Starting phenix.real_space_refine on Sat Mar 7 07:35:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kni_22950/03_2026/7kni_22950.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kni_22950/03_2026/7kni_22950.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7kni_22950/03_2026/7kni_22950.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kni_22950/03_2026/7kni_22950.map" model { file = "/net/cci-nas-00/data/ceres_data/7kni_22950/03_2026/7kni_22950.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kni_22950/03_2026/7kni_22950.cif" } resolution = 3.91 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 198 5.16 5 C 25249 2.51 5 N 6476 2.21 5 O 7651 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 244 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: 39574 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 8012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8012 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 978} 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: "B" Number of atoms: 8012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8012 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 978} 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: "C" Number of atoms: 8012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8012 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 978} 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: "F" 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: "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: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" 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: "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: "C" 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: "F" 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 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 Chain: "E" 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: 8.86, per 1000 atoms: 0.22 Number of scatterers: 39574 At special positions: 0 Unit cell: (168.222, 171.396, 239.108, 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 198 16.00 O 7651 8.00 N 6476 7.00 C 25249 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS F 133 " - pdb=" SG CYS F 141 " distance=2.03 Simple disulfide: pdb=" SG CYS F 344 " - pdb=" SG CYS F 361 " distance=2.03 Simple disulfide: pdb=" SG CYS F 530 " - pdb=" SG CYS F 542 " 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=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS E 133 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 344 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 530 " - pdb=" SG CYS E 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 G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A1134 " " NAG A1303 " - " ASN A1098 " " NAG A1304 " - " ASN A 282 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 801 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A 61 " " NAG A1311 " - " ASN A 234 " " NAG A1312 " - " ASN A 165 " " NAG A1313 " - " ASN A 603 " " 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 B 61 " " NAG B1310 " - " ASN B 234 " " NAG B1311 " - " ASN B 165 " " NAG B1312 " - " ASN B 343 " " NAG B1313 " - " ASN B 603 " " NAG B1314 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 616 " " NAG C1307 " - " ASN C 801 " " NAG C1308 " - " ASN C 709 " " NAG C1309 " - " ASN C1074 " " NAG C1310 " - " ASN C 61 " " NAG C1311 " - " ASN C 234 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 343 " " NAG C1314 " - " ASN C 603 " " 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 701 " - " ASN E 322 " " NAG E 702 " - " ASN E 432 " " NAG E 703 " - " ASN E 103 " " NAG E 704 " - " ASN E 90 " " NAG E 705 " - " ASN E 53 " " NAG F 701 " - " ASN F 322 " " NAG F 702 " - " ASN F 432 " " NAG F 703 " - " ASN F 103 " " NAG F 704 " - " ASN F 90 " " NAG F 705 " - " ASN F 53 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN B 717 " " NAG I 1 " - " ASN C 717 " " NAG J 1 " - " ASN F 546 " " NAG K 1 " - " ASN D 546 " " NAG L 1 " - " ASN E 546 " Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 2.1 seconds 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9186 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 51 sheets defined 38.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.52 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.660A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.814A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.897A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.740A 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 417 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 738 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 4.391A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 removed outlier: 4.006A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.647A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 946 through 968 removed outlier: 3.923A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N SER A 967 " --> pdb=" O VAL A 963 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.518A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.858A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.859A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.565A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N THR B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.902A pdb=" N TYR B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) removed outlier: 3.741A 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 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.563A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.716A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 774 " --> pdb=" O ILE B 770 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.556A pdb=" N LYS B 825 " --> pdb=" O LEU B 821 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.523A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.831A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.553A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.328A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 946 through 968 removed outlier: 3.599A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL B 963 " --> pdb=" O LEU B 959 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.984A pdb=" N ARG B 983 " --> pdb=" O ASP B 979 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.797A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU B 996 " --> pdb=" O GLN B 992 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (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: 3.888A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B1148 " --> pdb=" O GLU B1144 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.536A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR C 302 " --> pdb=" O GLU C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 341 Processing helix chain 'C' and resid 365 through 370 removed outlier: 4.006A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 405 through 407 No H-bonds generated for 'chain 'C' and resid 405 through 407' Processing helix chain 'C' and resid 417 through 422 Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 3.627A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.522A pdb=" N ARG C 765 " --> pdb=" O THR C 761 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.582A pdb=" N LYS C 825 " --> pdb=" O LEU C 821 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 883 removed outlier: 3.770A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.755A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 4.193A pdb=" N ALA C 903 " --> pdb=" O ALA C 899 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.533A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.793A pdb=" N SER C 929 " --> pdb=" O ASN C 925 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 946 through 965 removed outlier: 3.897A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ASN C 953 " --> pdb=" O GLN C 949 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.011A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1148 removed outlier: 3.815A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE C1148 " --> pdb=" O GLU C1144 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 51 removed outlier: 3.781A pdb=" N HIS F 34 " --> pdb=" O ASP F 30 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 38 " --> pdb=" O HIS F 34 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 80 removed outlier: 3.797A pdb=" N VAL F 59 " --> pdb=" O THR F 55 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 65 " --> pdb=" O ASN F 