-01 1.08e+01 angle pdb=" CA THR B 523 " pdb=" C THR B 523 " pdb=" O THR B 523 " ideal model delta sigma weight residual 121.94 118.25 3.69 1.15e+00 7.56e-01 1.03e+01 ... (remaining 40624 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16702 17.96 - 35.92: 1422 35.92 - 53.88: 260 53.88 - 71.84: 67 71.84 - 89.79: 34 Dihedral angle restraints: 18485 sinusoidal: 7887 harmonic: 10598 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 33.21 59.79 1 1.00e+01 1.00e-02 4.77e+01 dihedral pdb=" CB CYS B 738 " pdb=" SG CYS B 738 " pdb=" SG CYS B 760 " pdb=" CB CYS B 760 " ideal model delta sinusoidal sigma weight residual 93.00 34.34 58.66 1 1.00e+01 1.00e-02 4.61e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual 93.00 35.48 57.52 1 1.00e+01 1.00e-02 4.44e+01 ... (remaining 18482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 4177 0.073 - 0.146: 555 0.146 - 0.219: 9 0.219 - 0.292: 1 0.292 - 0.365: 5 Chirality restraints: 4747 Sorted by residual: chirality pdb=" C1 NAG B1313 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1313 " pdb=" O5 NAG B1313 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" C1 NAG B1311 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1311 " pdb=" O5 NAG B1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.49e+00 ... (remaining 4744 not shown) Planarity restraints: 5237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1313 " -0.236 2.00e-02 2.50e+03 1.96e-01 4.78e+02 pdb=" C7 NAG B1313 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B1313 " -0.167 2.00e-02 2.50e+03 pdb=" N2 NAG B1313 " 0.321 2.00e-02 2.50e+03 pdb=" O7 NAG B1313 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.088 5.00e-02 4.00e+02 1.32e-01 2.81e+01 pdb=" N PRO C 521 " 0.229 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 461 " 0.036 2.00e-02 2.50e+03 2.63e-02 1.74e+01 pdb=" CG TRP D 461 " -0.070 2.00e-02 2.50e+03 pdb=" CD1 TRP D 461 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP D 461 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP D 461 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 461 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 461 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 461 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 461 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP D 461 " 0.010 2.00e-02 2.50e+03 ... (remaining 5234 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 481 2.65 - 3.21: 27552 3.21 - 3.77: 43112 3.77 - 4.34: 59069 4.34 - 4.90: 95282 Nonbonded interactions: 225496 Sorted by model distance: nonbonded pdb=" O THR B1006 " pdb=" OG1 THR B1009 " model vdw 2.083 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.083 3.040 nonbonded pdb=" OG SER A 514 " pdb=" OE2 GLU A 516 " model vdw 2.110 3.040 nonbonded pdb=" O LYS C 964 " pdb=" OG SER C 967 " model vdw 2.138 3.040 nonbonded pdb=" O GLU A 309 " pdb=" OH TYR A 313 " model vdw 2.139 3.040 ... (remaining 225491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 66 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 209 or (resid 210 \ and (name N or name CA or name C or name O or name CB )) or resid 211 through 28 \ 9 or (resid 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 620 or resid 640 through 676 or resid 690 through 1312)) selection = (chain 'B' and (resid 26 through 66 or resid 81 through 95 or (resid 96 through \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 or (resi \ d 99 through 100 and (name N or name CA or name C or name O or name CB )) or res \ id 101 or (resid 102 and (name N or name CA or name C or name O or name CB )) or \ resid 103 through 139 or (resid 140 through 141 and (name N or name CA or name \ C or name O or name CB )) or (resid 156 and (name N or name CA or name C or name \ O or name CB )) or resid 157 through 158 or (resid 159 through 160 and (name N \ or name CA or name C or name O or name CB )) or resid 161 through 176 or (resid \ 187 through 188 and (name N or name CA or name C or name O or name CB )) or resi \ d 189 through 194 or (resid 195 through 198 and (name N or name CA or name C or \ name O or name CB )) or resid 199 or (resid 200 and (name N or name CA or name C \ or name O or name CB )) or resid 201 through 243 or resid 264 through 620 or re \ sid 640 through 811 or resid 815 through 828 or resid 853 through 1146 or resid \ 1303 through 1314)) selection = (chain 'C' and (resid 26 through 66 or (resid 81 and (name N or name CA or name \ C or name O or name CB )) or resid 82 through 189 or (resid 190 and (name N or n \ ame CA or name C or name O or name CB )) or resid 191 through 209 or (resid 210 \ and (name N or name CA or name C or name O or name CB )) or resid 211 through 28 \ 9 or (resid 290 and (name N or name CA or name C or name O or name CB )) or resi \ d 291 through 620 or resid 640 through 676 or resid 690 through 1312)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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 group one per residue 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: 5.