Starting phenix.real_space_refine on Fri Mar 6 21:33:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kmz_22932/03_2026/7kmz_22932.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kmz_22932/03_2026/7kmz_22932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kmz_22932/03_2026/7kmz_22932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kmz_22932/03_2026/7kmz_22932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kmz_22932/03_2026/7kmz_22932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kmz_22932/03_2026/7kmz_22932.map" } resolution = 3.62 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.033 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 167 5.16 5 C 21969 2.51 5 N 5637 2.21 5 O 6680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 195 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: 34453 Number of models: 1 Model: "" Number of chains: 14 Chain: "C" Number of atoms: 7837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1007, 7837 Classifications: {'peptide': 1007} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 49, 'TRANS': 957} Chain breaks: 8 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 8020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1030, 8020 Classifications: {'peptide': 1030} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 51, 'TRANS': 978} Chain breaks: 7 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 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: "B" Number of atoms: 8018 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1031, 8018 Classifications: {'peptide': 1031} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 51, 'TRANS': 979} Chain breaks: 7 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "A" Number of atoms: 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: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 196 Unusual residues: {'NAG': 14} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 8.86, per 1000 atoms: 0.26 Number of scatterers: 34453 At special positions: 0 Unit cell: (136.482, 162.932, 242.282, 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 167 16.00 O 6680 8.00 N 5637 7.00 C 21969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.04 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 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 A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 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 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 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 F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 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 343 " " NAG A1314 " - " 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 B1074 " " NAG B1310 " - " ASN B 61 " " NAG B1311 " - " ASN B 234 " " NAG B1312 " - " ASN B 165 " " NAG B1313 " - " ASN B 343 " " NAG B1314 " - " ASN B 603 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C1134 " " NAG C1303 " - " ASN C1098 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 801 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 61 " " NAG C1310 " - " ASN C 234 " " NAG C1311 " - " ASN C 603 " " NAG C1312 " - " ASN C 165 " " NAG C1313 " - " ASN C 657 " " NAG D 701 " - " ASN D 546 " " NAG D 702 " - " ASN D 322 " " NAG D 703 " - " ASN D 432 " " NAG D 704 " - " ASN D 103 " " NAG D 705 " - " ASN D 90 " " NAG D 706 " - " ASN D 53 " " NAG E 701 " - " ASN E 546 " " NAG E 702 " - " ASN E 322 " " NAG E 703 " - " ASN E 432 " " NAG E 704 " - " ASN E 103 " " NAG E 705 " - " ASN E 90 " " NAG E 706 " - " ASN E 53 " " NAG F 1 " - " ASN C 717 " " NAG G 1 " - " ASN C 343 " " NAG H 1 " - " ASN A 717 " " NAG I 1 " - " ASN B 717 " Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.6 seconds 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8012 Finding SS restraints... Secondary structure from input PDB file: 122 helices and 47 sheets defined 35.8% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'C' and resid 294 through 304 removed outlier: 3.631A pdb=" N LYS C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.932A pdb=" N TYR C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 4.063A 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 385 through 390 removed outlier: 4.127A pdb=" N ASP C 389 " --> pdb=" O THR C 385 " (cutoff:3.500A) 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 542 through 546 removed outlier: 3.842A pdb=" N GLY C 545 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 757 removed outlier: 4.009A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 757 " --> pdb=" O LEU C 753 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.611A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.674A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.287A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS C 964 " --> pdb=" O ASN C 960 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN C 965 " --> pdb=" O THR C 961 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 removed outlier: 4.045A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER C 982 " --> pdb=" O ASN C 978 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.834A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLN C1002 " --> pdb=" O THR C 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 3.794A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.542A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N THR A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.951A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.752A 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 405 through 410 removed outlier: 5.173A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 619 through 623 Processing helix chain 'A' and resid 738 through 743 removed outlier: 3.543A pdb=" N CYS A 743 " --> pdb=" O THR A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 3.691A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.658A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.672A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 removed outlier: 3.632A pdb=" N ALA A 871 " --> pdb=" O ASP A 867 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLN A 872 " --> pdb=" O GLU A 868 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR A 873 " --> pdb=" O MET A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.636A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.581A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ALA A 903 " --> pdb=" O ALA A 899 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 905 " --> pdb=" O GLN A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.671A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.527A pdb=" N LEU A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 946 through 965 removed outlier: 3.531A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASN A 953 " --> pdb=" O GLN A 949 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.919A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1118 No H-bonds generated for 'chain 'A' and resid 1116 through 1118' Processing helix chain 'A' and resid 1140 through 1148 removed outlier: 3.901A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE A1148 " --> pdb=" O GLU A1144 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 53 removed outlier: 3.668A pdb=" N THR E 27 " --> pdb=" O GLU E 23 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS E 34 " --> pdb=" O ASP E 30 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TYR E 50 " --> pdb=" O ALA E 46 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN E 51 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR E 52 " --> pdb=" O TRP E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 80 removed outlier: 3.874A pdb=" N VAL E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASN E 63 " --> pdb=" O VAL E 59 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU E 73 " --> pdb=" O TRP E 69 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS E 74 " --> pdb=" O SER E 70 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.889A pdb=" N GLN E 96 " --> pdb=" O THR E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 128 removed outlier: 3.505A pdb=" N LYS E 114 " --> pdb=" O GLU E 110 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ARG E 115 " --> pdb=" O ASP E 111 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N LEU E 116 " --> pdb=" O LYS E 112 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ASN E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR E 122 " --> pdb=" O THR E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 154 removed outlier: 3.920A pdb=" N ASN E 149 " --> pdb=" O GLU E 145 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU E 150 " --> pdb=" O PRO E 146 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE E 151 " --> pdb=" O GLY E 147 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 170 removed outlier: 3.883A pdb=" N ARG E 161 " --> pdb=" O ASP E 157 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N TRP E 168 " --> pdb=" O ALA E 164 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG E 169 " --> pdb=" O TRP E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 175 No H-bonds generated for 'chain 'E' and resid 173 through 175' Processing helix chain 'E' and resid 176 through 188 removed outlier: 3.509A pdb=" N GLU E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU E 182 " --> pdb=" O PRO E 178 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU E 186 " --> pdb=" O GLU E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 194 removed outlier: 3.503A pdb=" N ALA E 193 " --> pdb=" O GLU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 204 removed outlier: 3.713A pdb=" N TRP E 203 " --> pdb=" O TYR E 199 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG E 204 " --> pdb=" O GLY E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 218 through 252 removed outlier: 4.072A pdb=" N LEU E 222 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ILE E 223 " --> pdb=" O ARG E 219 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU E 224 " --> pdb=" O GLY E 220 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU E 231 " --> pdb=" O GLU E 227 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU E 232 " --> pdb=" O HIS E 228 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE E 233 " --> pdb=" O THR E 229 " (cutoff:3.500A) Proline residue: E 235 - end of helix removed outlier: 3.546A pdb=" N ARG E 245 " --> pdb=" O HIS E 241 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALA E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N LYS E 247 " --> pdb=" O TYR E 243 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LEU E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET E 249 " --> pdb=" O ARG E 245 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ASN E 250 " --> pdb=" O ALA E 246 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ALA E 251 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR E 252 " --> pdb=" O LEU E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 4.425A pdb=" N LEU E 281 " --> pdb=" O ASN E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 299 removed outlier: 3.768A pdb=" N MET E 297 " --> pdb=" O VAL E 293 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL E 298 " --> pdb=" O THR E 294 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ASP E 299 " --> pdb=" O ASP E 295 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 293 through 299' Processing helix chain 'E' and resid 303 through 319 removed outlier: 3.616A pdb=" N LYS E 313 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE E 314 " --> pdb=" O GLU E 310 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 315 " --> pdb=" O ALA E 311 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 316 " --> pdb=" O GLU E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 383 removed outlier: 3.579A pdb=" N HIS E 378 " --> pdb=" O HIS E 374 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N MET E 383 " --> pdb=" O ILE E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 397 through 413 removed outlier: 3.865A pdb=" N HIS E 401 " --> pdb=" O ASN E 397 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU E 402 " --> pdb=" O GLU E 398 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY E 405 " --> pdb=" O HIS E 401 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU E 406 " --> pdb=" O GLU E 402 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N MET E 408 " --> pdb=" O VAL E 404 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 411 " --> pdb=" O ILE E 407 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 422 Processing helix chain 'E' and resid 431 through 447 removed outlier: 3.772A pdb=" N GLU E 435 " --> pdb=" O ASP E 431 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR E 445 " --> pdb=" O LYS E 441 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 466 removed outlier: 4.566A pdb=" N PHE E 452 " --> pdb=" O GLY E 448 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET E 462 " --> pdb=" O LYS E 458 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL E 463 " --> pdb=" O TRP E 459 " (cutoff:3.500A) 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: 4.050A pdb=" N MET E 480 " --> pdb=" O LYS E 476 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS E 481 " --> pdb=" O TRP E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 502 removed outlier: 3.533A pdb=" N ALA E 501 " --> pdb=" O CYS E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 503 through 508 Processing helix chain 'E' and resid 512 through 534 removed outlier: 4.283A pdb=" N TYR E 516 " --> pdb=" O PHE E 512 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR E 517 " --> pdb=" O ILE E 513 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR E 519 " --> pdb=" O TYR E 515 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU E 520 " --> pdb=" O TYR E 516 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE E 523 " --> pdb=" O THR E 519 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN E 524 " --> pdb=" O LEU E 520 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 532 " --> pdb=" O ALA E 528 " (cutoff:3.500A) Processing helix chain 'E' and resid 538 through 542 Processing helix chain 'E' and resid 547 through 559 Processing helix chain 'E' and resid 565 through 572 removed outlier: 3.706A pdb=" N ALA E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 570 " --> pdb=" O TRP E 566 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU E 571 " --> pdb=" O THR E 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 585 removed outlier: 3.595A pdb=" N LEU E 585 " --> pdb=" O ARG E 582 " (cutoff:3.500A) Processing helix chain 'E' and resid 588 through 599 removed outlier: 3.818A pdb=" N ASP E 597 " --> pdb=" O THR E 593 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN E 598 " --> pdb=" O TRP E 594 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN E 599 " --> pdb=" O LEU E 595 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.748A pdb=" N LYS B 300 " --> pdb=" O LEU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.647A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.138A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 738 through 743 removed outlier: 3.617A pdb=" N ILE B 742 " --> pdb=" O CYS B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.692A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.606A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU B 763 " --> pdb=" O PHE B 759 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLU B 773 " --> pdb=" O GLY B 769 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.942A pdb=" N ALA B 871 " --> pdb=" O ASP B 867 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLN B 872 " --> pdb=" O GLU B 868 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TYR B 873 " --> pdb=" O MET