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR F 78 " --> pdb=" O LYS F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 81 through 83 No H-bonds generated for 'chain 'F' and resid 81 through 83' Processing helix chain 'F' and resid 90 through 101 removed outlier: 3.561A pdb=" N LYS F 94 " --> pdb=" O ASN F 90 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLN F 96 " --> pdb=" O THR F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 128 removed outlier: 3.568A pdb=" N LYS F 114 " --> pdb=" O GLU F 110 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ARG F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASN F 117 " --> pdb=" O SER F 113 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE F 119 " --> pdb=" O ARG F 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 143 through 154 removed outlier: 3.976A pdb=" N ASN F 149 " --> pdb=" O GLU F 145 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N GLU F 150 " --> pdb=" O PRO F 146 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ILE F 151 " --> pdb=" O GLY F 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 170 removed outlier: 3.767A pdb=" N TRP F 168 " --> pdb=" O ALA F 164 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER F 170 " --> pdb=" O GLU F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.682A pdb=" N GLN F 175 " --> pdb=" O VAL F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 176 through 187 removed outlier: 3.858A pdb=" N GLU F 182 " --> pdb=" O PRO F 178 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 194 removed outlier: 3.537A pdb=" N ALA F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 204 removed outlier: 3.775A pdb=" N ARG F 204 " --> pdb=" O GLY F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 245 removed outlier: 4.043A pdb=" N GLU F 224 " --> pdb=" O GLY F 220 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLU F 231 " --> pdb=" O GLU F 227 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU F 232 " --> pdb=" O HIS F 228 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE F 233 " --> pdb=" O THR F 229 " (cutoff:3.500A) Proline residue: F 235 - end of helix Processing helix chain 'F' and resid 265 through 267 No H-bonds generated for 'chain 'F' and resid 265 through 267' Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 293 through 300 removed outlier: 3.965A pdb=" N VAL F 298 " --> pdb=" O THR F 294 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASP F 299 " --> pdb=" O ASP F 295 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN F 300 " --> pdb=" O ALA F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 303 through 319 removed outlier: 3.543A pdb=" N PHE F 308 " --> pdb=" O ALA F 304 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA F 311 " --> pdb=" O ILE F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 329 removed outlier: 4.489A pdb=" N TRP F 328 " --> pdb=" O THR F 324 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N GLU F 329 " --> pdb=" O GLN F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 324 through 329' Processing helix chain 'F' and resid 365 through 383 removed outlier: 3.890A pdb=" N HIS F 378 " --> pdb=" O HIS F 374 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE F 379 " --> pdb=" O GLU F 375 " (cutoff:3.500A) Processing helix chain 'F' and resid 399 through 413 removed outlier: 4.076A pdb=" N GLY F 405 " --> pdb=" O HIS F 401 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU F 406 " --> pdb=" O GLU F 402 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N MET F 408 " --> pdb=" O VAL F 404 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N SER F 409 " --> pdb=" O GLY F 405 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 422 removed outlier: 3.505A pdb=" N ILE F 421 " --> pdb=" O HIS F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 432 through 447 removed outlier: 4.111A pdb=" N PHE F 438 " --> pdb=" O THR F 434 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N THR F 445 " --> pdb=" O LYS F 441 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 466 removed outlier: 4.405A pdb=" N PHE F 452 " --> pdb=" O GLY F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 469 through 471 No H-bonds generated for 'chain 'F' and resid 469 through 471' Processing helix chain 'F' and resid 472 through 484 removed outlier: 3.560A pdb=" N LYS F 476 " --> pdb=" O GLN F 472 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU F 479 " --> pdb=" O LYS F 475 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 502 Processing helix chain 'F' and resid 503 through 508 Processing helix chain 'F' and resid 512 through 523 removed outlier: 4.043A pdb=" N TYR F 516 " --> pdb=" O PHE F 512 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR F 519 " --> pdb=" O TYR F 515 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU F 520 " --> pdb=" O TYR F 516 " (cutoff:3.500A) Processing helix chain 'F' and resid 523 through 533 Processing helix chain 'F' and resid 547 through 559 removed outlier: 4.116A pdb=" N MET F 557 " --> pdb=" O LYS F 553 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 572 removed outlier: 3.670A pdb=" N GLU F 571 " --> pdb=" O THR F 567 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 586 removed outlier: 4.143A pdb=" N LEU F 585 " --> pdb=" O VAL F 581 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN F 586 " --> pdb=" O ARG F 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 581 through 586' Processing helix chain 'F' and resid 588 through 599 removed outlier: 3.633A pdb=" N TRP F 594 " --> pdb=" O PRO F 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 3.776A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 3.843A pdb=" N VAL D 59 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU D 75 " --> pdb=" O ALA D 71 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA D 80 " --> pdb=" O GLN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 91 through 101 removed outlier: 3.709A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 128 removed outlier: 4.594A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE D 119 " --> pdb=" O ARG D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 4.340A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE D 151 " --> pdb=" O GLY D 147 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.764A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.637A 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: 4.505A pdb=" N GLU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 194 removed outlier: 4.366A pdb=" N ARG D 192 " --> pdb=" O ASN D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.643A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 247 removed outlier: 3.743A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU D 231 " --> pdb=" O GLU D 227 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Proline residue: D 235 - end of helix removed outlier: 3.824A pdb=" N HIS D 239 " --> pdb=" O PRO D 235 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS D 247 " --> pdb=" O TYR D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.865A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP D 299 " --> pdb=" O ASP D 295 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.504A pdb=" N GLU D 310 " --> pdb=" O ARG D 306 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 383 removed outlier: 3.616A pdb=" N MET D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 4.123A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 removed outlier: 3.512A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 447 removed outlier: 4.090A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 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: 3.667A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET D 480 " --> pdb=" O LYS D 476 " (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: 4.097A pdb=" N TYR D 516 " --> pdb=" O PHE D 512 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.793A 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: 3.946A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.694A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 586 removed outlier: 3.989A pdb=" N LEU D 585 " --> pdb=" O VAL D 581 " (cutoff:3.500A) removed outlier: 3.611A 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: 3.931A pdb=" N TRP D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 51 removed outlier: 3.777A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ASP E 38 " --> pdb=" O HIS E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 82 removed outlier: 