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 27.540 Find NCS groups from input model: 0.710 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 29953 Z= 0.183 Angle : 0.648 11.810 40881 Z= 0.328 Chirality : 0.045 0.365 4747 Planarity : 0.005 0.196 5187 Dihedral : 13.762 89.795 11527 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.06 % Allowed : 0.16 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.17 (0.14), residues: 3583 helix: -0.56 (0.17), residues: 877 sheet: 0.26 (0.24), residues: 538 loop : -1.15 (0.13), residues: 2168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 177 TYR 0.020 0.001 TYR D 613 PHE 0.052 0.001 PHE D 504 TRP 0.070 0.001 TRP D 461 HIS 0.022 0.001 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.00376 (29855) covalent geometry : angle 0.63101 (40629) SS BOND : bond 0.00395 ( 42) SS BOND : angle 0.91697 ( 84) hydrogen bonds : bond 0.29749 ( 902) hydrogen bonds : angle 9.43114 ( 2532) link_BETA1-4 : bond 0.00827 ( 6) link_BETA1-4 : angle 2.25651 ( 18) link_NAG-ASN : bond 0.01285 ( 50) link_NAG-ASN : angle 2.37367 ( 150) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 141 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 460 ASN cc_start: 0.7606 (t0) cc_final: 0.7205 (t0) REVERT: A 896 ILE cc_start: 0.8788 (pt) cc_final: 0.8586 (mt) REVERT: B 153 MET cc_start: 0.6259 (pmm) cc_final: 0.5384 (pmm) REVERT: D 82 MET cc_start: 0.6266 (ppp) cc_final: 0.5770 (ppp) REVERT: D 123 MET cc_start: -0.1606 (ptp) cc_final: -0.2609 (mmm) REVERT: D 366 MET cc_start: 0.0174 (tpt) cc_final: -0.0464 (mmm) REVERT: D 408 MET cc_start: 0.0476 (ptm) cc_final: 0.0009 (ttt) outliers start: 2 outliers final: 0 residues processed: 143 average time/residue: 0.1688 time to fit residues: 40.1277 Evaluate side-chains 98 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.3980 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN C 955 ASN C1005 GLN A 218 GLN A 394 ASN B 450 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 992 GLN D 493 HIS D 508 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.108633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.069046 restraints weight = 140489.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.063567 restraints weight = 68253.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.064165 restraints weight = 41556.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.064359 restraints weight = 29035.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.064639 restraints weight = 24141.305| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 29953 Z= 0.165 Angle : 0.598 9.467 40881 Z= 0.306 Chirality : 0.045 0.323 4747 Planarity : 0.004 0.087 5187 Dihedral : 6.383 59.390 5057 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 0.22 % Allowed : 5.72 % Favored : 94.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.14), residues: 3583 helix: 0.04 (0.17), residues: 952 sheet: 0.01 (0.22), residues: 540 loop : -1.18 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 214 TYR 0.020 0.001 TYR C 904 PHE 0.012 0.001 PHE A 759 TRP 0.028 0.002 TRP A 886 HIS 0.005 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00361 (29855) covalent geometry : angle 0.58181 (40629) SS BOND : bond 0.00327 ( 42) SS BOND : angle 0.87420 ( 84) hydrogen bonds : bond 0.05387 ( 902) hydrogen bonds : angle 6.41919 ( 2532) link_BETA1-4 : bond 0.00202 ( 6) link_BETA1-4 : angle 1.33550 ( 18) link_NAG-ASN : bond 0.00442 ( 50) link_NAG-ASN : angle 2.29435 ( 150) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 115 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8601 (t0) cc_final: 0.8270 (t0) REVERT: C 756 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7929 (t80) REVERT: C 869 MET cc_start: 0.8893 (pmm) cc_final: 0.8568 (pmm) REVERT: A 1050 MET cc_start: 0.8188 (ptt) cc_final: 0.7669 (ptt) REVERT: B 614 ASP cc_start: 0.8699 (m-30) cc_final: 0.8264 (p0) REVERT: D 123 MET cc_start: -0.2520 (ptp) cc_final: -0.2746 (ptt) REVERT: D 366 MET cc_start: 0.0872 (tpt) cc_final: 0.0512 (mmm) outliers start: 7 outliers final: 3 residues processed: 120 average time/residue: 0.1618 time to fit residues: 32.8844 Evaluate side-chains 95 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain D residue 505 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 249 optimal weight: 0.2980 chunk 321 optimal weight: 0.1980 chunk 53 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 269 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 218 optimal weight: 10.0000 chunk 213 optimal weight: 9.9990 chunk 157 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 81 ASN C 134 GLN C 448 ASN C 658 ASN C1010 GLN C1058 HIS A 450 ASN A 992 GLN A1011 GLN B 334 ASN B 655 HIS ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1135 ASN D 121 ASN D 194 ASN D 250 ASN D 373 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.108393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072469 restraints weight = 168944.