B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.613A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.747A pdb=" N MET B 902 " --> pdb=" O PHE B 898 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 903 " --> pdb=" O ALA B 899 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG B 905 " --> pdb=" O GLN B 901 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.731A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 938 removed outlier: 3.670A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 4.415A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASN B 953 " --> pdb=" O GLN B 949 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN B 955 " --> pdb=" O VAL B 951 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 964 " --> pdb=" O ASN B 960 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 965 " --> pdb=" O THR B 961 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 removed outlier: 4.259A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEU B 984 " --> pdb=" O ILE B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.685A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1148 removed outlier: 4.025A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 51 removed outlier: 4.183A pdb=" N LYS D 31 " --> pdb=" O THR D 27 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TRP D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN D 49 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN D 51 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 removed outlier: 4.127A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 73 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS D 74 " --> pdb=" O SER D 70 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR D 78 " --> pdb=" O LYS D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 101 removed outlier: 3.580A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.105A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 removed outlier: 4.098A pdb=" N ARG D 115 " --> pdb=" O ASP D 111 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU D 116 " --> pdb=" O LYS D 112 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 154 removed outlier: 3.811A pdb=" N ASN D 149 " --> pdb=" O GLU D 145 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 170 removed outlier: 3.663A pdb=" N TRP D 168 " --> pdb=" O ALA D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 188 removed outlier: 4.235A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU D 182 " --> pdb=" O PRO D 178 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU D 186 " --> pdb=" O GLU D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 194 Processing helix chain 'D' and resid 198 through 204 removed outlier: 3.798A pdb=" N TRP D 203 " --> pdb=" O TYR D 199 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG D 204 " --> pdb=" O GLY D 200 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 229 removed outlier: 3.754A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 249 removed outlier: 4.241A pdb=" N LEU D 236 " --> pdb=" O GLU D 232 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 246 " --> pdb=" O ALA D 242 " (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 277 through 282 removed outlier: 4.303A pdb=" N LEU D 281 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 300 removed outlier: 3.509A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 319 removed outlier: 3.524A pdb=" N PHE D 308 " --> pdb=" O ALA D 304 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA D 311 " --> pdb=" O ILE D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 329 removed outlier: 4.430A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLU D 329 " --> pdb=" O GLN D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 324 through 329' Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.565A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE D 379 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 413 removed outlier: 3.856A pdb=" N HIS D 401 " --> pdb=" O ASN D 397 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLU D 402 " --> pdb=" O GLU D 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU D 406 " --> pdb=" O GLU D 402 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER D 411 " --> pdb=" O ILE D 407 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.263A pdb=" N PHE D 438 " --> pdb=" O THR D 434 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.390A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP D 459 " --> pdb=" O MET D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.593A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.621A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 removed outlier: 3.506A pdb=" N ALA D 569 " --> pdb=" O PRO D 565 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU D 571 " --> pdb=" O THR D 567 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 583 No H-bonds generated for 'chain 'D' and resid 581 through 583' Processing helix chain 'D' and resid 584 through 599 removed outlier: 4.143A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Proline residue: D 590 - end of helix removed outlier: 3.621A pdb=" N ASP D 597 " --> pdb=" O THR D 593 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.828A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR C 265 " --> pdb=" O PHE C 65 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N HIS C 207 " --> pdb=" O ALA C 222 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N ALA C 222 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 5.513A pdb=" N PHE C 43 " --> pdb=" O ARG B 567 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU B 583 " --> pdb=" O ASP B 578 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 51 removed outlier: 4.058A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 54 through 55 Processing sheet with id=AA5, first strand: chain 'C' and resid 104 through 107 Processing sheet with id=AA6, first strand: chain 'C' and resid 118 through 121 removed outlier: 3.802A pdb=" N LEU C 118 " --> pdb=" O LYS C 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 311 through 318 removed outlier: 5.244A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 593 " --> pdb=" O PHE C 318 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 354 through 356 removed outlier: 3.901A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL C 510 " --> pdb=" O PHE C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'C' and resid 539 through 541 removed outlier: 3.501A pdb=" N THR C 588 " --> pdb=" O VAL C 551 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 653 through 655 removed outlier: 3.661A pdb=" N ALA C 694 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 703 through 704 removed outlier: 6.938A pdb=" N ASN C 703 " --> pdb=" O LYS A 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.280A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.404A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 1122 through 1125 removed outlier: 4.325A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.511A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS A 195 " --> pdb=" O LYS A 202 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.511A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG A 190 " --> pdb=" O SER A 94 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.665A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AC3, first strand: chain 'A' and resid 311 through 318 removed outlier: 7.126A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 354 through 356 removed outlier: 3.974A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 452 through 453 removed outlier: 3.756A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 538 through 542 removed outlier: 3.519A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AC8, first strand: chain 'A' and resid 703 through 704 removed outlier: 7.211A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.610A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 