Starting phenix.real_space_refine on Mon Aug 25 12:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8c_39041/08_2025/8y8c_39041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8c_39041/08_2025/8y8c_39041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y8c_39041/08_2025/8y8c_39041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8c_39041/08_2025/8y8c_39041.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y8c_39041/08_2025/8y8c_39041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8c_39041/08_2025/8y8c_39041.map" } resolution = 2.95 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= 0.094 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 165 5.16 5 C 17707 2.51 5 N 4513 2.21 5 O 5404 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27789 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1188, 9118 Classifications: {'peptide': 1188} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1132} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 5, 'GLN:plan1': 2, 'GLU:plan': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 98 Chain: "B" Number of atoms: 9107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1173, 9107 Classifications: {'peptide': 1173} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1116} Chain breaks: 4 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 2, 'ARG:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 9214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1187, 9214 Classifications: {'peptide': 1187} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1130} Chain breaks: 2 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ARG:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 5.33, per 1000 atoms: 0.19 Number of scatterers: 27789 At special positions: 0 Unit cell: (147.6, 151.7, 163.18, 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 165 16.00 O 5404 8.00 N 4513 7.00 C 17707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 Simple disulfide: pdb=" SG CYS A 151 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 242 " distance=2.03 Simple disulfide: pdb=" SG CYS A 282 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 352 " distance=2.03 Simple disulfide: pdb=" SG CYS A 370 " - pdb=" SG CYS A 423 " distance=2.03 Simple disulfide: pdb=" SG CYS A 382 " - pdb=" SG CYS A 603 " distance=2.03 Simple disulfide: pdb=" SG CYS A 466 " - pdb=" SG CYS A 546 " distance=2.03 Simple disulfide: pdb=" SG CYS A 474 " - pdb=" SG CYS A 495 " distance=2.03 Simple disulfide: pdb=" SG CYS A 476 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 516 " distance=2.03 Simple disulfide: pdb=" SG CYS A 504 " - pdb=" SG CYS A 518 " distance=2.03 Simple disulfide: pdb=" SG CYS A 520 " - pdb=" SG CYS A 533 " distance=2.03 Simple disulfide: pdb=" SG CYS A 556 " - pdb=" SG CYS A 567 " distance=2.03 Simple disulfide: pdb=" SG CYS A 580 " - pdb=" SG CYS A 586 " distance=2.03 Simple disulfide: pdb=" SG CYS A 619 " - pdb=" SG CYS A 672 " distance=2.03 Simple disulfide: pdb=" SG CYS A 697 " - pdb=" SG CYS A 719 " distance=2.03 Simple disulfide: pdb=" SG CYS A 734 " - pdb=" SG CYS A 743 " distance=2.03 Simple disulfide: pdb=" SG CYS A 814 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A 819 " - pdb=" SG CYS A 825 " distance=2.03 Simple disulfide: pdb=" SG CYS A 890 " - pdb=" SG CYS A 895 " distance=2.03 Simple disulfide: pdb=" SG CYS A 925 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A1113 " - pdb=" SG CYS A1124 " distance=2.03 Simple disulfide: pdb=" SG CYS A1163 " - pdb=" SG CYS A1208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 20 " - pdb=" SG CYS B 156 " distance=2.03 Simple disulfide: pdb=" SG CYS B 151 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 242 " distance=2.03 Simple disulfide: pdb=" SG CYS B 282 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 370 " - pdb=" SG CYS B 423 " distance=2.03 Simple disulfide: pdb=" SG CYS B 382 " - pdb=" SG CYS B 603 " distance=2.03 Simple disulfide: pdb=" SG CYS B 466 " - pdb=" SG CYS B 546 " distance=2.03 Simple disulfide: pdb=" SG CYS B 474 " - pdb=" SG CYS B 495 " distance=2.03 Simple disulfide: pdb=" SG CYS B 476 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 520 " - pdb=" SG CYS B 533 " distance=2.03 Simple disulfide: pdb=" SG CYS B 556 " - pdb=" SG CYS B 567 " distance=2.03 Simple disulfide: pdb=" SG CYS B 580 " - pdb=" SG CYS B 586 " distance=2.03 Simple disulfide: pdb=" SG CYS B 619 " - pdb=" SG CYS B 672 " distance=2.03 Simple disulfide: pdb=" SG CYS B 697 " - pdb=" SG CYS B 719 " distance=2.03 Simple disulfide: pdb=" SG CYS B 734 " - pdb=" SG CYS B 743 " distance=2.03 Simple disulfide: pdb=" SG CYS B 814 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B 819 " - pdb=" SG CYS B 825 " distance=2.03 Simple disulfide: pdb=" SG CYS B 890 " - pdb=" SG CYS B 895 " distance=2.03 Simple disulfide: pdb=" SG CYS B 925 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B1113 " - pdb=" SG CYS B1124 " distance=2.03 Simple disulfide: pdb=" SG CYS B1163 " - pdb=" SG CYS B1208 " distance=2.03 Simple disulfide: pdb=" SG CYS C 20 " - pdb=" SG CYS C 156 " distance=2.03 Simple disulfide: pdb=" SG CYS C 151 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 163 " - pdb=" SG CYS C 242 " distance=2.03 Simple disulfide: pdb=" SG CYS C 282 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 327 " - pdb=" SG CYS C 352 " distance=2.03 Simple disulfide: pdb=" SG CYS C 370 " - pdb=" SG CYS C 423 " distance=2.03 Simple disulfide: pdb=" SG CYS C 382 " - pdb=" SG CYS C 603 " distance=2.03 Simple disulfide: pdb=" SG CYS C 466 " - pdb=" SG CYS C 546 " distance=2.03 Simple disulfide: pdb=" SG CYS C 474 " - pdb=" SG CYS C 495 " distance=2.03 Simple disulfide: pdb=" SG CYS C 476 " - pdb=" SG CYS C 565 " distance=2.03 Simple disulfide: pdb=" SG CYS C 504 " - pdb=" SG CYS C 518 " distance=2.03 Simple disulfide: pdb=" SG CYS C 520 " - pdb=" SG CYS C 533 " distance=2.03 Simple disulfide: pdb=" SG CYS C 556 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 580 " - pdb=" SG CYS C 586 " distance=2.03 Simple disulfide: pdb=" SG CYS C 619 " - pdb=" SG CYS C 672 " distance=2.03 Simple disulfide: pdb=" SG CYS C 697 " - pdb=" SG CYS C 719 " distance=2.03 Simple disulfide: pdb=" SG CYS C 734 " - pdb=" SG CYS C 743 " distance=2.03 Simple disulfide: pdb=" SG CYS C 814 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C 819 " - pdb=" SG CYS C 825 " distance=2.03 Simple disulfide: pdb=" SG CYS C 890 " - pdb=" SG CYS C 895 " distance=2.03 Simple disulfide: pdb=" SG CYS C 925 " - pdb=" SG CYS C 936 " distance=2.03 Simple disulfide: pdb=" SG CYS C1113 " - pdb=" SG CYS C1124 " distance=2.03 Simple disulfide: pdb=" SG CYS C1163 " - pdb=" SG CYS C1208 " 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 NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 58 " " NAG A1303 " - " ASN A 355 " " NAG A1304 " - " ASN A 703 " " NAG A1305 " - " ASN A 192 " " NAG A1306 " - " ASN A 771 " " NAG A1307 " - " ASN A 335 " " NAG A1308 " - " ASN A 664 " " NAG A1309 " - " ASN A 793 " " NAG B1301 " - " ASN B 703 " " NAG B1302 " - " ASN B 725 " " NAG B1303 " - " ASN B 793 " " NAG B1304 " - " ASN B 664 " " NAG B1305 " - " ASN B 335 " " NAG B1306 " - " ASN B 192 " " NAG B1307 " - " ASN B1211 " " NAG B1308 " - " ASN B 355 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 132 " " NAG C1303 " - " ASN C 192 " " NAG C1304 " - " ASN C 725 " " NAG C1305 " - " ASN C 188 " " NAG C1306 " - " ASN C 355 " " NAG C1307 " - " ASN C1211 " " NAG C1308 " - " ASN C 19 " Time building additional restraints: 1.68 Conformation dependent library (CDL) restraints added in 836.