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.072259 restraints weight = 78901.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.070507 restraints weight = 57112.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.071282 restraints weight = 44203.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.071557 restraints weight = 29096.700| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 29953 Z= 0.232 Angle : 0.631 9.613 40881 Z= 0.319 Chirality : 0.046 0.352 4747 Planarity : 0.004 0.082 5187 Dihedral : 5.922 59.796 5057 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.80 % Allowed : 10.20 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.14), residues: 3583 helix: 0.34 (0.17), residues: 963 sheet: -0.45 (0.22), residues: 549 loop : -1.26 (0.13), residues: 2071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.025 0.002 TYR C 904 PHE 0.018 0.002 PHE A 906 TRP 0.060 0.002 TRP A 886 HIS 0.009 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00504 (29855) covalent geometry : angle 0.61304 (40629) SS BOND : bond 0.00418 ( 42) SS BOND : angle 1.04140 ( 84) hydrogen bonds : bond 0.04661 ( 902) hydrogen bonds : angle 5.78966 ( 2532) link_BETA1-4 : bond 0.00279 ( 6) link_BETA1-4 : angle 1.24196 ( 18) link_NAG-ASN : bond 0.00480 ( 50) link_NAG-ASN : angle 2.44416 ( 150) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8603 (t0) cc_final: 0.8359 (t0) REVERT: C 756 TYR cc_start: 0.9033 (OUTLIER) cc_final: 0.8266 (t80) REVERT: A 740 MET cc_start: 0.9183 (tpp) cc_final: 0.8579 (tpp) REVERT: A 896 ILE cc_start: 0.9246 (mt) cc_final: 0.8908 (pt) REVERT: B 614 ASP cc_start: 0.8850 (m-30) cc_final: 0.8392 (p0) REVERT: B 714 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8658 (mt) REVERT: B 869 MET cc_start: 0.9015 (ptm) cc_final: 0.8792 (ptm) REVERT: B 904 TYR cc_start: 0.7675 (t80) cc_final: 0.7202 (t80) REVERT: B 1050 MET cc_start: 0.8086 (mtm) cc_final: 0.7803 (mtm) REVERT: D 82 MET cc_start: 0.6726 (tmm) cc_final: 0.6392 (ppp) REVERT: D 366 MET cc_start: 0.0219 (tpt) cc_final: -0.0290 (mmm) REVERT: D 408 MET cc_start: 0.1780 (ptm) cc_final: 0.1420 (ttt) outliers start: 25 outliers final: 9 residues processed: 124 average time/residue: 0.1520 time to fit residues: 33.3068 Evaluate side-chains 96 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain D residue 505 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 338 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 192 optimal weight: 2.9990 chunk 265 optimal weight: 0.0060 chunk 334 optimal weight: 30.0000 chunk 346 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 overall best weight: 1.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 764 ASN C 919 ASN A 675 GLN A 955 ASN A1011 GLN B 52 GLN B 245 HIS B 644 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.110475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.077326 restraints weight = 167177.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.076326 restraints weight = 87745.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.074611 restraints weight = 54396.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.075531 restraints weight = 39688.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.075392 restraints weight = 26408.057| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29953 Z= 0.126 Angle : 0.539 9.683 40881 Z= 0.270 Chirality : 0.044 0.334 4747 Planarity : 0.004 0.078 5187 Dihedral : 5.482 57.908 5057 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.02 % Allowed : 11.54 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.85 (0.14), residues: 3583 helix: 0.65 (0.17), residues: 957 sheet: -0.39 (0.21), residues: 545 loop : -1.22 (0.13), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.033 0.001 TYR C 904 PHE 0.014 0.001 PHE C 392 TRP 0.053 0.001 TRP A 886 HIS 0.003 0.000 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00279 (29855) covalent geometry : angle 0.52105 (40629) SS BOND : bond 0.00263 ( 42) SS BOND : angle 0.83341 ( 84) hydrogen bonds : bond 0.03768 ( 902) hydrogen bonds : angle 5.41146 ( 2532) link_BETA1-4 : bond 0.00306 ( 6) link_BETA1-4 : angle 1.11609 ( 18) link_NAG-ASN : bond 0.00444 ( 50) link_NAG-ASN : angle 2.25966 ( 150) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 98 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8466 (t0) cc_final: 0.8199 (t0) REVERT: C 756 TYR cc_start: 0.8865 (OUTLIER) cc_final: 0.8083 (t80) REVERT: C 869 MET cc_start: 0.8915 (pmm) cc_final: 0.8636 (pmm) REVERT: C 1122 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9153 (m) REVERT: A 740 MET cc_start: 0.8981 (tpp) cc_final: 0.8398 (tpp) REVERT: A 896 ILE cc_start: 0.9214 (mt) cc_final: 0.8965 (pt) REVERT: A 1050 MET cc_start: 0.8563 (ptt) cc_final: 0.8312 (ptt) REVERT: A 1122 VAL cc_start: 0.9533 (OUTLIER) cc_final: 0.9276 (m) REVERT: B 532 ASN cc_start: 0.8737 (t0) cc_final: 0.8520 (t0) REVERT: B 614 ASP cc_start: 0.8542 (m-30) cc_final: 0.8171 (p0) REVERT: B 869 MET cc_start: 0.8862 (ptm) cc_final: 0.8490 (ptm) REVERT: B 904 TYR cc_start: 0.7315 (t80) cc_final: 0.6983 (t80) REVERT: D 82 MET cc_start: 0.6614 (tmm) cc_final: 0.6313 (ppp) REVERT: D 366 MET cc_start: -0.0044 (tpt) cc_final: -0.0518 (mmm) outliers start: 32 outliers final: 15 residues processed: 122 average time/residue: 0.1413 time to fit residues: 30.9326 Evaluate side-chains 109 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 28 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 122 optimal weight: 10.0000 chunk 318 optimal weight: 8.9990 chunk 163 optimal weight: 0.8980 chunk 300 optimal weight: 3.9990 chunk 230 optimal weight: 30.0000 chunk 289 optimal weight: 2.9990 chunk 147 optimal weight: 0.4980 chunk 138 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 450 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.107745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.067832 restraints weight = 131811.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.062779 restraints weight = 69401.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.063311 restraints weight = 44971.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063771 restraints weight = 33194.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.063905 restraints weight = 26300.731| |-----------------------------------------------------------------------------| r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29953 Z= 0.118 Angle : 0.521 9.676 40881 Z= 0.259 Chirality : 0.044 0.336 4747 Planarity : 0.003 0.076 5187 Dihedral : 5.165 57.417 5057 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.37 % Allowed : 12.37 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.74 (0.14), residues: 3583 helix: 0.83 (0.17), residues: 944 sheet: -0.37 (0.21), residues: 559 loop : -1.17 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 44 TYR 0.020 0.001 TYR C 904 PHE 0.015 0.001 PHE C 855 TRP 0.051 0.001 TRP A 886 HIS 0.002 0.000 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00260 (29855) covalent geometry : angle 0.50309 (40629) SS BOND : bond 0.00260 ( 42) SS BOND : angle 0.78420 ( 84) hydrogen bonds : bond 0.03556 ( 902) hydrogen bonds : angle 5.14771 ( 2532) link_BETA1-4 : bond 0.00407 ( 6) link_BETA1-4 : angle 1.06339 ( 18) link_NAG-ASN : bond 0.00443 ( 50) link_NAG-ASN : angle 2.21651 ( 150) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 96 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8408 (t0) cc_final: 0.8137 (t0) REVERT: C 754 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9065 (pp) REVERT: C 756 TYR cc_start: 0.8849 (OUTLIER) cc_final: 0.8105 (t80) REVERT: C 869 MET cc_start: 0.8866 (pmm) cc_final: 0.8542 (pmm) REVERT: C 900 MET cc_start: 0.8733 (mpp) cc_final: 0.8232 (mpp) REVERT: C 1122 VAL cc_start: 0.9504 (OUTLIER) cc_final: 0.9156 (m) REVERT: A 740 MET cc_start: 0.9051 (tpp) cc_final: 0.8459 (tpp) REVERT: A 896 ILE cc_start: 0.9188 (mt) cc_final: 0.8950 (pt) REVERT: A 1122 VAL cc_start: 0.9553 (OUTLIER) cc_final: 0.9297 (m) REVERT: B 532 ASN cc_start: 0.8747 (t0) cc_final: 0.8459 (t0) REVERT: B 614 ASP cc_start: 0.8404 (m-30) cc_final: 0.8097 (p0) REVERT: B 774 GLN cc_start: 0.8854 (mp10) cc_final: 0.8576 (mp10) REVERT: B 869 MET cc_start: 0.8669 (ptm) cc_final: 0.8363 (ptm) REVERT: D 366 MET cc_start: 0.0666 (tpt) cc_final: 0.0169 (mmm) outliers start: 43 outliers final: 23 residues processed: 132 average time/residue: 0.1532 time to fit residues: 36.2034 Evaluate side-chains 119 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 220 optimal weight: 7.9990 chunk 316 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 309 optimal weight: 10.0000 chunk 339 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 242 optimal weight: 0.7980 chunk 99 optimal weight: 0.8980 chunk 29 optimal weight: 7.9990 chunk 185 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.108402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.070128 restraints weight = 133041.