712 through 728 removed outlier: 6.610A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 725 " --> pdb=" O PHE A1062 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AD3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.683A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'E' and resid 347 through 352 removed outlier: 6.077A pdb=" N ALA E 348 " --> pdb=" O LEU E 359 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU E 359 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ASP E 350 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ARG E 357 " --> pdb=" O ASP E 350 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.703A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 90 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LYS B 202 " --> pdb=" O LYS B 195 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 48 through 51 removed outlier: 3.818A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 54 through 55 Processing sheet with id=AD9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.583A pdb=" N ARG B 237 " --> pdb=" O GLY B 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR B 170 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 130 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 187 through 189 removed outlier: 3.955A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE B 210 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR B 208 " --> pdb=" O LEU B 189 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 311 through 318 removed outlier: 3.506A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 650 " --> pdb=" O PHE B 643 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE B 643 " --> pdb=" O LEU B 650 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 354 through 356 removed outlier: 3.802A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS B 356 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 452 through 453 removed outlier: 3.673A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.259A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 712 through 728 removed outlier: 6.598A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AE8, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.617A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AF1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.416A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.219A pdb=" N ALA D 348 " --> pdb=" O LEU D 359 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU D 359 " --> pdb=" O ALA D 348 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASP D 350 " --> pdb=" O ARG D 357 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ARG D 357 " --> pdb=" O ASP D 350 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY D 352 " --> pdb=" O ASP D 355 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3429 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: 8.04 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10972 1.34 - 1.46: 8813 1.46 - 1.58: 15246 1.58 - 1.70: 0 1.70 - 1.82: 237 Bond restraints: 35268 Sorted by residual: bond pdb=" C PHE A 329 " pdb=" N PRO A 330 " ideal model delta sigma weight residual 1.328 1.355 -0.027 1.25e-02 6.40e+03 4.78e+00 bond pdb=" C1 NAG G 1 " pdb=" O5 NAG G 1 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" C1 NAG A1311 " pdb=" O5 NAG A1311 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 bond pdb=" C1 NAG C1312 " pdb=" O5 NAG C1312 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG C1308 " pdb=" O5 NAG C1308 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.19e+00 ... (remaining 35263 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 46904 1.37 - 2.74: 828 2.74 - 4.12: 204 4.12 - 5.49: 28 5.49 - 6.86: 5 Bond angle restraints: 47969 Sorted by residual: angle pdb=" N ILE D 259 " pdb=" CA ILE D 259 " pdb=" C ILE D 259 " ideal model delta sigma weight residual 113.71 110.18 3.53 9.50e-01 1.11e+00 1.38e+01 angle pdb=" N THR B 33 " pdb=" CA THR B 33 " pdb=" C THR B 33 " ideal model delta sigma weight residual 114.56 111.74 2.82 1.27e+00 6.20e-01 4.91e+00 angle pdb=" CA ILE D 259 " pdb=" C ILE D 259 " pdb=" N GLY D 260 " ideal model delta sigma weight residual 119.87 117.02 2.85 1.34e+00 5.57e-01 4.53e+00 angle pdb=" N ASN D 338 " pdb=" CA ASN D 338 " pdb=" C ASN D 338 " ideal model delta sigma weight residual 113.18 110.44 2.74 1.33e+00 5.65e-01 4.26e+00 angle pdb=" N PRO A 330 " pdb=" CA PRO A 330 " pdb=" C PRO A 330 " ideal model delta sigma weight residual 111.03 114.53 -3.50 1.78e+00 3.16e-01 3.86e+00 ... (remaining 47964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19562 17.91 - 35.83: 1701 35.83 - 53.74: 366 53.74 - 71.65: 92 71.65 - 89.56: 34 Dihedral angle restraints: 21755 sinusoidal: 9323 harmonic: 12432 Sorted by residual: 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 -151.97 65.97 1 1.00e+01 1.00e-02 5.69e+01 dihedral pdb=" CB CYS C 738 " pdb=" SG CYS C 738 " pdb=" SG CYS C 760 " pdb=" CB CYS C 760 " ideal model delta sinusoidal sigma weight residual 93.00 37.74 55.26 1 1.00e+01 1.00e-02 4.13e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 39.46 53.54 1 1.00e+01 1.00e-02 3.90e+01 ... (remaining 21752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4825 0.060 - 0.119: 637 0.119 - 0.179: 48 0.179 - 0.239: 4 0.239 - 0.298: 3 Chirality restraints: 5517 Sorted by residual: chirality pdb=" C1 NAG A1311 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1311 " pdb=" O5 NAG A1311 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C1 NAG A1312 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1312 " pdb=" O5 NAG A1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1 NAG C1312 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG C1312 " pdb=" O5 NAG C1312 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.17e+00 ... (remaining 5514 not shown) Planarity restraints: 6184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " 0.048 5.00e-02 4.00e+02 7.31e-02 8.54e+00 pdb=" N PRO C 521 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 811 " 0.034 5.00e-02 4.00e+02 5.18e-02 4.30e+00 pdb=" N PRO A 812 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 812 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 812 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 811 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 812 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 812 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 812 " -0.024 5.00e-02 4.00e+02 ... (remaining 6181 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.58: 367 2.58 - 3.16: 30083 3.16 - 3.74: 51904 3.74 - 4.32: 70834 4.32 - 4.90: 116820 Nonbonded interactions: 270008 Sorted by model distance: nonbonded pdb=" OG1 THR B 323 " pdb=" OE1 GLU B 324 " model vdw 2.006 3.040 nonbonded pdb=" OD1 ASN A 540 " pdb=" OG1 THR A 549 " model vdw 2.017 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.135 3.040 nonbonded pdb=" O ALA E 501 " pdb=" OG SER E 507 " model vdw 2.147 3.040 nonbonded pdb=" OG1 THR B1116 " pdb=" OD1 ASP B1118 " model vdw 2.201 3.040 ... (remaining 270003 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 141 o \ r resid 156 through 176 or (resid 187 through 188 and (name N or name CA or name \ C or name O or name CB )) or resid 189 through 194 or (resid 195 through 198 an \ d (name N or name CA or name C or name O or name CB )) or resid 199 or (resid 20 \ 0 and (name N or name CA or name C or name O or name CB )) or resid 201 through \ 243 or resid 264 through 620 or resid 640 through 811 or resid 815 through 828 o \ r resid 853 through 1147 or resid 1302 through 1314)) selection = (chain 'B' and (resid 26 through 66 or resid 81 through 141 or resid 156 through \ 176 or (resid 187 through 188 and (name N or name CA or name C or name O or nam \ e CB )) or resid 189 through 194 or (resid 195 through 198 and (name N or name C \ A or name C or name O or name CB )) or resid 199 or (resid 200 and (name N or na \ me CA or name C or name O or name CB )) or resid 201 through 243 or resid 264 th \ rough 620 or resid 640 through 811 or resid 815 through 828 or resid 853 through \ 1147 or resid 1302 through 1314)) selection = (chain 'C' and (resid 26 through 59 or (resid 60 and (name N or name CA or name \ C or name O or name CB )) or resid 61 through 66 or (resid 81 and (name N or nam \ e CA or name C or name O or name CB )) or resid 82 through 114 or (resid 115 and \ (name N or name CA or name C or name O or name CB )) or resid 116 through 134 o \ r (resid 135 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 36 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 189 or (resid 190 and (name N or name CA or name C or \ name O or name CB )) or resid 191 through 209 or (resid 210 and (name N or name \ CA or name C or name O or name CB )) or resid 211 through 280 or (resid 281 and \ (name N or name CA or name C or name O or name CB )) or resid 282 through 289 o \ r (resid 290 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 91 through 620 or resid 640 through 676 or resid 690 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 6.