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6688 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 68 sheets defined 25.1% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.560A pdb=" N TRP A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N TYR A 90 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 91' Processing helix chain 'A' and resid 285 through 295 Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.675A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 4.010A pdb=" N TRP A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.508A pdb=" N ASP A 400 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 397 through 402' Processing helix chain 'A' and resid 408 through 413 Processing helix chain 'A' and resid 445 through 449 removed outlier: 3.531A pdb=" N GLY A 449 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 696 through 704 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 Processing helix chain 'A' and resid 831 through 833 No H-bonds generated for 'chain 'A' and resid 831 through 833' Processing helix chain 'A' and resid 834 through 862 Processing helix chain 'A' and resid 885 through 888 Processing helix chain 'A' and resid 901 through 909 Processing helix chain 'A' and resid 914 through 924 Processing helix chain 'A' and resid 933 through 940 removed outlier: 3.503A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 removed outlier: 3.529A pdb=" N ILE A 955 " --> pdb=" O SER A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.778A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 removed outlier: 3.753A pdb=" N ALA A1005 " --> pdb=" O GLN A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1046 Processing helix chain 'A' and resid 1047 through 1049 No H-bonds generated for 'chain 'A' and resid 1047 through 1049' Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.643A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 5.321A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.860A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 344 removed outlier: 4.151A pdb=" N TRP B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 341 through 344' Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.808A pdb=" N LEU B 360 " --> pdb=" O LEU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.839A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 447 removed outlier: 3.793A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.515A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 703 Processing helix chain 'B' and resid 814 through 819 Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.526A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 835 through 862 Processing helix chain 'B' and resid 870 through 872 No H-bonds generated for 'chain 'B' and resid 870 through 872' Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 910 removed outlier: 3.796A pdb=" N LYS B 910 " --> pdb=" O LEU B 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 Processing helix chain 'B' and resid 933 through 941 removed outlier: 3.591A pdb=" N VAL B 937 " --> pdb=" O ASP B 933 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 965 Processing helix chain 'B' and resid 971 through 975 removed outlier: 3.972A pdb=" N ALA B 975 " --> pdb=" O SER B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 989 Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.822A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1019 Processing helix chain 'B' and resid 1023 through 1046 Processing helix chain 'B' and resid 1047 through 1049 No H-bonds generated for 'chain 'B' and resid 1047 through 1049' Processing helix chain 'B' and resid 1057 through 1065 Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 3.879A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1202 removed outlier: 3.882A pdb=" N ASN B1201 " --> pdb=" O SER B1198 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B1202 " --> pdb=" O ASP B1199 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1198 through 1202' Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.664A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.567A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 363 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.859A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.541A pdb=" N LEU C 401 " --> pdb=" O ARG C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 413 Processing helix chain 'C' and resid 442 through 448 removed outlier: 3.775A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N TYR C 448 " --> pdb=" O TRP C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.974A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.691A pdb=" N THR C 532 " --> pdb=" O SER C 529 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N CYS C 533 " --> pdb=" O PRO C 530 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 529 through 533' Processing helix chain 'C' and resid 696 through 704 Processing helix chain 'C' and resid 813 through 820 Processing helix chain 'C' and resid 822 through 830 removed outlier: 3.797A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 862 Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.636A pdb=" N LEU C 888 " --> pdb=" O LYS C 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 885 through 888' Processing helix chain 'C' and resid 901 through 910 removed outlier: 3.761A pdb=" N LYS C 910 " --> pdb=" O LEU C 906 " (cutoff:3.500A) Processing helix chain 'C' and resid 914 through 924 removed outlier: 4.253A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 933 through 940 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.597A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 971 through 975 removed outlier: 3.760A pdb=" N ALA C 975 " --> pdb=" O SER C 972 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 999 removed outlier: 3.832A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1019 removed outlier: 3.694A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.891A pdb=" N LYS C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE C1029 " --> pdb=" O ALA C1025 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN C1030 " --> pdb=" O LEU C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.799A pdb=" N ASN C1049 " --> pdb=" O GLN C1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1046 through 1049' Processing helix chain 'C' and resid 1057 through 1065 removed outlier: 3.666A pdb=" N ILE C1061 " --> pdb=" O SER C1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 5.224A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 68 removed outlier: 4.259A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.592A pdb=" N VAL A 280 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ASN A 278 " --> pdb=" O ASN A 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 80 through 81 removed outlier: 6.567A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.627A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR A 123 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS A 151 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE A 145 " --> pdb=" O HIS A 142 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 302 through 305 Processing sheet with id=AA6, first strand: chain 'A' and resid 309 through 310 Processing sheet with id=AA7, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA8, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.873A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.745A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.745A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 385 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 