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.067972 restraints weight = 77949.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.067736 restraints weight = 48314.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.067626 restraints weight = 37770.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.067449 restraints weight = 36753.064| |-----------------------------------------------------------------------------| r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 29953 Z= 0.103 Angle : 0.517 9.655 40881 Z= 0.256 Chirality : 0.044 0.335 4747 Planarity : 0.003 0.072 5187 Dihedral : 4.989 56.958 5057 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.60 % Allowed : 12.95 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.14), residues: 3583 helix: 0.93 (0.17), residues: 952 sheet: -0.22 (0.22), residues: 536 loop : -1.15 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 44 TYR 0.030 0.001 TYR A 904 PHE 0.028 0.001 PHE C 392 TRP 0.020 0.001 TRP C 886 HIS 0.002 0.000 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00229 (29855) covalent geometry : angle 0.49707 (40629) SS BOND : bond 0.00227 ( 42) SS BOND : angle 1.36842 ( 84) hydrogen bonds : bond 0.03408 ( 902) hydrogen bonds : angle 5.00763 ( 2532) link_BETA1-4 : bond 0.00320 ( 6) link_BETA1-4 : angle 1.02739 ( 18) link_NAG-ASN : bond 0.00447 ( 50) link_NAG-ASN : angle 2.16086 ( 150) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 102 time to evaluate : 1.044 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 460 ASN cc_start: 0.8626 (t0) cc_final: 0.8388 (t0) REVERT: C 754 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.8963 (pp) REVERT: C 756 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8045 (t80) REVERT: C 869 MET cc_start: 0.8871 (pmm) cc_final: 0.8515 (pmm) REVERT: C 1122 VAL cc_start: 0.9528 (OUTLIER) cc_final: 0.9202 (m) REVERT: A 427 ASP cc_start: 0.9133 (p0) cc_final: 0.8887 (p0) REVERT: A 697 MET cc_start: 0.8782 (tpp) cc_final: 0.8518 (tpp) REVERT: A 740 MET cc_start: 0.9046 (tpp) cc_final: 0.8432 (tpp) REVERT: A 762 GLN cc_start: 0.9073 (pp30) cc_final: 0.8761 (pp30) REVERT: A 896 ILE cc_start: 0.9158 (mt) cc_final: 0.8918 (pt) REVERT: A 1122 VAL cc_start: 0.9535 (OUTLIER) cc_final: 0.9289 (m) REVERT: B 532 ASN cc_start: 0.8897 (t0) cc_final: 0.8613 (t0) REVERT: B 614 ASP cc_start: 0.8431 (m-30) cc_final: 0.8079 (p0) REVERT: B 714 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8673 (mt) REVERT: B 774 GLN cc_start: 0.8742 (mp10) cc_final: 0.8506 (mp10) REVERT: B 869 MET cc_start: 0.8647 (ptm) cc_final: 0.8368 (ptm) REVERT: D 366 MET cc_start: 0.0192 (tpt) cc_final: -0.0266 (mmm) outliers start: 50 outliers final: 29 residues processed: 144 average time/residue: 0.1514 time to fit residues: 40.0604 Evaluate side-chains 126 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 318 optimal weight: 5.9990 chunk 214 optimal weight: 10.0000 chunk 359 optimal weight: 40.0000 chunk 292 optimal weight: 4.9990 chunk 139 optimal weight: 10.0000 chunk 321 optimal weight: 40.0000 chunk 174 optimal weight: 2.9990 chunk 176 optimal weight: 4.9990 chunk 182 optimal weight: 0.1980 chunk 289 optimal weight: 0.8980 chunk 205 optimal weight: 20.0000 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 542 ASN A 965 GLN ** A1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS B 388 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** B 969 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.108328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.075024 restraints weight = 167089.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.076128 restraints weight = 85817.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.075507 restraints weight = 47858.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.075449 restraints weight = 43735.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.075157 restraints weight = 38690.235| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29953 Z= 0.209 Angle : 0.602 11.528 40881 Z= 0.304 Chirality : 0.045 0.345 4747 Planarity : 0.004 0.073 5187 Dihedral : 5.241 58.198 5057 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.53 % Allowed : 14.10 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.76 (0.14), residues: 3583 helix: 0.85 (0.17), residues: 965 sheet: -0.47 (0.22), residues: 565 loop : -1.19 (0.14), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 905 TYR 0.016 0.001 TYR C 904 PHE 0.019 0.002 PHE C 855 TRP 0.031 0.002 TRP A 886 HIS 0.004 0.001 HIS A1083 Details of bonding type rmsd