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.240 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 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 : 0.003 0.036 35374 Z= 0.139 Angle : 0.492 9.118 48242 Z= 0.237 Chirality : 0.042 0.298 5517 Planarity : 0.003 0.073 6127 Dihedral : 14.197 89.565 13608 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: -0.09 (0.13), residues: 4206 helix: 1.18 (0.16), residues: 1224 sheet: 0.00 (0.23), residues: 518 loop : -0.71 (0.13), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.000 ARG B 815 TYR 0.007 0.000 TYR C 904 PHE 0.012 0.001 PHE B 275 TRP 0.005 0.000 TRP D 594 HIS 0.003 0.000 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00291 (35268) covalent geometry : angle 0.48344 (47969) SS BOND : bond 0.00216 ( 45) SS BOND : angle 0.67837 ( 90) hydrogen bonds : bond 0.27538 ( 1201) hydrogen bonds : angle 8.74408 ( 3429) link_BETA1-4 : bond 0.00279 ( 4) link_BETA1-4 : angle 0.85553 ( 12) link_NAG-ASN : bond 0.00345 ( 57) link_NAG-ASN : angle 1.56883 ( 171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.264 Fit side-chains REVERT: C 697 MET cc_start: 0.8294 (mpp) cc_final: 0.7660 (mpp) REVERT: A 153 MET cc_start: 0.3500 (ptt) cc_final: 0.2662 (ppp) REVERT: E 82 MET cc_start: 0.6135 (pmm) cc_final: 0.5864 (pmm) REVERT: E 190 MET cc_start: 0.0475 (ppp) cc_final: 0.0218 (ppp) REVERT: D 579 MET cc_start: 0.2114 (tpt) cc_final: 0.1522 (tpp) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1980 time to fit residues: 39.7305 Evaluate side-chains 94 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 7.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 401 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 487 ASN C 644 GLN C 804 GLN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN C1002 GLN A 115 GLN A 487 ASN A 625 HIS ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1083 HIS ** A1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN B 901 GLN B 926 GLN B1002 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1083 HIS D 522 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.094083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.060187 restraints weight = 198027.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.060747 restraints weight = 91383.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.060270 restraints weight = 54264.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.060765 restraints weight = 40036.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.060703 restraints weight = 32441.638| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.081 35374 Z= 0.433 Angle : 0.817 10.995 48242 Z= 0.418 Chirality : 0.050 0.316 5517 Planarity : 0.005 0.057 6127 Dihedral : 7.246 59.975 5836 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.51 % Allowed : 7.31 % Favored : 92.18 % 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: -0.88 (0.12), residues: 4206 helix: 0.32 (0.14), residues: 1289 sheet: -0.61 (0.21), residues: 568 loop : -1.09 (0.12), residues: 2349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1039 TYR 0.026 0.002 TYR A 279 PHE 0.028 0.003 PHE B1089 TRP 0.018 0.002 TRP A 64 HIS 0.010 0.002 HIS C1083 Details of bonding type rmsd covalent geometry : bond 0.00955 (35268) covalent geometry : angle 0.80220 (47969) SS BOND : bond 0.00706 ( 45) SS BOND : angle 1.65162 ( 90) hydrogen bonds : bond 0.05733 ( 1201) hydrogen bonds : angle 6.46874 ( 3429) link_BETA1-4 : bond 0.01155 ( 4) link_BETA1-4 : angle 1.56987 ( 12) link_NAG-ASN : bond 0.00608 ( 57) link_NAG-ASN : angle 2.45246 ( 171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 1.342 Fit side-chains REVERT: C 487 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6980 (p0) REVERT: A 153 MET cc_start: 0.3638 (ptt) cc_final: 0.3004 (ppp) REVERT: A 697 MET cc_start: 0.8612 (mmp) cc_final: 0.8399 (mmp) REVERT: A 739 THR cc_start: 0.8510 (p) cc_final: 0.8288 (p) REVERT: A 740 MET cc_start: 0.7163 (ptm) cc_final: 0.6851 (tmm) REVERT: A 869 MET cc_start: 0.9377 (ptp) cc_final: 0.9049 (ttp) REVERT: E 323 MET cc_start: -0.2604 (tpt) cc_final: -0.2814 (tpt) REVERT: E 557 MET cc_start: 0.7134 (ttt) cc_final: 0.6611 (ppp) REVERT: B 200 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8599 (t80) REVERT: B 740 MET cc_start: 0.8400 (ppp) cc_final: 0.8151 (ppp) REVERT: B 902 MET cc_start: 0.9277 (mmt) cc_final: 0.8936 (tpt) REVERT: D 323 MET cc_start: 0.3939 (tpp) cc_final: 0.3666 (tpp) REVERT: D 579 MET cc_start: 0.3465 (tpt) cc_final: 0.2494 (tpp) outliers start: 19 outliers final: 9 residues processed: 119 average time/residue: 0.1853 time to fit residues: 39.9407 Evaluate side-chains 103 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 365 TYR Chi-restraints excluded: chain C residue 487 ASN Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain E residue 360 MET Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 542 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 103 optimal weight: 0.7980 chunk 352 optimal weight: 0.9990 chunk 401 optimal weight: 20.0000 chunk 375 optimal weight: 7.9990 chunk 371 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 175 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 394 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.096082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062107 restraints weight = 188796.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.061711 restraints weight = 77072.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.062271 restraints weight = 44675.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.062616 restraints weight = 32056.