459 through 463 Processing sheet with id=AB3, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.718A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 504 through 505 Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.743A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AB7, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.798A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.299A pdb=" N ASN A 725 " --> pdb=" O TYR A 762 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE A 764 " --> pdb=" O ASN A 725 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N THR A 766 " --> pdb=" O THR A 727 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N TYR A 729 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE A 742 " --> pdb=" O MET A 738 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.214A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 786 through 804 removed outlier: 6.945A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.060A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 866 through 868 Processing sheet with id=AC4, first strand: chain 'A' and resid 878 through 879 Processing sheet with id=AC5, first strand: chain 'A' and resid 1202 through 1205 removed outlier: 3.700A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A1169 " --> pdb=" O MET A1205 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 1175 through 1179 Processing sheet with id=AC7, first strand: chain 'B' and resid 34 through 35 removed outlier: 4.379A pdb=" N ARG B 34 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 75 " --> pdb=" O VAL B 258 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 34 through 35 removed outlier: 4.379A pdb=" N ARG B 34 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG B 75 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N GLY B 101 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 60 through 61 removed outlier: 6.925A pdb=" N ASN B 269 " --> pdb=" O THR B 277 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 80 through 81 removed outlier: 6.883A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.764A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE B 124 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 109 through 113 removed outlier: 3.792A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL B 113 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD5, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.669A pdb=" N GLY B 675 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 316 through 319 removed outlier: 3.568A pdb=" N ARG B 319 " --> pdb=" O ASP B 623 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 622 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N ILE B 656 " --> pdb=" O ILE B 669 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.986A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.520A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N CYS B 586 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.520A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AE2, first strand: chain 'B' and resid 459 through 463 Processing sheet with id=AE3, first strand: chain 'B' and resid 467 through 468 Processing sheet with id=AE4, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.517A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.496A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.703A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 744 " --> pdb=" O ARG B 737 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ARG B 737 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 786 through 791 Processing sheet with id=AE7, first strand: chain 'B' and resid 794 through 804 removed outlier: 6.147A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.213A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 866 through 868 Processing sheet with id=AF1, first strand: chain 'B' and resid 1162 through 1163 removed outlier: 3.673A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 1175 through 1180 Processing sheet with id=AF3, first strand: chain 'C' and resid 59 through 68 removed outlier: 3.616A pdb=" N LEU C 261 " --> pdb=" O GLY C 101 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 59 through 68 removed outlier: 6.750A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.743A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.628A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR C 235 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR C 123 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE C 124 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.745A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AF9, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG1, first strand: chain 'C' and resid 316 through 319 removed outlier: 3.694A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 636 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE C 658 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AG3, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.881A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER C 385 " --> pdb=" O ASN C 595 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS C 586 " --> pdb=" O LEU C 429 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU C 429 " --> pdb=" O CYS C 586 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N TYR C 427 " --> pdb=" O ILE C 588 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.866A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG6, first strand: chain 'C' and resid 466 through 468 removed outlier: 4.586A pdb=" N CYS C 466 " --> pdb=" O VAL C 538 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'C' and resid 550 through 551 Processing sheet with id=AG8, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AG9, first strand: chain 'C' and resid 724 through 731 removed outlier: 6.515A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.688A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 9.581A pdb=" N LEU C 726 " --> pdb=" O THR C 766 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'C' and resid 786 through 804 removed outlier: 7.000A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 809 through 812 removed outlier: 3.999A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH4, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.531A pdb=" N ALA C1171 " --> pdb=" O VAL C1203 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 1175 through 1179 1046 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.11 Time building geometry restraints manager: 2.24 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: 8852 1.34 - 1.46: 7039 1.46 - 1.58: 12371 1.58 - 1.70: 0 1.70 - 1.82: 192 Bond restraints: 28454 Sorted by residual: 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 2.30e+00 bond pdb=" C1 NAG C1305 " pdb=" O5 NAG C1305 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.11e+00 bond pdb=" C1 NAG B1307 " pdb=" O5 NAG B1307 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 bond pdb=" C1 NAG C1303 " pdb=" O5 NAG C1303 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.04e+00 bond pdb=" C1 NAG A1305 " pdb=" O5 NAG A1305 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 28449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 38071 1.28 - 2.56: 561 2.56 - 3.83: 138 3.83 - 5.11: 9 5.11 - 6.39: 4 Bond angle restraints: 38783 Sorted by residual: angle pdb=" N THR C 532 " pdb=" CA THR C 532 " pdb=" C THR C 532 " ideal model delta sigma weight residual 114.56 110.53 4.03 1.27e+00 6.20e-01 1.01e+01 angle pdb=" C ASN C 19 " pdb=" N CYS C 20 " pdb=" CA CYS C 20 " ideal model delta sigma weight