covalent geometry : bond 0.00458 (29855) covalent geometry : angle 0.58244 (40629) SS BOND : bond 0.00399 ( 42) SS BOND : angle 1.37629 ( 84) hydrogen bonds : bond 0.03740 ( 902) hydrogen bonds : angle 5.15030 ( 2532) link_BETA1-4 : bond 0.00383 ( 6) link_BETA1-4 : angle 1.22567 ( 18) link_NAG-ASN : bond 0.00471 ( 50) link_NAG-ASN : angle 2.37337 ( 150) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 86 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9083 (pp) REVERT: C 756 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8181 (t80) REVERT: C 1122 VAL cc_start: 0.9514 (OUTLIER) cc_final: 0.9199 (m) REVERT: A 740 MET cc_start: 0.8999 (tpp) cc_final: 0.8366 (tpp) REVERT: A 1122 VAL cc_start: 0.9501 (OUTLIER) cc_final: 0.9279 (m) REVERT: B 532 ASN cc_start: 0.9159 (t0) cc_final: 0.8910 (t0) REVERT: B 614 ASP cc_start: 0.8753 (m-30) cc_final: 0.8393 (p0) REVERT: B 714 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8735 (mt) REVERT: B 756 TYR cc_start: 0.9039 (OUTLIER) cc_final: 0.8243 (t80) REVERT: B 774 GLN cc_start: 0.8908 (mp10) cc_final: 0.8648 (mp10) REVERT: B 869 MET cc_start: 0.8768 (ptm) cc_final: 0.8401 (ptm) REVERT: B 904 TYR cc_start: 0.7590 (t80) cc_final: 0.7198 (t80) REVERT: D 366 MET cc_start: -0.0150 (tpt) cc_final: -0.0397 (mmm) outliers start: 48 outliers final: 37 residues processed: 129 average time/residue: 0.1486 time to fit residues: 34.4940 Evaluate side-chains 126 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 46 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 330 optimal weight: 0.0270 chunk 305 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 139 optimal weight: 9.9990 chunk 219 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 356 optimal weight: 0.7980 chunk 103 optimal weight: 0.9980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 969 ASN D 60 GLN D 228 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.107431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.068112 restraints weight = 132918.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.061831 restraints weight = 71616.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.062359 restraints weight = 45091.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.062770 restraints weight = 32893.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.062929 restraints weight = 26599.790| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 29953 Z= 0.101 Angle : 0.528 9.968 40881 Z= 0.262 Chirality : 0.044 0.335 4747 Planarity : 0.003 0.072 5187 Dihedral : 5.000 56.642 5057 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.57 % Allowed : 14.16 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.65 (0.14), residues: 3583 helix: 0.96 (0.17), residues: 958 sheet: -0.36 (0.22), residues: 540 loop : -1.15 (0.13), residues: 2085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.023 0.001 TYR C 707 PHE 0.011 0.001 PHE C 392 TRP 0.021 0.001 TRP A 886 HIS 0.002 0.000 HIS D 228 Details of bonding type rmsd covalent geometry : bond 0.00222 (29855) covalent geometry : angle 0.50968 (40629) SS BOND : bond 0.00236 ( 42) SS BOND : angle 1.09587 ( 84) hydrogen bonds : bond 0.03361 ( 902) hydrogen bonds : angle 4.94387 ( 2532) link_BETA1-4 : bond 0.00331 ( 6) link_BETA1-4 : angle 1.01717 ( 18) link_NAG-ASN : bond 0.00450 ( 50) link_NAG-ASN : angle 2.19983 ( 150) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 92 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9069 (pp) REVERT: C 756 TYR cc_start: 0.8743 (OUTLIER) cc_final: 0.8060 (t80) REVERT: C 869 MET cc_start: 0.8884 (pmm) cc_final: 0.8675 (pmm) REVERT: C 1122 VAL cc_start: 0.9541 (OUTLIER) cc_final: 0.9218 (m) REVERT: A 427 ASP cc_start: 0.8913 (p0) cc_final: 0.8680 (p0) REVERT: A 740 MET cc_start: 0.8954 (tpp) cc_final: 0.8332 (tpp) REVERT: A 896 ILE cc_start: 0.9204 (mt) cc_final: 0.8987 (pt) REVERT: A 1122 VAL cc_start: 0.9553 (OUTLIER) cc_final: 0.9318 (m) REVERT: B 532 ASN cc_start: 0.8866 (t0) cc_final: 0.8516 (t0) REVERT: B 614 ASP cc_start: 0.8440 (m-30) cc_final: 0.8188 (p0) REVERT: B 714 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8702 (mt) REVERT: B 756 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 774 GLN cc_start: 0.8799 (mp10) cc_final: 0.8549 (mp10) REVERT: B 869 MET cc_start: 0.8522 (ptm) cc_final: 0.8237 (ptm) REVERT: B 904 TYR cc_start: 0.7224 (t80) cc_final: 0.6912 (t80) REVERT: D 82 MET cc_start: 0.7104 (tmm) cc_final: 0.6880 (ppp) REVERT: D 366 MET cc_start: 0.0553 (tpt) cc_final: 0.0249 (mmm) outliers start: 49 outliers final: 35 residues processed: 134 average time/residue: 0.1466 time to fit residues: 35.5251 Evaluate side-chains 132 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 