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.062885 restraints weight = 26492.406| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35374 Z= 0.119 Angle : 0.532 9.395 48242 Z= 0.271 Chirality : 0.044 0.308 5517 Planarity : 0.004 0.056 6127 Dihedral : 6.207 55.271 5836 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.76 % Allowed : 9.68 % Favored : 89.56 % 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: -0.71 (0.13), residues: 4206 helix: 0.50 (0.14), residues: 1295 sheet: -0.52 (0.20), residues: 585 loop : -1.00 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 214 TYR 0.020 0.001 TYR A1067 PHE 0.011 0.001 PHE D 315 TRP 0.010 0.001 TRP D 165 HIS 0.005 0.001 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00253 (35268) covalent geometry : angle 0.51736 (47969) SS BOND : bond 0.00355 ( 45) SS BOND : angle 1.19416 ( 90) hydrogen bonds : bond 0.04754 ( 1201) hydrogen bonds : angle 5.67137 ( 3429) link_BETA1-4 : bond 0.00222 ( 4) link_BETA1-4 : angle 0.91542 ( 12) link_NAG-ASN : bond 0.00418 ( 57) link_NAG-ASN : angle 1.98651 ( 171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 1.255 Fit side-chains revert: symmetry clash REVERT: A 153 MET cc_start: 0.3526 (ptt) cc_final: 0.2971 (ppp) REVERT: A 869 MET cc_start: 0.9301 (ptp) cc_final: 0.8836 (ptp) REVERT: E 190 MET cc_start: 0.2180 (ppp) cc_final: 0.1954 (ppp) REVERT: E 557 MET cc_start: 0.7383 (ttt) cc_final: 0.6803 (ppp) REVERT: D 323 MET cc_start: 0.3842 (tpp) cc_final: 0.3545 (tpp) REVERT: D 579 MET cc_start: 0.5252 (tpt) cc_final: 0.4327 (tpp) outliers start: 28 outliers final: 10 residues processed: 122 average time/residue: 0.1888 time to fit residues: 41.4786 Evaluate side-chains 100 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain D residue 60 GLN Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 392 optimal weight: 0.9980 chunk 210 optimal weight: 5.9990 chunk 307 optimal weight: 0.9990 chunk 285 optimal weight: 5.9990 chunk 213 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 232 optimal weight: 0.8980 chunk 243 optimal weight: 0.8980 chunk 102 optimal weight: 7.9990 chunk 370 optimal weight: 20.0000 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 ASN ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 ASN A1108 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN D 96 GLN D 239 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.095931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.062260 restraints weight = 197802.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.060912 restraints weight = 84350.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.061359 restraints weight = 48805.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.061675 restraints weight = 34951.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.061934 restraints weight = 28960.626| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 35374 Z= 0.163 Angle : 0.573 23.470 48242 Z= 0.282 Chirality : 0.049 1.526 5517 Planarity : 0.003 0.055 6127 Dihedral : 5.905 54.011 5836 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 0.89 % Allowed : 11.95 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.68 (0.13), residues: 4206 helix: 0.52 (0.14), residues: 1296 sheet: -0.61 (0.20), residues: 588 loop : -0.95 (0.13), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1107 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE A 392 TRP 0.037 0.001 TRP B 886 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00359 (35268) covalent geometry : angle 0.54126 (47969) SS BOND : bond 0.00370 ( 45) SS BOND : angle 0.97692 ( 90) hydrogen bonds : bond 0.04206 ( 1201) hydrogen bonds : angle 5.45296 ( 3429) link_BETA1-4 : bond 0.00390 ( 4) link_BETA1-4 : angle 0.86276 ( 12) link_NAG-ASN : bond 0.00379 ( 57) link_NAG-ASN : angle 3.15226 ( 171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 96 time to evaluate : 1.250 Fit side-chains REVERT: A 153 MET cc_start: 0.3625 (ptt) cc_final: 0.3007 (ppp) REVERT: A 869 MET cc_start: 0.9277 (ptp) cc_final: 0.8963 (ptp) REVERT: A 1031 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8094 (mp0) REVERT: E 323 MET cc_start: -0.0992 (tpt) cc_final: -0.1406 (tpt) REVERT: E 408 MET cc_start: -0.1491 (ttt) cc_final: -0.1952 (ttt) REVERT: E 557 MET cc_start: 0.7661 (ttt) cc_final: 0.7023 (ppp) REVERT: B 200 TYR cc_start: 0.8719 (m-80) cc_final: 0.8282 (t80) REVERT: B 697 MET cc_start: 0.8789 (mmm) cc_final: 0.8587 (tpt) REVERT: D 323 MET cc_start: 0.3312 (tpp) cc_final: 0.3071 (tpp) REVERT: D 579 MET cc_start: 0.5772 (tpt) cc_final: 0.5204 (tpp) outliers start: 33 outliers final: 21 residues processed: 125 average time/residue: 0.1705 time to fit residues: 38.3912 Evaluate side-chains 112 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 915 VAL Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain E residue 427 ASP Chi-restraints excluded: chain E residue 548 THR Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 49 optimal weight: 0.7980 chunk 201 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 131 optimal weight: 0.0570 chunk 326 optimal weight: 0.7980 chunk 420 optimal weight: 3.9990 chunk 186 optimal weight: 0.8980 chunk 271 optimal weight: 9.9990 chunk 369 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.096094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.062348 restraints weight = 188963.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.061869 restraints weight = 77355.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.062569 restraints weight = 44938.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.062883 restraints weight = 31390.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.063119 restraints weight = 25999.421| |-----------------------------------------------------------------------------| r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 35374 Z= 0.104 Angle : 0.520 19.834 48242 Z= 0.258 Chirality : 0.044 0.619 5517 Planarity : 0.003 0.055 6127 Dihedral : 5.395 55.025 5836 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.92 % Allowed : 13.03 % Favored : 86.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.62 (0.13), residues: 4206 helix: 0.63 (0.14), residues: 1292 sheet: -0.59 (0.20), residues: 620 loop : -0.94 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.018 0.001 TYR A1067 PHE 0.014 0.001 PHE A 392 TRP 0.021 0.001 TRP B 886 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00226 (35268) covalent geometry : angle 0.49222 (47969) SS BOND : bond 0.00288 ( 45) SS BOND : angle 0.82979 ( 90) hydrogen bonds : bond 0.03791 ( 1201) hydrogen bonds : angle 5.13657 ( 3429) link_BETA1-4 : bond 0.00242 ( 4) link_BETA1-4 : angle 0.84075 ( 12) link_NAG-ASN : bond 0.00422 ( 57) link_NAG-ASN : angle 2.79608 ( 171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 98 time to evaluate : 1.356 Fit side-chains REVERT: C 754 LEU cc_start: 0.9191 (mt) cc_final: 0.8925 (pp) REVERT: A 153 MET cc_start: 0.3466 (ptt) cc_final: 0.2878 (ppp) REVERT: A 1031 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8141 (mp0) REVERT: E 323 MET cc_start: -0.1840 (tpt) cc_final: -0.2149 (tpt) REVERT: E 408 MET cc_start: -0.1450 (ttt) cc_final: -0.1906 (ttt) REVERT: E 557 MET cc_start: 0.7429 (ttt) cc_final: 0.6816 (ppp) REVERT: B 200 TYR cc_start: 0.8727 (m-80) cc_final: 0.8330 (t80) REVERT: B 697 MET cc_start: 0.8804 (mmm) cc_final: 0.8603 (tpt) REVERT: D 323 MET cc_start: 0.3477 (tpp) cc_final: 0.3204 (tpp) REVERT: D 579 MET cc_start: 0.5644 (tpt) cc_final: 0.4662 (tpp) outliers start: 34 outliers final: 22 residues processed: 129 average time/residue: 0.1779 time to fit residues: 41.7695 Evaluate side-chains 115 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 376 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 360 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 342 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 chunk 237 optimal weight: 20.0000 chunk 92 optimal weight: 0.9990 chunk 294 optimal weight: 7.9990 chunk 164 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 324 optimal weight: 0.7980 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN C1106 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 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 = 0.4227 r_free = 0.4227 target = 0.096202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.062641 restraints weight = 189146.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.062095 restraints weight = 77512.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.062725 restraints weight = 44714.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.063045 restraints weight = 31845.