4.070A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR E 78 " --> pdb=" O LYS E 74 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET E 82 " --> pdb=" O THR E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.722A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 4.573A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 3.881A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N MET E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN E 154 " --> pdb=" O GLU E 150 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 169 removed outlier: 3.705A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.654A pdb=" N GLN E 175 " --> pdb=" O VAL E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 176 through 187 removed outlier: 3.577A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 194 removed outlier: 4.425A pdb=" N ARG E 192 " --> pdb=" O ASN E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.584A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 245 removed outlier: 3.719A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.682A pdb=" N HIS E 239 " --> pdb=" O PRO E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 275 through 279 Processing helix chain 'E' and resid 293 through 300 removed outlier: 3.856A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.590A pdb=" N PHE E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU E 310 " --> pdb=" O ARG E 306 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA E 311 " --> pdb=" O ILE E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 329 removed outlier: 4.148A pdb=" N TRP E 328 " --> pdb=" O THR E 324 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU E 329 " --> pdb=" O GLN E 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 324 through 329' Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.874A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 399 through 413 removed outlier: 4.096A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 432 through 447 removed outlier: 4.039A pdb=" N PHE E 438 " --> pdb=" O THR E 434 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 466 Processing helix chain 'E' and resid 469 through 471 No H-bonds generated for 'chain 'E' and resid 469 through 471' Processing helix chain 'E' and resid 472 through 484 removed outlier: 3.594A pdb=" N LYS E 476 " --> pdb=" O GLN E 472 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU E 479 " --> pdb=" O LYS E 475 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 523 removed outlier: 4.038A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) Processing helix chain 'E' and resid 523 through 533 Processing helix chain 'E' and resid 547 through 559 removed outlier: 3.938A pdb=" N MET E 557 " --> pdb=" O LYS E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.674A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 586 removed outlier: 4.201A pdb=" N LEU E 585 " --> pdb=" O VAL E 581 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN E 586 " --> pdb=" O ARG E 582 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 581 through 586' Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.691A pdb=" N TRP E 594 " --> pdb=" O PRO E 590 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.806A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 204 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.806A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.640A pdb=" N TYR A 279 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.808A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.212A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356 removed outlier: 4.065A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.773A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.582A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLU A 583 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 578 " --> pdb=" O GLU A 583 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 642 through 645 removed outlier: 3.677A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 660 removed outlier: 4.333A pdb=" N THR A 696 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 658 " --> pdb=" O THR A 696 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.243A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 712 through 719 removed outlier: 6.484A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N TYR A1047 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 722 through 728 removed outlier: 3.666A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.241A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.534A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'B' and resid 28 through 31 removed outlier: 7.975A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.906A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 83 through 85 removed outlier: 4.633A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.955A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 356 removed outlier: 4.027A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.760A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 538 through 542 removed outlier: 3.534A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 642 through 645 removed outlier: 3.577A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.812A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N CYS B 671 " --> pdb=" O TYR B 695 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 703 through 704 removed outlier: 7.169A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.478A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 714 through 728 removed outlier: 6.478A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR B1066 " --> pdb=" O SER B 721 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 734 through 735 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 removed outlier: 3.533A pdb=" N LYS B1086 " --> pdb=" O HIS B1083 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N CYS B1082 " --> pdb=" O VAL B1133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 28 through 31 removed outlier: 8.134A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG C 190 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.066A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.623A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS C 129 " --> pdb=" O LEU C 118 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ILE C 128 " --> pdb=" O TYR C 170 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TYR C 170 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.776A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 356 removed outlier: 4.094A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS C 356 " --> pdb=" O ALA C 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 452 through 453 removed outlier: 3.795A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 538 through 542 removed outlier: 3.607A pdb=" N GLY C 550 " --> pdb=" O VAL C 539 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 642 through 644 removed outlier: 3.639A pdb=" N PHE C 643 " --> pdb=" O LEU C 650 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU C 650 " --> pdb=" O PHE C 643 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.946A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 712 through 719 removed outlier: 6.901A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 722 through 728 removed outlier: 3.546A pdb=" N GLU C 725 " --> pdb=" O PHE C1062 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.277A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.769A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'F' and resid 262 through 263 removed outlier: 5.601A pdb=" N LEU F 262 " --> pdb=" O VAL F 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'F' and resid 347 through 352 removed outlier: 5.969A pdb=" N ASP F 355 " --> pdb=" O LEU F 351 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 262 through 263 removed outlier: 5.537A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'D' and resid 347 through 352 removed outlier: 3.527A pdb=" N LEU D 359 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 263 removed outlier: 5.969A pdb=" N LEU E 262 " --> pdb=" O VAL E 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'E' and resid 347 through 352 removed outlier: 5.964A pdb=" N ASP E 355 " --> pdb=" O LEU E 351 " (cutoff:3.500A) 1412 hydrogen bonds defined for protein. 3966 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: 8.90 Time building geometry restraints manager: 5.