91 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 896 ILE Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 714 ILE Chi-restraints excluded: chain B residue 739 THR Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 438 PHE Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 345 optimal weight: 20.0000 chunk 93 optimal weight: 5.9990 chunk 221 optimal weight: 20.0000 chunk 22 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 307 optimal weight: 20.0000 chunk 169 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 chunk 227 optimal weight: 30.0000 chunk 220 optimal weight: 1.9990 chunk 251 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 955 ASN A1048 HIS A1106 GLN B 804 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.103352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.057628 restraints weight = 125676.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058051 restraints weight = 74299.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058376 restraints weight = 54714.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058376 restraints weight = 44424.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.058376 restraints weight = 44423.739| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29953 Z= 0.230 Angle : 0.635 9.861 40881 Z= 0.320 Chirality : 0.045 0.350 4747 Planarity : 0.004 0.070 5187 Dihedral : 5.413 57.981 5057 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.63 % Allowed : 14.39 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.87 (0.14), residues: 3583 helix: 0.73 (0.17), residues: 976 sheet: -0.59 (0.22), residues: 565 loop : -1.25 (0.14), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 44 TYR 0.027 0.002 TYR A 741 PHE 0.023 0.002 PHE C 855 TRP 0.024 0.001 TRP C 886 HIS 0.004 0.001 HIS C1064 Details of bonding type rmsd covalent geometry : bond 0.00498 (29855) covalent geometry : angle 0.61504 (40629) SS BOND : bond 0.00462 ( 42) SS BOND : angle 1.41713 ( 84) hydrogen bonds : bond 0.03846 ( 902) hydrogen bonds : angle 5.21107 ( 2532) link_BETA1-4 : bond 0.00363 ( 6) link_BETA1-4 : angle 1.24795 ( 18) link_NAG-ASN : bond 0.00513 ( 50) link_NAG-ASN : angle 2.48495 ( 150) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 85 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9515 (OUTLIER) cc_final: 0.9137 (pp) REVERT: C 756 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8214 (t80) REVERT: C 869 MET cc_start: 0.9037 (pmm) cc_final: 0.8812 (pmm) REVERT: C 1122 VAL cc_start: 0.9544 (OUTLIER) cc_final: 0.9265 (m) REVERT: A 740 MET cc_start: 0.9219 (tpp) cc_final: 0.8780 (tpp) REVERT: A 1122 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9285 (m) REVERT: B 532 ASN cc_start: 0.9247 (t0) cc_final: 0.8925 (t0) REVERT: B 756 TYR cc_start: 0.9121 (OUTLIER) cc_final: 0.8351 (t80) REVERT: B 869 MET cc_start: 0.8744 (ptm) cc_final: 0.8442 (ptm) REVERT: B 904 TYR cc_start: 0.7696 (t80) cc_final: 0.7265 (t80) REVERT: D 82 MET cc_start: 0.7097 (tmm) cc_final: 0.6869 (ppp) REVERT: D 366 MET cc_start: 0.0327 (tpt) cc_final: -0.0012 (mmm) outliers start: 51 outliers final: 39 residues processed: 133 average time/residue: 0.1542 time to fit residues: 35.9694 Evaluate side-chains 125 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 81 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1106 GLN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 503 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 20 optimal weight: 10.0000 chunk 228 optimal weight: 0.9980 chunk 7 optimal weight: 20.0000 chunk 211 optimal weight: 8.9990 chunk 244 optimal weight: 30.0000 chunk 214 optimal weight: 10.0000 chunk 174 optimal weight: 0.6980 chunk 343 optimal weight: 0.9990 chunk 336 optimal weight: 30.0000 chunk 202 optimal weight: 9.9990 chunk 181 optimal weight: 0.9980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.107520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073110 restraints weight = 165005.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.073025 restraints weight = 85062.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.071583 restraints weight = 55011.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.072190 restraints weight = 43396.