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.063281 restraints weight = 26218.415| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 35374 Z= 0.098 Angle : 0.511 18.537 48242 Z= 0.252 Chirality : 0.043 0.373 5517 Planarity : 0.003 0.054 6127 Dihedral : 5.012 54.985 5836 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.05 % Allowed : 13.62 % Favored : 85.33 % 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: -0.56 (0.13), residues: 4206 helix: 0.70 (0.15), residues: 1291 sheet: -0.56 (0.20), residues: 614 loop : -0.92 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.018 0.001 TYR A1067 PHE 0.017 0.001 PHE B 759 TRP 0.018 0.001 TRP B 886 HIS 0.003 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00213 (35268) covalent geometry : angle 0.48720 (47969) SS BOND : bond 0.00185 ( 45) SS BOND : angle 0.73036 ( 90) hydrogen bonds : bond 0.03588 ( 1201) hydrogen bonds : angle 4.96982 ( 3429) link_BETA1-4 : bond 0.00225 ( 4) link_BETA1-4 : angle 0.84652 ( 12) link_NAG-ASN : bond 0.00395 ( 57) link_NAG-ASN : angle 2.61506 ( 171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 1.358 Fit side-chains REVERT: A 153 MET cc_start: 0.3462 (ptt) cc_final: 0.2880 (ppp) REVERT: A 1031 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8096 (mp0) REVERT: E 408 MET cc_start: -0.1904 (ttt) cc_final: -0.2145 (ttt) REVERT: E 474 MET cc_start: -0.0714 (tpp) cc_final: -0.1054 (tpp) REVERT: E 557 MET cc_start: 0.7332 (ttt) cc_final: 0.6743 (ppp) REVERT: B 200 TYR cc_start: 0.8742 (m-80) cc_final: 0.8440 (t80) REVERT: B 563 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7916 (mm-40) REVERT: D 323 MET cc_start: 0.3514 (tpp) cc_final: 0.3194 (tpp) REVERT: D 579 MET cc_start: 0.5938 (tpt) cc_final: 0.4982 (tpp) outliers start: 39 outliers final: 24 residues processed: 130 average time/residue: 0.1878 time to fit residues: 43.7148 Evaluate side-chains 118 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1106 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 736 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 374 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 221 optimal weight: 40.0000 chunk 37 optimal weight: 8.9990 chunk 72 optimal weight: 0.5980 chunk 247 optimal weight: 6.9990 chunk 399 optimal weight: 10.0000 chunk 406 optimal weight: 0.9990 chunk 422 optimal weight: 5.9990 chunk 327 optimal weight: 3.9990 chunk 412 optimal weight: 0.6980 chunk 166 optimal weight: 0.8980 chunk 285 optimal weight: 5.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.095645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.061980 restraints weight = 189450.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.062099 restraints weight = 78207.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.062474 restraints weight = 44758.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.062902 restraints weight = 33503.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.063206 restraints weight = 27093.904| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 35374 Z= 0.127 Angle : 0.522 18.508 48242 Z= 0.257 Chirality : 0.043 0.319 5517 Planarity : 0.003 0.053 6127 Dihedral : 4.888 54.578 5836 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.29 % Allowed : 13.65 % Favored : 85.06 % 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: -0.52 (0.13), residues: 4206 helix: 0.78 (0.15), residues: 1287 sheet: -0.52 (0.20), residues: 608 loop : -0.93 (0.13), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 34 TYR 0.017 0.001 TYR A1067 PHE 0.018 0.001 PHE B 759 TRP 0.030 0.001 TRP D 168 HIS 0.004 0.001 HIS D 417 Details of bonding type rmsd covalent geometry : bond 0.00282 (35268) covalent geometry : angle 0.49877 (47969) SS BOND : bond 0.00276 ( 45) SS BOND : angle 0.80827 ( 90) hydrogen bonds : bond 0.03524 ( 1201) hydrogen bonds : angle 4.93960 ( 3429) link_BETA1-4 : bond 0.00264 ( 4) link_BETA1-4 : angle 0.93281 ( 12) link_NAG-ASN : bond 0.00368 ( 57) link_NAG-ASN : angle 2.60986 ( 171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 94 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9231 (mt) cc_final: 0.8945 (pp) REVERT: C 900 MET cc_start: 0.8556 (mtt) cc_final: 0.8345 (mtt) REVERT: A 153 MET cc_start: 0.3462 (ptt) cc_final: 0.2988 (ppp) REVERT: E 408 MET cc_start: -0.1786 (ttt) cc_final: -0.2041 (ttt) REVERT: E 557 MET cc_start: 0.7194 (ttt) cc_final: 0.6626 (ppp) REVERT: B 200 TYR cc_start: 0.8752 (m-80) cc_final: 0.8454 (t80) REVERT: B 563 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7952 (mm-40) REVERT: D 323 MET cc_start: 0.3692 (tpp) cc_final: 0.3367 (tpp) REVERT: D 332 MET cc_start: 0.5274 (pmm) cc_final: 0.4885 (pmm) REVERT: D 579 MET cc_start: 0.5630 (tpt) cc_final: 0.4545 (tpp) outliers start: 48 outliers final: 33 residues processed: 137 average time/residue: 0.1819 time to fit residues: 45.1656 Evaluate side-chains 126 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 92 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 187 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 34 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 249 optimal weight: 9.9990 chunk 314 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 236 optimal weight: 30.0000 chunk 35 optimal weight: 0.0970 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 599 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.095954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.061772 restraints weight = 187726.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 67)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.061530 restraints weight = 76939.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.061997 restraints weight = 45604.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.062454 restraints weight = 33692.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.062780 restraints weight = 26448.611| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 35374 Z= 0.115 Angle : 0.521 17.633 48242 Z= 0.256 Chirality : 0.043 0.318 5517 Planarity : 0.003 0.053 6127 Dihedral : 4.761 54.813 5836 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.16 % Allowed : 14.19 % Favored : 84.65 % 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: -0.51 (0.13), residues: 4206 helix: 0.77 (0.15), residues: 1291 sheet: -0.51 (0.20), residues: 605 loop : -0.92 (0.13), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.018 0.001 TYR A1067 PHE 0.022 0.001 PHE B 759 TRP 0.018 0.001 TRP D 168 HIS 0.003 0.001 HIS E 540 Details of bonding type rmsd covalent geometry : bond 0.00255 (35268) covalent geometry : angle 0.49925 (47969) SS BOND : bond 0.00262 ( 45) SS BOND : angle 0.79826 ( 90) hydrogen bonds : bond 0.03423 ( 1201) hydrogen bonds : angle 4.85306 ( 3429) link_BETA1-4 : bond 0.00198 ( 4) link_BETA1-4 : angle 0.87306 ( 12) link_NAG-ASN : bond 0.00379 ( 57) link_NAG-ASN : angle 2.52446 ( 171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 97 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9238 (mt) cc_final: 0.8945 (pp) REVERT: C 900 MET cc_start: 0.8505 (mtt) cc_final: 0.8276 (mtt) REVERT: A 153 MET cc_start: 0.3738 (ptt) cc_final: 0.3414 (ppp) REVERT: A 731 MET cc_start: 0.8704 (ptm) cc_final: 0.8421 (ptm) REVERT: E 323 MET cc_start: -0.0168 (tpt) cc_final: -0.0457 (tpt) REVERT: E 462 MET cc_start: 0.6248 (mpp) cc_final: 0.5903 (pmm) REVERT: E 474 MET cc_start: -0.0285 (tpp) cc_final: -0.0537 (tpp) REVERT: E 557 MET cc_start: 0.7488 (ttt) cc_final: 0.6842 (ppp) REVERT: B 563 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8021 (mm-40) REVERT: B 902 MET cc_start: 0.9119 (tpp) cc_final: 0.8610 (tpt) REVERT: D 323 MET cc_start: 0.3617 (tpp) cc_final: 0.3351 (tpp) REVERT: D 579 MET cc_start: 0.6356 (tpt) cc_final: 0.5768 (tpp) outliers start: 43 outliers final: 34 residues processed: 138 average time/residue: 0.1905 time to fit residues: 47.1994 Evaluate side-chains 127 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 92 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 563 GLN Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 15 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 268 optimal weight: 8.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 chunk 358 optimal weight: 0.7980 chunk 364 optimal weight: 0.9980 chunk 176 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 305 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.095370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061244 restraints weight = 186090.