residual 121.54 126.64 -5.10 1.91e+00 2.74e-01 7.12e+00 angle pdb=" C VAL A 113 " pdb=" N ASN A 114 " pdb=" CA ASN A 114 " ideal model delta sigma weight residual 121.54 126.05 -4.51 1.91e+00 2.74e-01 5.56e+00 angle pdb=" CA THR C 532 " pdb=" C THR C 532 " pdb=" N CYS C 533 " ideal model delta sigma weight residual 119.26 116.70 2.56 1.14e+00 7.69e-01 5.04e+00 angle pdb=" C THR B 834 " pdb=" N PHE B 835 " pdb=" CA PHE B 835 " ideal model delta sigma weight residual 121.54 125.03 -3.49 1.91e+00 2.74e-01 3.34e+00 ... (remaining 38778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 16832 17.11 - 34.22: 371 34.22 - 51.34: 60 51.34 - 68.45: 11 68.45 - 85.56: 2 Dihedral angle restraints: 17276 sinusoidal: 6871 harmonic: 10405 Sorted by residual: dihedral pdb=" CB CYS C 619 " pdb=" SG CYS C 619 " pdb=" SG CYS C 672 " pdb=" CB CYS C 672 " ideal model delta sinusoidal sigma weight residual -86.00 -115.40 29.40 1 1.00e+01 1.00e-02 1.24e+01 dihedral pdb=" CB CYS A 466 " pdb=" SG CYS A 466 " pdb=" SG CYS A 546 " pdb=" CB CYS A 546 " ideal model delta sinusoidal sigma weight residual -86.00 -113.91 27.91 1 1.00e+01 1.00e-02 1.12e+01 dihedral pdb=" CB CYS C 466 " pdb=" SG CYS C 466 " pdb=" SG CYS C 546 " pdb=" CB CYS C 546 " ideal model delta sinusoidal sigma weight residual -86.00 -113.63 27.63 1 1.00e+01 1.00e-02 1.10e+01 ... (remaining 17273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2733 0.026 - 0.053: 1048 0.053 - 0.079: 299 0.079 - 0.106: 258 0.106 - 0.132: 126 Chirality restraints: 4464 Sorted by residual: chirality pdb=" CA ILE A 790 " pdb=" N ILE A 790 " pdb=" C ILE A 790 " pdb=" CB ILE A 790 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.37e-01 chirality pdb=" CA VAL C 977 " pdb=" N VAL C 977 " pdb=" C VAL C 977 " pdb=" CB VAL C 977 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.16e-01 ... (remaining 4461 not shown) Planarity restraints: 5004 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 521 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO C 522 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 522 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 522 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PRO B1067 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C1066 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.78e+00 pdb=" N PRO C1067 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C1067 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C1067 " 0.018 5.00e-02 4.00e+02 ... (remaining 5001 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2753 2.76 - 3.29: 26115 3.29 - 3.83: 44351 3.83 - 4.36: 51852 4.36 - 4.90: 92884 Nonbonded interactions: 217955 Sorted by model distance: nonbonded pdb=" OG SER A 340 " pdb=" OD1 ASN A 343 " model vdw 2.219 3.040 nonbonded pdb=" OD2 ASP A 374 " pdb=" OG SER A 376 " model vdw 2.226 3.040 nonbonded pdb=" OG SER A 568 " pdb=" OD1 ASP A 570 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR B 448 " pdb=" O PHE B 473 " model vdw 2.256 3.040 nonbonded pdb=" OD1 ASN C 108 " pdb=" OG SER C 119 " model vdw 2.257 3.040 ... (remaining 217950 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 14 through 21 or (resid 22 and (name N or name CA or name \ C or name O or name CB )) or resid 23 or (resid 24 and (name N or name CA or nam \ e C or name O or name CB )) or resid 25 through 179 or (resid 180 and (name N or \ name CA or name C or name O or name CB )) or resid 181 through 247 or (resid 24 \ 8 and (name N or name CA or name C or name O or name CB )) or resid 249 through \ 311 or (resid 312 and (name N or name CA or name C or name O or name CB )) or re \ sid 313 through 374 or (resid 375 and (name N or name CA or name C or name O or \ name CB )) or resid 376 through 483 or resid 490 through 501 or (resid 502 and ( \ name N or name CA or name C or name O or name CB )) or resid 519 through 558 or \ resid 563 through 569 or (resid 570 through 571 and (name N or name CA or name C \ or name O or name CB )) or resid 572 through 705 or (resid 706 and (name N or n \ ame CA or name C or name O or name CB )) or resid 707 through 781 or (resid 782 \ and (name N or name CA or name C or name O or name CB )) or resid 783 through 87 \ 5 or (resid 876 and (name N or name CA or name C or name O or name CB )) or resi \ d 877 through 1065 or (resid 1066 and (name N or name CA or name C or name O or \ name CB )) or resid 1067 through 1308)) selection = (chain 'B' and (resid 14 through 19 or resid 21 through 26 or (resid 34 and (nam \ e N or name CA or name C or name O or name CB )) or resid 35 through 83 or (resi \ d 84 and (name N or name CA or name C or name O or name CB )) or resid 85 throug \ h 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 113 or (resid 114 through 116 and (name N or name CA or name C \ or name O or name CB )) or resid 117 or (resid 118 and (name N or name CA or na \ me C or name O or name CB )) or resid 119 through 139 or (resid 140 and (name N \ or name CA or name C or name O or name CB )) or resid 141 through 156 or (resid \ 157 and (name N or name CA or name C or name O or name CB )) or resid 158 throug \ h 165 or (resid 166 and (name N or name CA or name C or name O or name CB )) or \ resid 167 through 173 or (resid 174 and (name N or name CA or name C or name O o \ r name CB )) or resid 175 through 179 or (resid 180 and (name N or name CA or na \ me C or name O or name CB )) or resid 181 through 185 or (resid 186 and (name N \ or name CA or name C or name O or name CB )) or resid 187 through 374 or (resid \ 375 and (name N or name CA or name C or name O or name CB )) or resid 376 throug \ h 533 or (resid 534 and (name N or name CA or name C or name O or name CB )) or \ resid 535 through 550 or (resid 551 and (name N or name CA or name C or name O o \ r name CB )) or resid 552 or (resid 553 through 555 and (name N or name CA or na \ me C or name O or name CB )) or resid 556 through 557 or (resid 558 through 563 \ and (name N or name CA or name C or name O or name CB )) or resid 564 through 87 \ 5 or (resid 876 and (name N or name CA or name C or name O or name CB )) or resi \ d 877 through 929 or (resid 930 through 932 and (name N or name CA or name C or \ name O or name CB )) or resid 933 through 998 or (resid 999 and (name N or name \ CA or name C or name O or name CB )) or resid 1000 through 1021 or (resid 1022 a \ nd (name N or name CA or name C or name O or name CB )) or resid 1023 through 11 \ 80 or (resid 1181 through 1182 and (name N or name CA or name C or name O or nam \ e CB )) or resid 1183 through 1199 or (resid 1200 and (name N or name CA or name \ C or name O or name CB )) or resid 1201 through 1308)) selection = (chain 'C' and (resid 14 through 19 or resid 21 or (resid 22 and (name N or name \ CA or name C or name O or name CB )) or resid 23 or (resid 24 and (name N or na \ me CA or name C or name O or name CB )) or resid 25 through 26 or resid 34 throu \ gh 109 or (resid 110 and (name N or name CA or name C or name O or name CB )) or \ resid 111 through 115 or (resid 116 and (name N or name CA or name C or name O \ or name CB )) or resid 117 or (resid 118 and (name N or name CA or name C or nam \ e O or name CB )) or resid 119 through 139 or (resid 140 and (name N or name CA \ or name C or name O or name CB )) or resid 141 through 156 or (resid 157 and (na \ me N or name CA or name C or name O or name CB )) or resid 158 through 173 or (r \ esid 174 and (name N or name CA or name C or name O or name CB )) or resid 175 t \ hrough 185 or (resid 186 and (name N or name CA or name C or name O or name CB ) \ ) or resid 187 through 247 