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.072156 restraints weight = 30070.202| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29953 Z= 0.185 Angle : 0.591 10.739 40881 Z= 0.295 Chirality : 0.045 0.346 4747 Planarity : 0.004 0.070 5187 Dihedral : 5.336 56.942 5057 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.57 % Allowed : 14.55 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.89 (0.14), residues: 3583 helix: 0.80 (0.17), residues: 977 sheet: -0.62 (0.22), residues: 558 loop : -1.31 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 44 TYR 0.020 0.001 TYR C 707 PHE 0.021 0.001 PHE C 392 TRP 0.018 0.001 TRP C 886 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00403 (29855) covalent geometry : angle 0.57182 (40629) SS BOND : bond 0.00381 ( 42) SS BOND : angle 1.26405 ( 84) hydrogen bonds : bond 0.03598 ( 902) hydrogen bonds : angle 5.10108 ( 2532) link_BETA1-4 : bond 0.00323 ( 6) link_BETA1-4 : angle 1.08778 ( 18) link_NAG-ASN : bond 0.00462 ( 50) link_NAG-ASN : angle 2.39393 ( 150) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7166 Ramachandran restraints generated. 3583 Oldfield, 0 Emsley, 3583 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 83 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 425 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9126 (tt) REVERT: C 754 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9102 (pp) REVERT: C 756 TYR cc_start: 0.8885 (OUTLIER) cc_final: 0.8163 (t80) REVERT: C 869 MET cc_start: 0.8992 (pmm) cc_final: 0.8759 (pmm) REVERT: C 1122 VAL cc_start: 0.9518 (OUTLIER) cc_final: 0.9236 (m) REVERT: A 740 MET cc_start: 0.9099 (tpp) cc_final: 0.8546 (tpp) REVERT: A 1122 VAL cc_start: 0.9494 (OUTLIER) cc_final: 0.9289 (m) REVERT: B 532 ASN cc_start: 0.9147 (t0) cc_final: 0.8775 (t0) REVERT: B 614 ASP cc_start: 0.8237 (p0) cc_final: 0.7987 (p0) REVERT: B 756 TYR cc_start: 0.9057 (OUTLIER) cc_final: 0.8296 (t80) REVERT: B 774 GLN cc_start: 0.8921 (mp10) cc_final: 0.8631 (mp10) REVERT: B 869 MET cc_start: 0.8773 (ptm) cc_final: 0.8470 (ptm) REVERT: B 904 TYR cc_start: 0.7556 (t80) cc_final: 0.7145 (t80) REVERT: D 82 MET cc_start: 0.7183 (tmm) cc_final: 0.6849 (ppp) REVERT: D 366 MET cc_start: -0.1028 (tpt) cc_final: -0.1287 (mmm) REVERT: D 603 PHE cc_start: 0.2838 (t80) cc_final: 0.2489 (p90) outliers start: 49 outliers final: 42 residues processed: 130 average time/residue: 0.1530 time to fit residues: 34.9975 Evaluate side-chains 132 residues out of total 3187 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 84 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain C residue 460 ASN Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 756 TYR Chi-restraints excluded: chain C residue 759 PHE Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 898 PHE Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1027 THR Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 756 TYR Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 610 VAL Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 699 LEU Chi-restraints excluded: chain B residue 756 TYR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 954 GLN Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1122 VAL Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain D residue 151 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 361 random chunks: chunk 270 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 17 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 949 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS A1106 GLN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.107860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.073690 restraints weight = 165778.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.072312 restraints weight = 85218.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.070598 restraints weight = 58904.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.071549 restraints weight = 41567.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.071254 restraints weight = 29840.648| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29953 Z= 0.158 Angle : 0.573 11.989 40881 Z= 0.284 Chirality : 0.044 0.349 4747 Planarity : 0.003 0.071 5187 Dihedral : 5.151 56.683 5057 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.50 % Allowed : 14.87 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.83 (0.14), residues: 3583 helix: 0.98 (0.17), residues: 958 sheet: -0.62 (0.22), residues: 553 loop : -1.30 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 44 TYR 0.012 0.001 TYR A 279 PHE 0.018 0.001 PHE C 392 TRP 0.014 0.001 TRP C 886 HIS 0.006 0.001 HIS C 519 Details of bonding type rmsd covalent geometry : bond 0.00347 (29855) covalent geometry : angle 0.55438 (40629) SS BOND : bond 0.00313 ( 42) SS BOND : angle 1.20807 ( 84) hydrogen bonds : bond 0.03421 ( 902) hydrogen bonds : angle 4.95003 ( 2532) link_BETA1-4 : bond 0.00341 ( 6) link_BETA1-4 : angle 1.06803 ( 18) link_NAG-ASN : bond 0.00450 ( 50) link_NAG-ASN : angle 2.31667 ( 150) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7259.13 seconds wall clock time: 125 minutes 1.85 seconds (7501.85 seconds total)