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12551 1.34 - 1.46: 10187 1.46 - 1.59: 17505 1.59 - 1.71: 0 1.71 - 1.84: 291 Bond restraints: 40534 Sorted by residual: bond pdb=" N ASN A1074 " pdb=" CA ASN A1074 " ideal model delta sigma weight residual 1.454 1.484 -0.030 1.17e-02 7.31e+03 6.62e+00 bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.455 1.486 -0.032 1.26e-02 6.30e+03 6.34e+00 bond pdb=" N ASN B1074 " pdb=" CA ASN B1074 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.27e-02 6.20e+03 6.16e+00 bond pdb=" N ASN C 709 " pdb=" CA ASN C 709 " ideal model delta sigma weight residual 1.457 1.490 -0.033 1.35e-02 5.49e+03 5.85e+00 bond pdb=" N ASN C 616 " pdb=" CA ASN C 616 " ideal model delta sigma weight residual 1.456 1.484 -0.029 1.22e-02 6.72e+03 5.56e+00 ... (remaining 40529 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.21: 54212 2.21 - 4.42: 830 4.42 - 6.63: 69 6.63 - 8.84: 10 8.84 - 11.05: 3 Bond angle restraints: 55124 Sorted by residual: angle pdb=" N TYR D 180 " pdb=" CA TYR D 180 " pdb=" C TYR D 180 " ideal model delta sigma weight residual 111.82 117.48 -5.66 1.16e+00 7.43e-01 2.38e+01 angle pdb=" CA MET D 152 " pdb=" CB MET D 152 " pdb=" CG MET D 152 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.76e+01 angle pdb=" N LEU D 179 " pdb=" CA LEU D 179 " pdb=" C LEU D 179 " ideal model delta sigma weight residual 112.45 117.80 -5.35 1.39e+00 5.18e-01 1.48e+01 angle pdb=" CB MET E 579 " pdb=" CG MET E 579 " pdb=" SD MET E 579 " ideal model delta sigma weight residual 112.70 123.75 -11.05 3.00e+00 1.11e-01 1.36e+01 angle pdb=" N TRP D 594 " pdb=" CA TRP D 594 " pdb=" CB TRP D 594 " ideal model delta sigma weight residual 110.16 115.51 -5.35 1.48e+00 4.57e-01 1.31e+01 ... (remaining 55119 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 22408 17.96 - 35.91: 2011 35.91 - 53.87: 412 53.87 - 71.83: 96 71.83 - 89.79: 33 Dihedral angle restraints: 24960 sinusoidal: 10707 harmonic: 14253 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -141.53 55.53 1 1.00e+01 1.00e-02 4.17e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -137.56 51.56 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -136.79 50.79 1 1.00e+01 1.00e-02 3.53e+01 ... (remaining 24957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 5719 0.084 - 0.168: 528 0.168 - 0.252: 18 0.252 - 0.336: 19 0.336 - 0.421: 2 Chirality restraints: 6286 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.28 -0.12 2.00e-02 2.50e+03 3.55e+01 chirality pdb=" C1 NAG A1309 " pdb=" ND2 ASN A1074 " pdb=" C2 NAG A1309 " pdb=" O5 NAG A1309 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.42e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.05 -0.35 2.00e-01 2.50e+01 3.15e+00 ... (remaining 6283 not shown) Planarity restraints: 7102 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1301 " 0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG A1301 " -0.081 2.00e-02 2.50e+03 pdb=" C8 NAG A1301 " 0.089 2.00e-02 2.50e+03 pdb=" N2 NAG A1301 " -0.537 2.00e-02 2.50e+03 pdb=" O7 NAG A1301 " 0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1301 " -0.339 2.00e-02 2.50e+03 2.90e-01 1.05e+03 pdb=" C7 NAG B1301 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B1301 " -0.172 2.00e-02 2.50e+03 pdb=" N2 NAG B1301 " 0.510 2.00e-02 2.50e+03 pdb=" O7 NAG B1301 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1301 " 0.293 2.00e-02 2.50e+03 2.46e-01 7.59e+02 pdb=" C7 NAG C1301 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG C1301 " 0.187 2.00e-02 2.50e+03 pdb=" N2 NAG C1301 " -0.420 2.00e-02 2.50e+03 pdb=" O7 NAG C1301 " 0.017 2.00e-02 2.50e+03 ... (remaining 7099 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 489 2.62 - 3.19: 35488 3.19 - 3.76: 61350 3.76 - 4.33: 83750 4.33 - 4.90: 134526 Nonbonded interactions: 315603 Sorted by model distance: nonbonded pdb=" OD1 ASN C 540 " pdb=" OG1 THR C 549 " model vdw 2.045 3.040 nonbonded pdb=" OD1 ASN B 540 " pdb=" OG1 THR B 549 " model vdw 2.048 3.040 nonbonded pdb=" O LEU B 966 " pdb=" OG SER B 975 " model vdw 2.059 3.040 nonbonded pdb=" O ALA D 501 " pdb=" OG SER D 507 " model vdw 2.088 3.040 nonbonded pdb=" NH2 ARG D 177 " pdb=" O TYR D 497 " model vdw 2.090 3.120 ... (remaining 315598 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' selection = (chain 'B' and resid 26 through 1313) selection = (chain 'C' and resid 26 through 1313) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 4.380 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: 0.050 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 38.790 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5677 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 0.054 40650 Z= 0.180 Angle : 0.655 11.050 55424 Z= 0.328 Chirality : 0.047 0.421 6286 Planarity : 0.008 0.302 7040 Dihedral : 14.194 89.785 15630 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.07 % Allowed : 0.45 % Favored : 99.48 % 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: -1.75 (0.11), residues: 4824 helix: -1.56 (0.12), residues: 1495 sheet: 0.08 (0.22), residues: 540 loop : -1.15 (0.11), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 306 TYR 0.017 0.001 TYR F 243 PHE 0.046 0.001 PHE D 315 TRP 0.047 0.001 TRP D 594 HIS 0.015 0.001 HIS F 540 Details of bonding type rmsd covalent geometry : bond 0.00378 (40534) covalent geometry : angle 0.63849 (55124) SS BOND : bond 0.00182 ( 48) SS BOND : angle 0.90846 ( 96) hydrogen bonds : bond 0.30018 ( 1386) hydrogen bonds : angle 9.27094 ( 3966) link_BETA1-4 : bond 0.00293 ( 6) link_BETA1-4 : angle 0.83903 ( 18) link_NAG-ASN : bond 0.00721 ( 62) link_NAG-ASN : angle 2.58868 ( 186) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 254 time to evaluate : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8023 (tm-30) cc_final: 0.7700 (tm-30) REVERT: B 153 MET cc_start: 0.1872 (pmm) cc_final: 0.1497 (pmm) REVERT: B 915 VAL cc_start: 0.7177 (p) cc_final: 0.6856 (p) REVERT: B 1038 LYS cc_start: 0.5522 (mmtt) cc_final: 0.5218 (mmmt) REVERT: C 42 VAL cc_start: 0.5356 (t) cc_final: 0.4886 (t) REVERT: F 247 LYS cc_start: 0.7651 (mppt) cc_final: 0.7236 (mtmm) REVERT: F 480 MET cc_start: 0.6131 (tmm) cc_final: 0.5915 (tmm) REVERT: F 557 MET cc_start: 0.0501 (ppp) cc_final: 0.0273 (ppp) REVERT: F 579 MET cc_start: 0.2043 (mtt) cc_final: 0.1629 (mtt) REVERT: D 292 ASP cc_start: 0.4617 (m-30) cc_final: 0.4306 (m-30) REVERT: D 376 MET cc_start: -0.0418 (mtt) cc_final: -0.0742 (mtm) REVERT: D 455 MET cc_start: 0.5995 (tmm) cc_final: 0.4909 (ppp) REVERT: D 610 TRP cc_start: 0.7677 (m-90) cc_final: 0.7438 (m-90) REVERT: E 50 TYR cc_start: 0.9496 (t80) cc_final: 0.9240 (t80) REVERT: E 361 CYS cc_start: 0.4262 (m) cc_final: 0.4020 (t) outliers start: 3 outliers final: 2 residues processed: 256 average time/residue: 0.2054 time to fit residues: 92.6571 Evaluate side-chains 194 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 192 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain D residue 152 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 5.9990 chunk 455 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.0050 chunk 470 optimal weight: 9.9990 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 644 GLN A 655 HIS A1023 ASN A1054 GLN B 450 ASN B1106 GLN C 121 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 751 ASN C 895 GLN C 901 GLN F 330 ASN F 373 HIS D 188 ASN D 330 ASN E 188 ASN E 265 HIS E 330 ASN E 373 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.123796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.084594 restraints weight = 291882.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.085101 restraints weight = 173867.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.084529 restraints weight = 119644.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.084637 restraints weight = 116510.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.085682 restraints weight = 114930.349| |-----------------------------------------------------------------------------| r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 40650 Z= 0.177 Angle : 0.647 11.689 55424 Z= 0.326 Chirality : 0.047 0.299 6286 Planarity : 0.004 0.054 7040 Dihedral : 5.831 59.868 6654 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 0.57 % Allowed : 7.68 % Favored : 91.76 % 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: -1.31 (0.11), residues: 4824 helix: -0.54 (0.12), residues: 1592 sheet: 0.10 (0.23), residues: 500 loop : -1.26 (0.11), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 177 TYR 0.023 0.002 TYR B 917 PHE 0.023 0.002 PHE B 718 TRP 0.024 0.002 TRP D 163 HIS 0.006 0.001 HIS E 378 Details of bonding type rmsd covalent geometry : bond 0.00367 (40534) covalent geometry : angle 0.61640 (55124) SS BOND : bond 0.00360 ( 48) SS BOND : angle 1.08045 ( 96) hydrogen bonds : bond 0.05456 ( 1386) hydrogen bonds : angle 6.03308 ( 3966) link_BETA1-4 : bond 0.01841 ( 6) link_BETA1-4 : angle 1.54367 ( 18) link_NAG-ASN : bond 0.00842 ( 62) link_NAG-ASN : angle 3.36752 ( 186) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 227 time to evaluate : 1.