or (resid 248 and (name N or name CA or name C or nam \ e O or name CB )) or resid 249 through 483 or resid 490 through 501 or (resid 50 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 519 through \ 533 or (resid 534 and (name N or name CA or name C or name O or name CB )) or re \ sid 535 through 550 or (resid 551 and (name N or name CA or name C or name O or \ name CB )) or resid 552 or (resid 553 through 555 and (name N or name CA or name \ C or name O or name CB )) or resid 556 through 557 or (resid 558 and (name N or \ name CA or name C or name O or name CB )) or (resid 563 and (name N or name CA \ or name C or name O or name CB )) or resid 564 through 569 or (resid 570 through \ 571 and (name N or name CA or name C or name O or name CB )) or resid 572 throu \ gh 705 or (resid 706 and (name N or name CA or name C or name O or name CB )) or \ resid 707 through 779 or (resid 780 and (name N or name CA or name C or name O \ or name CB )) or resid 781 or (resid 782 and (name N or name CA or name C or nam \ e O or name CB )) or resid 783 through 929 or (resid 930 through 932 and (name N \ or name CA or name C or name O or name CB )) or resid 933 through 998 or (resid \ 999 and (name N or name CA or name C or name O or name CB )) or resid 1000 thro \ ugh 1021 or (resid 1022 and (name N or name CA or name C or name O or name CB )) \ or resid 1023 through 1065 or (resid 1066 and (name N or name CA or name C or n \ ame O or name CB )) or resid 1067 through 1180 or (resid 1181 through 1182 and ( \ name N or name CA or name C or name O or name CB )) or resid 1183 through 1199 o \ r (resid 1200 and (name N or name CA or name C or name O or name CB )) or resid \ 1201 through 1308)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.130 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.030 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:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 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 : 0.002 0.039 28546 Z= 0.101 Angle : 0.401 6.388 38992 Z= 0.211 Chirality : 0.040 0.132 4464 Planarity : 0.003 0.036 4979 Dihedral : 6.857 85.559 10387 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.80 % Allowed : 3.12 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -1.59 (0.13), residues: 3522 helix: 0.32 (0.18), residues: 764 sheet: -0.09 (0.19), residues: 676 loop : -2.04 (0.12), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 502 TYR 0.006 0.001 TYR C 832 PHE 0.006 0.001 PHE C 202 TRP 0.005 0.001 TRP B 444 HIS 0.002 0.000 HIS B 826 Details of bonding type rmsd covalent geometry : bond 0.00198 (28454) covalent geometry : angle 0.39984 (38783) SS BOND : bond 0.00081 ( 67) SS BOND : angle 0.40940 ( 134) hydrogen bonds : bond 0.22695 ( 1012) hydrogen bonds : angle 7.78824 ( 2931) link_NAG-ASN : bond 0.00162 ( 25) link_NAG-ASN : angle 0.87579 ( 75) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 555 time to evaluate : 1.034 Fit side-chains revert: symmetry clash REVERT: A 213 TYR cc_start: 0.8091 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 250 ASP cc_start: 0.6823 (m-30) cc_final: 0.6591 (m-30) REVERT: B 602 THR cc_start: 0.7791 (OUTLIER) cc_final: 0.7388 (t) REVERT: C 711 PHE cc_start: 0.7064 (m-80) cc_final: 0.6804 (m-80) REVERT: C 1216 PRO cc_start: 0.8420 (Cg_endo) cc_final: 0.8140 (Cg_exo) outliers start: 25 outliers final: 5 residues processed: 575 average time/residue: 0.4679 time to fit residues: 322.7754 Evaluate side-chains 282 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 275 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 1001 GLN Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 521 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 1.9990 chunk 298 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 424 GLN A 621 ASN A 826 HIS A 954 GLN A1135 GLN A1201 ASN A1211 ASN B 143 ASN B 188 ASN B 201 HIS B 621 ASN B 709 GLN B 789 GLN B 854 GLN B 998 ASN B1046 GLN B1059 GLN B1136 ASN B1180 GLN C 440 ASN C 583 ASN C 611 ASN C 642 ASN C1122 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.134829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.107911 restraints weight = 36417.275| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 1.83 r_work: 0.3029 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28546 Z= 0.171 Angle : 0.572 11.541 38992 Z= 0.301 Chirality : 0.046 0.224 4464 Planarity : 0.004 0.060 4979 Dihedral : 4.963 58.827 4347 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.54 % Allowed : 9.84 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.89 (0.14), residues: 3522 helix: 1.26 (0.20), residues: 789 sheet: 0.11 (0.19), residues: 652 loop : -1.66 (0.12), residues: 2081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 398 TYR 0.027 0.002 TYR B 712 PHE 0.025 0.002 PHE C 467 TRP 0.009 0.001 TRP C 174 HIS 0.015 0.002 HIS B 465 Details of bonding type rmsd covalent geometry : bond 0.00399 (28454) covalent geometry : angle 0.56471 (38783) SS BOND : bond 0.00572 ( 67) SS BOND : angle 1.48374 ( 134) hydrogen bonds : bond 0.05100 ( 1012) hydrogen bonds : angle 5.29075 ( 2931) link_NAG-ASN : bond 0.00302 ( 25) link_NAG-ASN : angle 1.16698 ( 75) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 269 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.7165 (m-30) cc_final: 0.6937 (m-30) REVERT: A 408 PHE cc_start: 0.8829 (m-10) cc_final: 0.8524 (m-80) REVERT: B 345 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7839 (mm-30) REVERT: B 464 ASP cc_start: 0.8286 (m-30) cc_final: 0.8019 (m-30) REVERT: B 553 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8279 (mt-10) REVERT: B 936 CYS cc_start: 0.8097 (m) cc_final: 0.7833 (m) REVERT: C 711 PHE cc_start: 0.7440 (m-80) cc_final: 0.7045 (m-80) REVERT: C 1091 GLN cc_start: 0.8476 (tt0) cc_final: 0.8271 (tt0) REVERT: C 1149 LYS cc_start: 0.8715 (tttm) cc_final: 0.8400 (tptp) REVERT: C 1216 PRO cc_start: 0.8494 (Cg_endo) cc_final: 0.8193 (Cg_exo) outliers start: 79 outliers final: 34 residues processed: 329 average time/residue: 0.4053 time to fit residues: 165.2540 Evaluate side-chains 269 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 233 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 374 ASP Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 1014 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 150 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 334 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 283 optimal weight: 1.9990 chunk 282 optimal weight: 7.9990 chunk 26 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 340 optimal weight: 0.8980 chunk 287 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 583 ASN A 863 GLN B 621 ASN B 876 HIS B1045 GLN C 175 HIS C 583 ASN C 652 ASN C 799 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.128761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101608 restraints weight = 36245.202| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.81 r_work: 0.2948 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 28546 Z= 0.180 Angle : 0.571 10.113 38992 Z= 0.299 Chirality : 0.045 0.171 4464 Planarity : 0.004 0.046 4979 Dihedral : 4.923 58.460 4340 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.73 % Allowed : 10.86 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.67 (0.14), residues: 3522 helix: 1.48 (0.20), residues: 779 sheet: 0.31 (0.19), residues: 666 loop : -1.54 (0.12), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.023 0.002 TYR B 712 PHE 0.021 0.002 PHE A 592 TRP 0.012 0.001 TRP A 444 HIS 0.007 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00435 (28454) covalent