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.062218 restraints weight = 80793.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.061587 restraints weight = 53948.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.062148 restraints weight = 37032.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.062117 restraints weight = 31946.263| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 35374 Z= 0.150 Angle : 0.597 31.308 48242 Z= 0.284 Chirality : 0.044 0.317 5517 Planarity : 0.003 0.053 6127 Dihedral : 5.089 54.198 5836 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.11 % Allowed : 14.35 % Favored : 84.54 % 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: -0.55 (0.13), residues: 4206 helix: 0.72 (0.15), residues: 1301 sheet: -0.58 (0.20), residues: 604 loop : -0.93 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 34 TYR 0.017 0.001 TYR A1067 PHE 0.026 0.001 PHE B 759 TRP 0.019 0.001 TRP D 168 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00332 (35268) covalent geometry : angle 0.54463 (47969) SS BOND : bond 0.00826 ( 45) SS BOND : angle 1.02522 ( 90) hydrogen bonds : bond 0.03498 ( 1201) hydrogen bonds : angle 4.93761 ( 3429) link_BETA1-4 : bond 0.00355 ( 4) link_BETA1-4 : angle 0.99792 ( 12) link_NAG-ASN : bond 0.00506 ( 57) link_NAG-ASN : angle 4.10515 ( 171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: C 900 MET cc_start: 0.8604 (mtt) cc_final: 0.8382 (mtt) REVERT: A 153 MET cc_start: 0.3798 (ptt) cc_final: 0.3590 (ppp) REVERT: A 1050 MET cc_start: 0.8682 (pmm) cc_final: 0.8053 (pmm) REVERT: E 360 MET cc_start: -0.3021 (mtm) cc_final: -0.3246 (ttp) REVERT: E 557 MET cc_start: 0.6866 (ttt) cc_final: 0.6332 (ppp) REVERT: B 563 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8103 (mm110) REVERT: D 323 MET cc_start: 0.3756 (tpp) cc_final: 0.3534 (tpp) REVERT: D 579 MET cc_start: 0.3622 (tpt) cc_final: 0.2516 (tpp) outliers start: 41 outliers final: 35 residues processed: 134 average time/residue: 0.1712 time to fit residues: 42.1826 Evaluate side-chains 128 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 357 optimal weight: 1.9990 chunk 388 optimal weight: 2.9990 chunk 221 optimal weight: 0.0170 chunk 102 optimal weight: 0.6980 chunk 142 optimal weight: 20.0000 chunk 213 optimal weight: 20.0000 chunk 10 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 345 optimal weight: 1.9990 chunk 383 optimal weight: 20.0000 chunk 180 optimal weight: 1.9990 overall best weight: 0.9422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.095461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 86)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.061907 restraints weight = 190444.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.062809 restraints weight = 77622.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.063447 restraints weight = 44767.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.063775 restraints weight = 31844.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.064010 restraints weight = 26578.200| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 35374 Z= 0.109 Angle : 0.539 16.301 48242 Z= 0.263 Chirality : 0.043 0.316 5517 Planarity : 0.003 0.053 6127 Dihedral : 5.457 111.396 5836 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.05 % Allowed : 14.59 % Favored : 84.35 % 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: -0.52 (0.13), residues: 4206 helix: 0.79 (0.15), residues: 1298 sheet: -0.56 (0.20), residues: 599 loop : -0.94 (0.13), residues: 2309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 34 TYR 0.017 0.001 TYR A1067 PHE 0.031 0.001 PHE B 759 TRP 0.016 0.001 TRP D 168 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00244 (35268) covalent geometry : angle 0.51459 (47969) SS BOND : bond 0.00365 ( 45) SS BOND : angle 1.14701 ( 90) hydrogen bonds : bond 0.03335 ( 1201) hydrogen bonds : angle 4.82048 ( 3429) link_BETA1-4 : bond 0.00219 ( 4) link_BETA1-4 : angle 0.85200 ( 12) link_NAG-ASN : bond 0.00378 ( 57) link_NAG-ASN : angle 2.60965 ( 171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8412 Ramachandran restraints generated. 4206 Oldfield, 0 Emsley, 4206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 93 time to evaluate : 1.262 Fit side-chains revert: symmetry clash REVERT: C 754 LEU cc_start: 0.9316 (mt) cc_final: 0.9002 (pp) REVERT: C 900 MET cc_start: 0.8594 (mtt) cc_final: 0.8378 (mtt) REVERT: A 153 MET cc_start: 0.3756 (ptt) cc_final: 0.3551 (ppp) REVERT: A 1050 MET cc_start: 0.8769 (pmm) cc_final: 0.8029 (pmm) REVERT: E 360 MET cc_start: -0.2770 (mtm) cc_final: -0.3069 (ttp) REVERT: E 557 MET cc_start: 0.7279 (ttt) cc_final: 0.6674 (ppp) REVERT: B 563 GLN cc_start: 0.8538 (OUTLIER) cc_final: 0.8258 (mm110) REVERT: D 323 MET cc_start: 0.3571 (tpp) cc_final: 0.3295 (tpp) REVERT: D 579 MET cc_start: 0.5803 (tpt) cc_final: 0.4683 (tpp) outliers start: 39 outliers final: 34 residues processed: 127 average time/residue: 0.1826 time to fit residues: 42.3491 Evaluate side-chains 128 residues out of total 3735 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 93 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 376 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 996 LEU Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 617 CYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 791 THR Chi-restraints excluded: chain A residue 860 VAL Chi-restraints excluded: chain A residue 900 MET Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain A residue 1031 GLU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain E residue 228 HIS Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 563 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain D residue 29 LEU Chi-restraints excluded: chain D residue 62 MET Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 374 HIS Chi-restraints excluded: chain D residue 597 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 424 random chunks: chunk 24 optimal weight: 0.5980 chunk 274 optimal weight: 3.9990 chunk 246 optimal weight: 8.9990 chunk 301 optimal weight: 8.9990 chunk 80 optimal weight: 6.9990 chunk 342 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 300 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 314 GLN C 856 ASN C1106 GLN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 58 ASN ** E 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.093853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.057569 restraints weight = 175736.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.058960 restraints weight = 85668.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.058338 restraints weight = 48187.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.058231 restraints weight = 37951.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.058170 restraints weight = 36211.916| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 35374 Z= 0.284 Angle : 0.683 15.109 48242 Z= 0.339 Chirality : 0.046 0.329 5517 Planarity : 0.004 0.054 6127 Dihedral : 5.965 109.115 5836 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.19 % Allowed : 14.54 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.13), residues: 4206 helix: 0.60 (0.15), residues: 1292 sheet: -0.95 (0.19), residues: 643 loop : -1.08 (0.13), residues: 2271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C1107 TYR 0.020 0.002 TYR A1067 PHE 0.036 0.002 PHE B 759 TRP 0.022 0.002 TRP B 886 HIS 0.006 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00627 (35268) covalent geometry : angle 0.66188 (47969) SS BOND : bond 0.00618 ( 45) SS BOND : angle 1.51027 ( 90) hydrogen bonds : bond 0.03911 ( 1201) hydrogen bonds : angle 5.31899 ( 3429) link_BETA1-4 : bond 0.00541 ( 4) link_BETA1-4 : angle 1.14106 ( 12) link_NAG-ASN : bond 0.00478 ( 57) link_NAG-ASN : angle 2.74243 ( 171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9734.55 seconds wall clock time: 167 minutes 14.84 seconds (10034.84 seconds total)