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 779 GLN cc_start: 0.8853 (tm-30) cc_final: 0.8473 (tm-30) REVERT: A 900 MET cc_start: 0.7931 (pmm) cc_final: 0.7578 (pmm) REVERT: A 1050 MET cc_start: 0.8004 (mtm) cc_final: 0.7740 (mtm) REVERT: B 269 TYR cc_start: 0.7052 (m-10) cc_final: 0.6637 (m-10) REVERT: B 731 MET cc_start: 0.8381 (ppp) cc_final: 0.8064 (ppp) REVERT: B 950 ASP cc_start: 0.8877 (p0) cc_final: 0.8638 (p0) REVERT: C 42 VAL cc_start: 0.6064 (t) cc_final: 0.5800 (t) REVERT: C 1031 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6349 (pp20) REVERT: C 1038 LYS cc_start: 0.8357 (tppt) cc_final: 0.8027 (mmpt) REVERT: F 557 MET cc_start: 0.4012 (ppp) cc_final: 0.2987 (ppp) REVERT: D 152 MET cc_start: 0.1044 (tmm) cc_final: 0.0602 (tmm) REVERT: D 455 MET cc_start: 0.5523 (tmm) cc_final: 0.5153 (ppp) REVERT: E 249 MET cc_start: 0.6757 (OUTLIER) cc_final: 0.6026 (ptt) outliers start: 24 outliers final: 10 residues processed: 242 average time/residue: 0.2036 time to fit residues: 86.5163 Evaluate side-chains 203 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 191 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1103 PHE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 249 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 128 optimal weight: 6.9990 chunk 407 optimal weight: 50.0000 chunk 196 optimal weight: 2.9990 chunk 434 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 308 optimal weight: 9.9990 chunk 243 optimal weight: 10.0000 chunk 201 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 804 GLN ** B 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 655 HIS ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 340 GLN F 417 HIS E 175 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.120986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.081400 restraints weight = 293474.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.082084 restraints weight = 176904.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.080889 restraints weight = 116853.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.080165 restraints weight = 108644.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.081431 restraints weight = 105255.387| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 40650 Z= 0.188 Angle : 0.624 13.978 55424 Z= 0.314 Chirality : 0.046 0.309 6286 Planarity : 0.004 0.064 7040 Dihedral : 5.277 58.882 6648 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.08 % Allowed : 10.48 % Favored : 88.43 % 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: -1.19 (0.12), residues: 4824 helix: -0.18 (0.12), residues: 1667 sheet: -0.52 (0.21), residues: 547 loop : -1.24 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 460 TYR 0.023 0.001 TYR A 707 PHE 0.017 0.002 PHE D 315 TRP 0.020 0.001 TRP D 163 HIS 0.008 0.001 HIS E 345 Details of bonding type rmsd covalent geometry : bond 0.00389 (40534) covalent geometry : angle 0.59604 (55124) SS BOND : bond 0.00676 ( 48) SS BOND : angle 1.16744 ( 96) hydrogen bonds : bond 0.05091 ( 1386) hydrogen bonds : angle 5.59140 ( 3966) link_BETA1-4 : bond 0.00584 ( 6) link_BETA1-4 : angle 0.93115 ( 18) link_NAG-ASN : bond 0.00709 ( 62) link_NAG-ASN : angle 3.16566 ( 186) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 200 time to evaluate : 1.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 950 ASP cc_start: 0.8854 (p0) cc_final: 0.8639 (p0) REVERT: C 1031 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.5975 (pp20) REVERT: F 123 MET cc_start: 0.2326 (ttp) cc_final: 0.1989 (ptm) REVERT: F 557 MET cc_start: 0.4392 (ppp) cc_final: 0.3371 (ppp) REVERT: D 152 MET cc_start: 0.0600 (tmm) cc_final: 0.0197 (tmm) REVERT: D 297 MET cc_start: 0.0682 (mtt) cc_final: 0.0027 (mmt) REVERT: D 455 MET cc_start: 0.5113 (tmm) cc_final: 0.4482 (ppp) REVERT: E 249 MET cc_start: 0.6825 (OUTLIER) cc_final: 0.6202 (ptt) outliers start: 46 outliers final: 25 residues processed: 234 average time/residue: 0.2055 time to fit residues: 84.9640 Evaluate side-chains 207 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 366 MET Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 476 optimal weight: 40.0000 chunk 443 optimal weight: 2.9990 chunk 447 optimal weight: 20.0000 chunk 166 optimal weight: 0.7980 chunk 156 optimal weight: 6.9990 chunk 41 optimal weight: 40.0000 chunk 301 optimal weight: 5.9990 chunk 168 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 225 optimal weight: 8.9990 chunk 383 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 245 HIS B 655 HIS B 762 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1101 HIS C 450 ASN C 644 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.121688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.081795 restraints weight = 290472.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.081459 restraints weight = 173510.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.080350 restraints weight = 125935.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.080532 restraints weight = 93968.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.080455 restraints weight = 84526.946| |-----------------------------------------------------------------------------| r_work (final): 0.3803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 40650 Z= 0.121 Angle : 0.556 11.063 55424 Z= 0.275 Chirality : 0.045 0.305 6286 Planarity : 0.004 0.067 7040 Dihedral : 4.927 55.544 6648 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.20 % Allowed : 12.25 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.12), residues: 4824 helix: 0.16 (0.13), residues: 1655 sheet: -0.47 (0.21), residues: 531 loop : -1.17 (0.12), residues: 2638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 905 TYR 0.013 0.001 TYR B 707 PHE 0.012 0.001 PHE A1095 TRP 0.017 0.001 TRP D 163 HIS 0.004 0.001 HIS E 417 Details of bonding type rmsd covalent geometry : bond 0.00256 (40534) covalent geometry : angle 0.52544 (55124) SS BOND : bond 0.00594 ( 48) SS BOND : angle 1.23951 ( 96) hydrogen bonds : bond 0.04001 ( 1386) hydrogen bonds : angle 5.18770 ( 3966) link_BETA1-4 : bond 0.00542 ( 6) link_BETA1-4 : angle 0.76749 ( 18) link_NAG-ASN : bond 0.00743 ( 62) link_NAG-ASN : angle 3.09104 ( 186) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 205 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 LEU cc_start: 0.9481 (tp) cc_final: 0.9256 (pp) REVERT: A 779 GLN cc_start: 0.8887 (tm-30) cc_final: 0.8497 (tm-30) REVERT: B 649 CYS cc_start: 0.4680 (OUTLIER) cc_final: 0.4207 (t) REVERT: B 913 GLN cc_start: 0.5392 (pt0) cc_final: 0.5136 (pt0) REVERT: B 950 ASP cc_start: 0.8747 (p0) cc_final: 0.8546 (p0) REVERT: C 1031 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6035 (pp20) REVERT: C 1050 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6691 (pmm) REVERT: F 297 MET cc_start: -0.0848 (mtt) cc_final: -0.1615 (mmt) REVERT: F 557 MET cc_start: 0.4245 (ppp) cc_final: 0.3664 (ppp) REVERT: D 152 MET cc_start: 0.0703 (tmm) cc_final: 0.0256 (tmm) REVERT: D 323 MET cc_start: 0.6487 (tpt) cc_final: 0.6252 (tpp) REVERT: D 383 MET cc_start: 0.0456 (mtt) cc_final: 0.0229 (mtt) REVERT: D 474 MET cc_start: 0.7152 (mmt) cc_final: 0.5890 (mmp) REVERT: E 249 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.5966 (ptt) outliers start: 51 outliers final: 28 residues processed: 241 average time/residue: 0.2053 time to fit residues: 86.3412 Evaluate side-chains 215 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 327 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1055 SER Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 249 MET Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 482 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 425 optimal weight: 30.0000 chunk 16 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 296 optimal weight: 1.9990 chunk 348 optimal weight: 20.0000 chunk 390 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 266 optimal weight: 2.9990 chunk 247 optimal weight: 7.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 321 GLN A 542 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN B 762 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 907 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 535 HIS E 194 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.117307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.077061 restraints weight = 289215.