geometry : angle 0.56189 (38783) SS BOND : bond 0.00331 ( 67) SS BOND : angle 1.51039 ( 134) hydrogen bonds : bond 0.06243 ( 1012) hydrogen bonds : angle 5.16419 ( 2931) link_NAG-ASN : bond 0.00190 ( 25) link_NAG-ASN : angle 1.39664 ( 75) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 245 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7738 (m-40) cc_final: 0.7299 (m110) REVERT: A 408 PHE cc_start: 0.9033 (m-10) cc_final: 0.8825 (m-80) REVERT: A 613 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7536 (mm-30) REVERT: A 831 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7228 (mp0) REVERT: A 903 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8784 (tt) REVERT: B 346 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8584 (ttt180) REVERT: B 776 ASN cc_start: 0.8495 (t0) cc_final: 0.8274 (t0) REVERT: C 711 PHE cc_start: 0.7571 (m-80) cc_final: 0.7176 (m-80) REVERT: C 1126 ASN cc_start: 0.8564 (p0) cc_final: 0.8350 (p0) outliers start: 85 outliers final: 36 residues processed: 310 average time/residue: 0.4210 time to fit residues: 162.1882 Evaluate side-chains 247 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 208 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 346 ARG Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 65 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 228 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 260 optimal weight: 4.9990 chunk 217 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 329 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 HIS A 248 ASN A 642 ASN A1201 ASN B 621 ASN B 876 HIS C 583 ASN C 684 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.101101 restraints weight = 36231.990| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.82 r_work: 0.2892 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28546 Z= 0.151 Angle : 0.542 9.413 38992 Z= 0.284 Chirality : 0.044 0.189 4464 Planarity : 0.004 0.047 4979 Dihedral : 4.790 58.426 4338 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.73 % Allowed : 11.70 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.58 (0.14), residues: 3522 helix: 1.56 (0.20), residues: 784 sheet: 0.30 (0.19), residues: 677 loop : -1.48 (0.13), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 398 TYR 0.020 0.001 TYR B 712 PHE 0.017 0.001 PHE A 592 TRP 0.012 0.001 TRP A 444 HIS 0.020 0.001 HIS B 876 Details of bonding type rmsd covalent geometry : bond 0.00359 (28454) covalent geometry : angle 0.53441 (38783) SS BOND : bond 0.00332 ( 67) SS BOND : angle 1.33923 ( 134) hydrogen bonds : bond 0.05831 ( 1012) hydrogen bonds : angle 5.04695 ( 2931) link_NAG-ASN : bond 0.00189 ( 25) link_NAG-ASN : angle 1.38804 ( 75) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 222 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7655 (m-40) cc_final: 0.7273 (m110) REVERT: A 218 MET cc_start: 0.8880 (mtt) cc_final: 0.8361 (mtt) REVERT: A 408 PHE cc_start: 0.9047 (m-10) cc_final: 0.8829 (m-80) REVERT: A 613 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7499 (mm-30) REVERT: A 831 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: A 903 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8750 (tt) REVERT: B 345 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7842 (mm-30) REVERT: B 1095 ASP cc_start: 0.8605 (m-30) cc_final: 0.8302 (m-30) REVERT: B 1105 ARG cc_start: 0.8439 (tpp80) cc_final: 0.8220 (tpp-160) REVERT: C 711 PHE cc_start: 0.7515 (m-80) cc_final: 0.7134 (m-80) REVERT: C 815 SER cc_start: 0.9275 (OUTLIER) cc_final: 0.8980 (m) outliers start: 85 outliers final: 46 residues processed: 290 average time/residue: 0.4113 time to fit residues: 147.4749 Evaluate side-chains 264 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 214 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 90 optimal weight: 3.9990 chunk 106 optimal weight: 3.9990 chunk 200 optimal weight: 2.9990 chunk 337 optimal weight: 4.9990 chunk 173 optimal weight: 3.9990 chunk 73 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 135 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 143 ASN B 621 ASN B 821 ASN B 838 ASN B 876 HIS B1073 GLN C 323 ASN C 684 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098259 restraints weight = 36467.776| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.79 r_work: 0.2913 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 28546 Z= 0.205 Angle : 0.605 10.664 38992 Z= 0.315 Chirality : 0.046 0.177 4464 Planarity : 0.004 0.052 4979 Dihedral : 5.131 59.734 4338 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.15 % Allowed : 11.64 % Favored : 85.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.69 (0.14), residues: 3522 helix: 1.40 (0.20), residues: 785 sheet: 0.17 (0.19), residues: 689 loop : -1.50 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 737 TYR 0.019 0.002 TYR B 712 PHE 0.022 0.002 PHE A 592 TRP 0.013 0.001 TRP A 444 HIS 0.030 0.002 HIS B 876 Details of bonding type rmsd covalent geometry : bond 0.00505 (28454) covalent geometry : angle 0.59425 (38783) SS BOND : bond 0.00348 ( 67) SS BOND : angle 1.76277 ( 134) hydrogen bonds : bond 0.06669 ( 1012) hydrogen bonds : angle 5.17458 ( 2931) link_NAG-ASN : bond 0.00231 ( 25) link_NAG-ASN : angle 1.53028 ( 75) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 225 time to evaluate : 1.147 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7765 (m-40) cc_final: 0.7358 (m110) REVERT: A 408 PHE cc_start: 0.9088 (m-10) cc_final: 0.8866 (m-80) REVERT: A 516 CYS cc_start: 0.6704 (m) cc_final: 0.6480 (m) REVERT: A 583 ASN cc_start: 0.8137 (m-40) cc_final: 0.7543 (t0) REVERT: A 821 ASN cc_start: 0.8348 (p0) cc_final: 0.8101 (p0) REVERT: A 831 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: A 903 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 345 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7868 (mm-30) REVERT: C 597 ILE cc_start: 0.9074 (OUTLIER) cc_final: 0.8770 (mm) REVERT: C 711 PHE cc_start: 0.7588 (m-80) cc_final: 0.7221 (m-80) REVERT: C 815 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9004 (m) outliers start: 98 outliers final: 51 residues processed: 298 average time/residue: 0.3957 time to fit residues: 148.1061 Evaluate side-chains 268 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 212 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 977 VAL Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain A residue 1211 ASN Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 996 VAL Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1181 ASN Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 743 CYS Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 179 optimal weight: 0.6980 chunk 122 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 152 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 138 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 340 optimal weight: 1.9990 chunk 126 optimal weight: 7.9990 chunk 139 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A1041 ASN B 621 ASN B 821 ASN C 583 ASN C 684 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100432 restraints weight = 36327.802| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.77 r_work: 0.2930 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28546 Z= 0.133 Angle : 0.534 8.719 38992 Z= 0.281 Chirality : 0.044 0.188 4464 Planarity : 0.004 0.050 4979 Dihedral : 4.892 58.987 4338 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.73 % Allowed : 12.38 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.55 (0.14), residues: 3522 helix: 1.53 (0.20), residues: 791 sheet: 0.22 (0.19), residues: 669 loop : -1.41 (0.13), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1105 TYR 0.016 0.001 TYR B 712 PHE 0.016 0.001 PHE A 592 TRP 0.012 0.001 TRP A 444 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00306 (28454) covalent geometry : angle 0.52470 (38783) SS BOND : bond 0.00266 ( 67) SS BOND : angle 1.44727 ( 134) hydrogen bonds : bond 0.05864 ( 1012) hydrogen bonds : angle 5.05175 ( 2931) link_NAG-ASN : bond 0.00136 ( 25) link_NAG-ASN : angle 1.48999 ( 75) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 217 time to evaluate : 0.743 Fit side-chains REVERT: A 132 ASN cc_start: 0.7691 (m-40) cc_final: 0.7305 (m110) REVERT: A 164 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7746 (ttmm) REVERT: A 408 PHE cc_start: 0.9072 (m-10) cc_final: 0.8847 (m-80) REVERT: A 583 ASN cc_start: 0.8120 (m-40) cc_final: 0.7513 (t0) REVERT: A 831 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: A 903 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8760 (tt) REVERT: B 853 THR cc_start: 0.9327 (OUTLIER) cc_final: 0.9094 (m) REVERT: C 711 PHE cc_start: 0.7507 (m-80) cc_final: 0.7173 (m-80) REVERT: C 815 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8997 (m) outliers start: 85 outliers final: 50 residues processed: 281 average time/residue: 0.4122 time to fit residues: 144.8453 Evaluate side-chains 262 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1181 ASN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 326 ASP Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 79 optimal weight: 0.8980 chunk 121 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 326 optimal weight: 6.9990 chunk 184 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 266 optimal weight: 1.9990 chunk 113 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 258 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A1041 ASN A1211 ASN B 621 ASN B 821 ASN C 29 ASN C 353 ASN C 684 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.125598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.098630 restraints weight = 36386.446| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 1.77 r_work: 0.2859 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 28546 Z= 0.162 Angle : 0.558 10.019 38992 Z= 0.291 Chirality : 0.044 0.177 4464 Planarity : 0.004 0.051 4979 Dihedral : 4.923 58.830 4338 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 2.76 % Allowed : 12.63 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.53 (0.14), residues: 3522 helix: 1.58 (0.20), residues: 785 sheet: 0.23 (0.19), residues: 669 loop : -1.39 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1105 TYR 0.016 0.001 TYR B 712 PHE 0.018 0.001 PHE A 592 TRP 0.012 0.001 TRP A 444 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00390 (28454) covalent geometry : angle 0.54831 (38783) SS BOND : bond 0.00293 ( 67) SS BOND : angle 1.50882 ( 134) hydrogen bonds : bond 0.06112 ( 1012) hydrogen bonds : angle 5.05221 ( 2931) link_NAG-ASN : bond 0.00185 ( 25) link_NAG-ASN : angle 1.52359 ( 75) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 210 time to evaluate : 0.828 Fit side-chains REVERT: A 132 ASN cc_start: 0.7604 (m-40) cc_final: 0.7245 (m110) REVERT: A 164 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7701 (ttmm) REVERT: A 516 CYS cc_start: 0.6632 (m) cc_final: 0.6397 (m) REVERT: A 583 ASN cc_start: 0.8147 (m-40) cc_final: 0.7490 (t0) REVERT: A 831 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: A 903 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8702 (tt) REVERT: B 1019 PHE cc_start: 0.7700 (OUTLIER) cc_final: 0.7472 (m-10) REVERT: C 597 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8693 (mm) REVERT: C 711 PHE cc_start: 0.7489 (m-80) cc_final: 0.7110 (m-80) REVERT: C 815 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.9007 (m) outliers start: 86 outliers final: 52 residues processed: 276 average time/residue: 0.4028 time to fit residues: 139.2207 Evaluate side-chains 266 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 209 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1181 ASN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 107 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 298 optimal weight: 0.9990 chunk 321 optimal weight: 4.9990 chunk 284 optimal weight: 6.9990 chunk 309 optimal weight: 6.9990 chunk 100 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 282 optimal weight: 7.9990 chunk 245 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A1211 ASN B 621 ASN B 821 ASN C 684 ASN C 799 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.125419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.098378 restraints weight = 36480.682| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 1.78 r_work: 0.2843 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 28546 Z= 0.173 Angle : 0.568 8.360 38992 Z= 0.296 Chirality : 0.045 0.197 4464 Planarity : 0.004 0.052 4979 Dihedral : 4.969 58.857 4338 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.89 % Allowed : 12.66 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.57 (0.14), residues: 3522 helix: 1.49 (0.20), residues: 791 sheet: 0.23 (0.19), residues: 668 loop : -1.41 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C1105 TYR 0.015 0.002 TYR C 203 PHE 0.018 0.001 PHE A 592 TRP 0.013 0.001 TRP A 444 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00422 (28454) covalent geometry : angle 0.55786 (38783) SS BOND : bond 0.00319 ( 67) SS BOND : angle 1.57548 ( 134) hydrogen bonds : bond 0.06264 ( 1012) hydrogen bonds : angle 5.08555 ( 2931) link_NAG-ASN : bond 0.00173 ( 25) link_NAG-ASN : angle 1.55408 ( 75) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 216 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7607 (m-40) cc_final: 0.7250 (m110) REVERT: A 164 LYS cc_start: 0.8128 (ttmm) cc_final: 0.7745 (ttmm) REVERT: A 408 PHE cc_start: 0.8981 (m-80) cc_final: 0.8748 (m-80) REVERT: A 583 ASN cc_start: 0.8153 (m-40) cc_final: 0.7496 (t0) REVERT: A 831 GLU cc_start: 0.8042 (OUTLIER) cc_final: 0.7549 (mp0) REVERT: A 903 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8699 (tt) REVERT: B 553 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: B 853 THR cc_start: 0.9416 (OUTLIER) cc_final: 0.9180 (m) REVERT: B 880 ASP cc_start: 0.8190 (t0) cc_final: 0.7911 (t0) REVERT: B 1019 PHE cc_start: 0.7706 (OUTLIER) cc_final: 0.7484 (m-10) REVERT: C 597 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8675 (mm) REVERT: C 711 PHE cc_start: 0.7569 (m-80) cc_final: 0.7199 (m-80) REVERT: C 815 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.9010 (m) REVERT: C 1149 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8346 (ttmm) outliers start: 90 outliers final: 58 residues processed: 284 average time/residue: 0.4005 time to fit residues: 142.5112 Evaluate side-chains 269 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 203 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 112 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 806 SER Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 903 LEU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 981 LEU Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 529 SER Chi-restraints excluded: chain B residue 553 GLU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 821 ASN Chi-restraints excluded: chain B residue 853 THR Chi-restraints excluded: chain B residue 869 SER Chi-restraints excluded: chain B residue 876 HIS Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1056 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1156 VAL Chi-restraints excluded: chain B residue 1181 ASN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 597 ILE Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 815 SER Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1149 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 191 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 337 optimal weight: 1.9990 chunk 348 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 314 optimal weight: 0.0670 chunk 100 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 chunk 273 optimal weight: 0.7980 chunk 272 optimal weight: 1.9990 chunk 284 optimal weight: 0.7980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A1041 ASN A1211 ASN B 621 ASN C 465 HIS C 583 ASN C 684 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.128406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.101518 restraints weight = 36288.771| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.78 r_work: 0.2936 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 28546 Z= 0.102 Angle : 0.507 8.495 38992 Z= 0.267 Chirality : 0.043 0.162 4464 Planarity : 0.004 0.049 4979 Dihedral : 4.658 57.380 4338 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.83 % Allowed : 13.89 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.31 (0.14), residues: 3522 helix: 1.82 (0.20), residues: 782 sheet: 0.36 (0.20), residues: 660 loop : -1.27 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1105 TYR 0.016 0.001 TYR B 203 PHE 0.013 0.001 PHE A 121 TRP 0.012 0.001 TRP A 444 HIS 0.005 0.001 HIS C 465 Details of bonding type rmsd covalent geometry : bond 0.00218 (28454) covalent geometry : angle 0.49908 (38783) SS BOND : bond 0.00227 ( 67) SS BOND : angle 1.25212 ( 134) hydrogen bonds : bond 0.05214 ( 1012) hydrogen bonds : angle 4.89954 ( 2931) link_NAG-ASN : bond 0.00144 ( 25) link_NAG-ASN : angle 1.46685 ( 75) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 211 time to evaluate : 0.737 Fit side-chains REVERT: A 132 ASN cc_start: 0.7686 (m-40) cc_final: 0.7285 (m110) REVERT: A 164 LYS cc_start: 0.8041 (ttmm) cc_final: 0.7657 (ttmm) REVERT: A 408 PHE cc_start: 0.9005 (m-80) cc_final: 0.8788 (m-80) REVERT: A 583 ASN cc_start: 0.8067 (m-40) cc_final: 0.7495 (t0) REVERT: A 831 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7520 (mp0) REVERT: B 1019 PHE cc_start: 0.7659 (OUTLIER) cc_final: 0.7206 (m-10) REVERT: C 711 PHE cc_start: 0.7572 (m-80) cc_final: 0.7238 (m-80) REVERT: C 815 SER cc_start: 0.9275 (t) cc_final: 0.9004 (m) outliers start: 57 outliers final: 36 residues processed: 258 average time/residue: 0.3932 time to fit residues: 127.4728 Evaluate side-chains 243 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 831 GLU Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1181 ASN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Chi-restraints excluded: chain C residue 1014 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 191 optimal weight: 6.9990 chunk 288 optimal weight: 0.4980 chunk 318 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 315 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 245 optimal weight: 0.0870 chunk 250 optimal weight: 0.9980 chunk 286 optimal weight: 0.9990 chunk 293 optimal weight: 6.9990 overall best weight: 0.6760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A 248 ASN A1211 ASN B 621 ASN B1136 ASN C 684 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.129221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102184 restraints weight = 36226.991| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.79 r_work: 0.2975 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28546 Z= 0.101 Angle : 0.496 8.422 38992 Z= 0.260 Chirality : 0.042 0.160 4464 Planarity : 0.004 0.049 4979 Dihedral : 4.434 55.919 4338 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.38 % Allowed : 14.50 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.19 (0.14), residues: 3522 helix: 1.85 (0.20), residues: 787 sheet: 0.44 (0.19), residues: 691 loop : -1.19 (0.13), residues: 2044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C1105 TYR 0.015 0.001 TYR B 203 PHE 0.012 0.001 PHE C 577 TRP 0.011 0.001 TRP C 174 HIS 0.004 0.001 HIS A 201 Details of bonding type rmsd covalent geometry : bond 0.00222 (28454) covalent geometry : angle 0.48961 (38783) SS BOND : bond 0.00216 ( 67) SS BOND : angle 1.10077 ( 134) hydrogen bonds : bond 0.04902 ( 1012) hydrogen bonds : angle 4.78075 ( 2931) link_NAG-ASN : bond 0.00125 ( 25) link_NAG-ASN : angle 1.41196 ( 75) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7044 Ramachandran restraints generated. 3522 Oldfield, 0 Emsley, 3522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7727 (m-40) cc_final: 0.7308 (m110) REVERT: A 164 LYS cc_start: 0.8077 (ttmm) cc_final: 0.7702 (ttmm) REVERT: A 408 PHE cc_start: 0.9003 (m-80) cc_final: 0.8549 (m-80) REVERT: B 880 ASP cc_start: 0.8081 (t70) cc_final: 0.7674 (t0) REVERT: B 1019 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7124 (m-10) REVERT: C 711 PHE cc_start: 0.7606 (m-80) cc_final: 0.7286 (m-80) REVERT: C 815 SER cc_start: 0.9315 (t) cc_final: 0.9025 (m) outliers start: 43 outliers final: 35 residues processed: 247 average time/residue: 0.3936 time to fit residues: 121.7334 Evaluate side-chains 235 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 199 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 916 VAL Chi-restraints excluded: chain A residue 1104 SER Chi-restraints excluded: chain A residue 1156 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 807 SER Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 926 THR Chi-restraints excluded: chain B residue 1019 PHE Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1181 ASN Chi-restraints excluded: chain B residue 1202 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 890 CYS Chi-restraints excluded: chain C residue 959 THR Chi-restraints excluded: chain C residue 1014 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 36 optimal weight: 3.9990 chunk 187 optimal weight: 6.9990 chunk 254 optimal weight: 2.9990 chunk 251 optimal weight: 0.4980 chunk 346 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 195 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 282 optimal weight: 0.0020 overall best weight: 1.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A1211 ASN B 621 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.126880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.100283 restraints weight = 36160.379| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.74 r_work: 0.2949 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28546 Z= 0.142 Angle : 0.540 9.032 38992 Z= 0.282 Chirality : 0.044 0.170 4464 Planarity : 0.004 0.050 4979 Dihedral : 4.675 56.648 4338 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.58 % Allowed : 14.37 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % 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 aren not related in a simple way. whole: -0.27 (0.14), residues: 3522 helix: 1.81 (0.20), residues: 781 sheet: 0.39 (0.19), residues: 684 loop : -1.24 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C1105 TYR 0.015 0.001 TYR B 203 PHE 0.016 0.001 PHE A 592 TRP 0.010 0.001 TRP A 444 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00339 (28454) covalent geometry : angle 0.53183 (38783) SS BOND : bond 0.00264 ( 67) SS BOND : angle 1.36916 ( 134) hydrogen bonds : bond 0.05677 ( 1012) hydrogen bonds : angle 4.90899 ( 2931) link_NAG-ASN : bond 0.00154 ( 25) link_NAG-ASN : angle 1.46396 ( 75) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7599.01 seconds wall clock time: 130 minutes 4.75 seconds (7804.75 seconds total)