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.076646 restraints weight = 168081.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.075776 restraints weight = 104244.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.074672 restraints weight = 88203.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.074847 restraints weight = 71233.108| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.158 40650 Z= 0.214 Angle : 0.672 12.697 55424 Z= 0.340 Chirality : 0.047 0.326 6286 Planarity : 0.005 0.070 7040 Dihedral : 5.228 59.205 6648 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.17 % Allowed : 13.45 % Favored : 84.38 % 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: -1.12 (0.12), residues: 4824 helix: 0.06 (0.13), residues: 1652 sheet: -0.91 (0.20), residues: 563 loop : -1.22 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B1107 TYR 0.045 0.002 TYR C 351 PHE 0.037 0.002 PHE C1075 TRP 0.017 0.002 TRP D 163 HIS 0.009 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00453 (40534) covalent geometry : angle 0.64412 (55124) SS BOND : bond 0.00627 ( 48) SS BOND : angle 1.76051 ( 96) hydrogen bonds : bond 0.04489 ( 1386) hydrogen bonds : angle 5.43145 ( 3966) link_BETA1-4 : bond 0.00442 ( 6) link_BETA1-4 : angle 1.16163 ( 18) link_NAG-ASN : bond 0.00697 ( 62) link_NAG-ASN : angle 3.12047 ( 186) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 187 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8674 (pt0) cc_final: 0.8455 (pt0) REVERT: B 900 MET cc_start: 0.6568 (mmt) cc_final: 0.6183 (mmt) REVERT: B 950 ASP cc_start: 0.8826 (p0) cc_final: 0.8519 (p0) REVERT: B 1031 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6683 (pp20) REVERT: C 1031 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6202 (pp20) REVERT: F 297 MET cc_start: -0.0661 (mtt) cc_final: -0.1168 (mmt) REVERT: F 455 MET cc_start: -0.0098 (ptt) cc_final: -0.0461 (ptt) REVERT: F 557 MET cc_start: 0.4838 (ppp) cc_final: 0.3898 (ppp) REVERT: D 297 MET cc_start: 0.0634 (mmt) cc_final: 0.0329 (mmt) REVERT: D 474 MET cc_start: 0.7276 (mmt) cc_final: 0.5971 (mmp) REVERT: D 579 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5876 (tpp) REVERT: E 249 MET cc_start: 0.6653 (mmt) cc_final: 0.6003 (ptt) outliers start: 92 outliers final: 40 residues processed: 260 average time/residue: 0.2062 time to fit residues: 93.5881 Evaluate side-chains 207 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 164 time to evaluate : 1.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 954 GLN Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 860 VAL Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 818 ILE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 304 optimal weight: 4.9990 chunk 479 optimal weight: 50.0000 chunk 241 optimal weight: 3.9990 chunk 227 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 259 optimal weight: 0.8980 chunk 332 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 73 optimal weight: 0.0470 chunk 372 optimal weight: 30.0000 chunk 262 optimal weight: 0.7980 overall best weight: 1.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN C 895 GLN ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.118547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.079356 restraints weight = 288250.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.080108 restraints weight = 170661.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.079251 restraints weight = 106885.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.078490 restraints weight = 96609.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.078045 restraints weight = 95355.210| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.4421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 40650 Z= 0.128 Angle : 0.577 11.526 55424 Z= 0.284 Chirality : 0.045 0.310 6286 Planarity : 0.004 0.070 7040 Dihedral : 4.943 56.088 6648 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.32 % Allowed : 14.84 % Favored : 83.84 % 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: -0.90 (0.12), residues: 4824 helix: 0.33 (0.13), residues: 1658 sheet: -0.85 (0.21), residues: 547 loop : -1.14 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.021 0.001 TYR B 707 PHE 0.026 0.001 PHE D 315 TRP 0.016 0.001 TRP D 163 HIS 0.005 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00276 (40534) covalent geometry : angle 0.54814 (55124) SS BOND : bond 0.00283 ( 48) SS BOND : angle 1.32642 ( 96) hydrogen bonds : bond 0.03828 ( 1386) hydrogen bonds : angle 5.11872 ( 3966) link_BETA1-4 : bond 0.00334 ( 6) link_BETA1-4 : angle 0.85959 ( 18) link_NAG-ASN : bond 0.00709 ( 62) link_NAG-ASN : angle 3.00771 ( 186) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 731 MET cc_start: 0.8490 (ptm) cc_final: 0.8168 (ttp) REVERT: A 753 LEU cc_start: 0.9486 (tp) cc_final: 0.9232 (pp) REVERT: A 779 GLN cc_start: 0.8906 (tm-30) cc_final: 0.8477 (tm-30) REVERT: A 780 GLU cc_start: 0.8608 (pt0) cc_final: 0.8326 (pt0) REVERT: B 900 MET cc_start: 0.6386 (mmt) cc_final: 0.5913 (mmt) REVERT: B 950 ASP cc_start: 0.8701 (p0) cc_final: 0.8423 (p0) REVERT: B 1031 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.6873 (pp20) REVERT: B 1038 LYS cc_start: 0.7531 (mmtt) cc_final: 0.7288 (mmpt) REVERT: C 1010 GLN cc_start: 0.9059 (mm-40) cc_final: 0.8810 (mm-40) REVERT: C 1031 GLU cc_start: 0.7321 (OUTLIER) cc_final: 0.6294 (pp20) REVERT: C 1050 MET cc_start: 0.7086 (OUTLIER) cc_final: 0.6272 (pmm) REVERT: F 297 MET cc_start: -0.0213 (mtt) cc_final: -0.0803 (mmt) REVERT: F 557 MET cc_start: 0.5246 (ppp) cc_final: 0.4698 (ppp) REVERT: D 123 MET cc_start: -0.0161 (tpt) cc_final: -0.0424 (tpp) REVERT: D 297 MET cc_start: 0.1345 (mmt) cc_final: 0.1072 (mmt) REVERT: D 474 MET cc_start: 0.7336 (mmt) cc_final: 0.6224 (mmp) REVERT: E 249 MET cc_start: 0.6635 (mmt) cc_final: 0.6158 (ptp) REVERT: E 332 MET cc_start: 0.4085 (ptt) cc_final: 0.3822 (pmm) REVERT: E 579 MET cc_start: 0.3396 (tmm) cc_final: 0.2967 (tpt) outliers start: 56 outliers final: 37 residues processed: 227 average time/residue: 0.2138 time to fit residues: 84.4238 Evaluate side-chains 213 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 173 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 786 LYS Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1109 PHE Chi-restraints excluded: chain F residue 85 LEU Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 366 MET Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 570 LEU Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 126 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 357 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 114 optimal weight: 4.9990 chunk 246 optimal weight: 0.6980 chunk 416 optimal weight: 9.9990 chunk 464 optimal weight: 40.0000 chunk 190 optimal weight: 0.9990 chunk 469 optimal weight: 30.0000 chunk 398 optimal weight: 30.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 334 ASN B 607 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 965 GLN ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 GLN ** F 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 ASN ** D 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 526 GLN E 81 GLN E 277 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.113892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.074408 restraints weight = 302188.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.074116 restraints weight = 184933.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.073729 restraints weight = 114550.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.075947 restraints weight = 89155.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.073711 restraints weight = 82224.623| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.5925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.097 40650 Z= 0.268 Angle : 0.743 12.571 55424 Z= 0.379 Chirality : 0.049 0.346 6286 Planarity : 0.005 0.072 7040 Dihedral : 5.676 58.772 6648 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.38 % Favored : 93.59 % Rotamer: Outliers : 1.93 % Allowed : 14.98 % Favored : 83.09 % 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: -1.23 (0.12), residues: 4824 helix: 0.03 (0.13), residues: 1637 sheet: -1.02 (0.22), residues: 499 loop : -1.32 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.001 ARG A1039 TYR 0.040 0.002 TYR B 707 PHE 0.032 0.002 PHE B1095 TRP 0.026 0.002 TRP B1102 HIS 0.010 0.002 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00564 (40534) covalent geometry : angle 0.71826 (55124) SS BOND : bond 0.00589 ( 48) SS BOND : angle 1.75274 ( 96) hydrogen bonds : bond 0.04790 ( 1386) hydrogen bonds : angle 5.59096 ( 3966) link_BETA1-4 : bond 0.00512 ( 6) link_BETA1-4 : angle 1.26023 ( 18) link_NAG-ASN : bond 0.00733 ( 62) link_NAG-ASN : angle 3.15394 ( 186) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 182 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8763 (pt0) cc_final: 0.8475 (pt0) REVERT: A 1019 ARG cc_start: 0.9312 (OUTLIER) cc_final: 0.8665 (mtp-110) REVERT: A 1110 TYR cc_start: 0.8424 (t80) cc_final: 0.8102 (t80) REVERT: B 900 MET cc_start: 0.6681 (mmt) cc_final: 0.6306 (mmt) REVERT: B 922 LEU cc_start: 0.8943 (tt) cc_final: 0.8669 (tt) REVERT: B 950 ASP cc_start: 0.8929 (p0) cc_final: 0.8568 (p0) REVERT: B 1031 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7075 (pp20) REVERT: C 886 TRP cc_start: 0.7869 (OUTLIER) cc_final: 0.7581 (p90) REVERT: C 1031 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6620 (pp20) REVERT: C 1050 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6218 (pmm) REVERT: F 297 MET cc_start: 0.1061 (mtt) cc_final: 0.0626 (mmt) REVERT: F 557 MET cc_start: 0.5683 (ppp) cc_final: 0.4869 (ppp) REVERT: D 123 MET cc_start: 0.1140 (tpt) cc_final: 0.0723 (tpp) REVERT: D 278 LEU cc_start: 0.3127 (OUTLIER) cc_final: 0.2833 (tt) REVERT: D 474 MET cc_start: 0.7512 (mmt) cc_final: 0.6793 (mmp) REVERT: E 123 MET cc_start: -0.4628 (ptt) cc_final: -0.5024 (ppp) REVERT: E 249 MET cc_start: 0.6682 (mmt) cc_final: 0.6334 (ptp) REVERT: E 270 MET cc_start: 0.4516 (ppp) cc_final: 0.3468 (mmp) REVERT: E 557 MET cc_start: -0.2592 (ttt) cc_final: -0.2832 (ttt) outliers start: 82 outliers final: 42 residues processed: 252 average time/residue: 0.2078 time to fit residues: 91.1841 Evaluate side-chains 203 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 155 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1019 ARG Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1040 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 293 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 886 TRP Chi-restraints excluded: chain C residue 915 VAL Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1076 THR Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 408 optimal weight: 0.0770 chunk 470 optimal weight: 40.0000 chunk 95 optimal weight: 0.9980 chunk 3 optimal weight: 9.9990 chunk 31 optimal weight: 0.0070 chunk 112 optimal weight: 8.9990 chunk 133 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 277 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 328 optimal weight: 0.5980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B1002 GLN C 751 ASN C 872 GLN ** C 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1106 GLN F 265 HIS F 330 ASN D 340 GLN E 188 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.117127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.079658 restraints weight = 288710.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.079328 restraints weight = 173019.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.079731 restraints weight = 96420.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.078530 restraints weight = 80480.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.078358 restraints weight = 77113.420| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.5831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 40650 Z= 0.118 Angle : 0.608 13.947 55424 Z= 0.301 Chirality : 0.046 0.324 6286 Planarity : 0.004 0.073 7040 Dihedral : 5.098 58.902 6648 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.13 % Allowed : 16.37 % Favored : 82.50 % 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: -0.95 (0.12), residues: 4824 helix: 0.32 (0.13), residues: 1653 sheet: -0.81 (0.22), residues: 537 loop : -1.21 (0.12), residues: 2634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 765 TYR 0.018 0.001 TYR B 707 PHE 0.026 0.001 PHE D 315 TRP 0.014 0.001 TRP D 271 HIS 0.004 0.001 HIS C1088 Details of bonding type rmsd covalent geometry : bond 0.00260 (40534) covalent geometry : angle 0.58264 (55124) SS BOND : bond 0.00251 ( 48) SS BOND : angle 1.12713 ( 96) hydrogen bonds : bond 0.03726 ( 1386) hydrogen bonds : angle 5.08166 ( 3966) link_BETA1-4 : bond 0.00284 ( 6) link_BETA1-4 : angle 1.03021 ( 18) link_NAG-ASN : bond 0.00726 ( 62) link_NAG-ASN : angle 2.95601 ( 186) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 183 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 LEU cc_start: 0.9536 (tp) cc_final: 0.9267 (pp) REVERT: A 779 GLN cc_start: 0.9024 (tm-30) cc_final: 0.8588 (tm-30) REVERT: A 780 GLU cc_start: 0.8643 (pt0) cc_final: 0.8357 (pt0) REVERT: A 802 PHE cc_start: 0.7797 (m-80) cc_final: 0.7097 (m-80) REVERT: B 177 MET cc_start: 0.3129 (mmt) cc_final: 0.2779 (mmt) REVERT: B 900 MET cc_start: 0.6521 (mmt) cc_final: 0.6127 (mmt) REVERT: B 950 ASP cc_start: 0.8667 (p0) cc_final: 0.8360 (p0) REVERT: B 1031 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: C 1010 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8974 (mm-40) REVERT: C 1031 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6395 (pp20) REVERT: F 297 MET cc_start: 0.0306 (mtt) cc_final: -0.0127 (mmt) REVERT: F 323 MET cc_start: 0.5772 (tpt) cc_final: 0.5487 (tpp) REVERT: F 557 MET cc_start: 0.4838 (ppp) cc_final: 0.3954 (ppp) REVERT: D 278 LEU cc_start: 0.3276 (OUTLIER) cc_final: 0.2978 (tt) REVERT: D 474 MET cc_start: 0.7455 (mmp) cc_final: 0.6534 (mmp) REVERT: E 249 MET cc_start: 0.6619 (mmt) cc_final: 0.6287 (ptp) REVERT: E 332 MET cc_start: 0.3961 (ptt) cc_final: 0.3520 (pmm) REVERT: E 579 MET cc_start: 0.3429 (tmm) cc_final: 0.3142 (tpt) outliers start: 48 outliers final: 31 residues processed: 228 average time/residue: 0.2040 time to fit residues: 81.7738 Evaluate side-chains 201 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 167 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 720 ILE Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 216 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 141 optimal weight: 40.0000 chunk 129 optimal weight: 9.9990 chunk 228 optimal weight: 1.9990 chunk 397 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 445 optimal weight: 40.0000 chunk 208 optimal weight: 8.9990 chunk 13 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 965 GLN ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 330 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 = 0.4416 r_free = 0.4416 target = 0.112936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.070941 restraints weight = 302330.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.071333 restraints weight = 173430.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.070908 restraints weight = 115670.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.070692 restraints weight = 104553.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.070529 restraints weight = 101481.144| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.6599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 40650 Z= 0.269 Angle : 0.734 12.156 55424 Z= 0.372 Chirality : 0.048 0.332 6286 Planarity : 0.005 0.090 7040 Dihedral : 5.515 56.166 6648 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.49 % Favored : 93.49 % Rotamer: Outliers : 1.34 % Allowed : 16.87 % Favored : 81.79 % 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: -1.22 (0.12), residues: 4824 helix: 0.11 (0.13), residues: 1643 sheet: -1.34 (0.21), residues: 540 loop : -1.27 (0.12), residues: 2641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B1039 TYR 0.041 0.002 TYR A 707 PHE 0.029 0.002 PHE A1089 TRP 0.020 0.002 TRP B1102 HIS 0.011 0.002 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00559 (40534) covalent geometry : angle 0.71032 (55124) SS BOND : bond 0.00680 ( 48) SS BOND : angle 1.61489 ( 96) hydrogen bonds : bond 0.04724 ( 1386) hydrogen bonds : angle 5.49939 ( 3966) link_BETA1-4 : bond 0.00378 ( 6) link_BETA1-4 : angle 1.09383 ( 18) link_NAG-ASN : bond 0.00712 ( 62) link_NAG-ASN : angle 3.09678 ( 186) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8723 (pt0) cc_final: 0.8450 (pt0) REVERT: A 802 PHE cc_start: 0.7444 (m-80) cc_final: 0.7211 (m-80) REVERT: B 177 MET cc_start: 0.3529 (mmt) cc_final: 0.2782 (mmt) REVERT: B 900 MET cc_start: 0.6828 (mmt) cc_final: 0.6437 (mmt) REVERT: B 950 ASP cc_start: 0.8879 (p0) cc_final: 0.8482 (p0) REVERT: C 201 PHE cc_start: 0.8838 (OUTLIER) cc_final: 0.8376 (t80) REVERT: C 1031 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.6880 (pp20) REVERT: F 123 MET cc_start: 0.3319 (tmm) cc_final: 0.2991 (ppp) REVERT: F 297 MET cc_start: 0.1110 (mtt) cc_final: 0.0660 (mmt) REVERT: F 323 MET cc_start: 0.6381 (tpt) cc_final: 0.6177 (tpp) REVERT: F 557 MET cc_start: 0.5694 (ppp) cc_final: 0.5235 (ppp) REVERT: D 278 LEU cc_start: 0.3433 (OUTLIER) cc_final: 0.3029 (tt) REVERT: D 474 MET cc_start: 0.7484 (mmp) cc_final: 0.6645 (mmp) REVERT: E 249 MET cc_start: 0.6648 (mmt) cc_final: 0.6331 (ptp) REVERT: E 270 MET cc_start: 0.4419 (ppp) cc_final: 0.3527 (mmm) REVERT: E 332 MET cc_start: 0.4407 (ptt) cc_final: 0.3779 (pmm) REVERT: E 376 MET cc_start: -0.4989 (ttp) cc_final: -0.5405 (ttp) outliers start: 57 outliers final: 42 residues processed: 209 average time/residue: 0.1946 time to fit residues: 73.1378 Evaluate side-chains 199 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 154 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 95 THR Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1040 VAL Chi-restraints excluded: chain A residue 1066 THR Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 53 ASP Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1013 ILE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 42 VAL Chi-restraints excluded: chain C residue 201 PHE Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 802 PHE Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1119 ASN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain E residue 488 VAL Chi-restraints excluded: chain E residue 573 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 170 optimal weight: 0.6980 chunk 368 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 chunk 267 optimal weight: 0.9990 chunk 366 optimal weight: 20.0000 chunk 483 optimal weight: 0.4980 chunk 199 optimal weight: 0.9990 chunk 111 optimal weight: 0.6980 chunk 335 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 263 optimal weight: 8.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 HIS D 526 GLN E 188 ASN ** E 330 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.115966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.074945 restraints weight = 298285.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.073793 restraints weight = 182309.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.073691 restraints weight = 121594.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.072777 restraints weight = 104933.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.073377 restraints weight = 100163.858| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7327 moved from start: 0.6519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 40650 Z= 0.119 Angle : 0.620 13.639 55424 Z= 0.305 Chirality : 0.046 0.326 6286 Planarity : 0.004 0.075 7040 Dihedral : 5.118 59.027 6648 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.01 % Allowed : 17.08 % Favored : 81.91 % 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: -1.01 (0.12), residues: 4824 helix: 0.27 (0.13), residues: 1674 sheet: -1.01 (0.21), residues: 566 loop : -1.21 (0.12), residues: 2584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B1014 TYR 0.020 0.001 TYR B 707 PHE 0.027 0.001 PHE D 315 TRP 0.017 0.001 TRP D 610 HIS 0.008 0.001 HIS B1083 Details of bonding type rmsd covalent geometry : bond 0.00262 (40534) covalent geometry : angle 0.59522 (55124) SS BOND : bond 0.00335 ( 48) SS BOND : angle 1.23233 ( 96) hydrogen bonds : bond 0.03725 ( 1386) hydrogen bonds : angle 5.09036 ( 3966) link_BETA1-4 : bond 0.00362 ( 6) link_BETA1-4 : angle 1.05106 ( 18) link_NAG-ASN : bond 0.00724 ( 62) link_NAG-ASN : angle 2.94152 ( 186) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9648 Ramachandran restraints generated. 4824 Oldfield, 0 Emsley, 4824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 177 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 753 LEU cc_start: 0.9327 (tt) cc_final: 0.9058 (pp) REVERT: A 779 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8596 (tm-30) REVERT: A 780 GLU cc_start: 0.8649 (pt0) cc_final: 0.8341 (pt0) REVERT: B 177 MET cc_start: 0.3291 (mmt) cc_final: 0.2825 (mmt) REVERT: B 900 MET cc_start: 0.6876 (mmt) cc_final: 0.6606 (mmt) REVERT: B 950 ASP cc_start: 0.8740 (p0) cc_final: 0.8398 (p0) REVERT: C 1031 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: F 123 MET cc_start: 0.3228 (OUTLIER) cc_final: 0.2722 (ptm) REVERT: F 297 MET cc_start: 0.1025 (mtt) cc_final: 0.0531 (mmt) REVERT: F 323 MET cc_start: 0.6362 (tpt) cc_final: 0.6160 (tpp) REVERT: F 557 MET cc_start: 0.5490 (ppp) cc_final: 0.4686 (ppp) REVERT: D 278 LEU cc_start: 0.3307 (OUTLIER) cc_final: 0.2995 (tt) REVERT: D 474 MET cc_start: 0.7490 (mmp) cc_final: 0.6630 (mmp) REVERT: E 249 MET cc_start: 0.6603 (mmt) cc_final: 0.6284 (ptp) REVERT: E 270 MET cc_start: 0.4599 (ppp) cc_final: 0.3566 (mmm) REVERT: E 332 MET cc_start: 0.4747 (ptt) cc_final: 0.4200 (pmm) REVERT: E 376 MET cc_start: -0.5126 (ttp) cc_final: -0.5541 (ttp) REVERT: E 579 MET cc_start: 0.3606 (tmm) cc_final: 0.3301 (tpt) outliers start: 43 outliers final: 35 residues processed: 213 average time/residue: 0.2015 time to fit residues: 76.2866 Evaluate side-chains 206 residues out of total 4278 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 505 TYR Chi-restraints excluded: chain A residue 767 LEU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 1084 ASP Chi-restraints excluded: chain A residue 1129 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 298 GLU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 915 VAL Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1061 VAL Chi-restraints excluded: chain B residue 1103 PHE Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 587 ILE Chi-restraints excluded: chain C residue 722 VAL Chi-restraints excluded: chain C residue 860 VAL Chi-restraints excluded: chain C residue 912 THR Chi-restraints excluded: chain C residue 917 TYR Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1031 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain F residue 123 MET Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 157 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain D residue 510 TYR Chi-restraints excluded: chain D residue 594 TRP Chi-restraints excluded: chain E residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 486 random chunks: chunk 255 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 404 optimal weight: 6.9990 chunk 191 optimal weight: 8.9990 chunk 385 optimal weight: 8.9990 chunk 223 optimal weight: 10.0000 chunk 405 optimal weight: 50.0000 chunk 477 optimal weight: 50.0000 chunk 32 optimal weight: 20.0000 chunk 324 optimal weight: 5.9990 chunk 370 optimal weight: 50.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 992 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 526 GLN D 526 GLN D 535 HIS ** E 330 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 = 0.4401 r_free = 0.4401 target = 0.112231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.070113 restraints weight = 302861.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.069814 restraints weight = 178177.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.068856 restraints weight = 119151.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067972 restraints weight = 89319.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.067916 restraints weight = 95255.855| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.7285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.116 40650 Z= 0.276 Angle : 0.735 12.124 55424 Z= 0.373 Chirality : 0.048 0.332 6286 Planarity : 0.005 0.070 7040 Dihedral : 5.602 56.940 6648 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 1.30 % Allowed : 17.31 % Favored : 81.39 % 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: -1.25 (0.12), residues: 4824 helix: 0.07 (0.13), residues: 1641 sheet: -1.19 (0.22), residues: 532 loop : -1.33 (0.12), residues: 2651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 460 TYR 0.046 0.002 TYR F 50 PHE 0.030 0.002 PHE A1089 TRP 0.023 0.002 TRP B1102 HIS 0.007 0.001 HIS B 49 Details of bonding type rmsd covalent geometry : bond 0.00575 (40534) covalent geometry : angle 0.71090 (55124) SS BOND : bond 0.00612 ( 48) SS BOND : angle 1.66937 ( 96) hydrogen bonds : bond 0.04675 ( 1386) hydrogen bonds : angle 5.49450 ( 3966) link_BETA1-4 : bond 0.00271 ( 6) link_BETA1-4 : angle 1.04788 ( 18) link_NAG-ASN : bond 0.00722 ( 62) link_NAG-ASN : angle 3.07702 ( 186) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18137.81 seconds wall clock time: 308 minutes 25.61 seconds (18505.61 seconds total)