Starting phenix.real_space_refine on Mon May 26 04:52:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8c_39041/05_2025/8y8c_39041.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8c_39041/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8c_39041/05_2025/8y8c_39041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8c_39041/05_2025/8y8c_39041.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8c_39041/05_2025/8y8c_39041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8c_39041/05_2025/8y8c_39041.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 1.38s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 2, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 3} 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: {'PHE:plan': 2, 'GLU:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'ARG:plan': 2} 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, '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: 17.02, per 1000 atoms: 0.61 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: 6.43 Conformation dependent library (CDL) restraints added in 3.7 seconds 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: 4.44 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: 13.96 Time building geometry restraints manager: 7.63 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 1221 or resid 1301 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 1221 or resid 1301 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 1221 or resid 1301 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.180 Check model and map are aligned: 0.200 Set scattering table: 0.260 Process input model: 65.970 Find NCS groups from input model: 1.780 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.090 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.005 0.001 TRP B 444 HIS 0.002 0.000 HIS B 826 PHE 0.006 0.001 PHE C 202 TYR 0.006 0.001 TYR C 832 ARG 0.002 0.000 ARG A 502 Details of bonding type rmsd link_NAG-ASN : bond 0.00162 ( 25) link_NAG-ASN : angle 0.87579 ( 75) hydrogen bonds : bond 0.22695 ( 1012) hydrogen bonds : angle 7.78824 ( 2931) SS BOND : bond 0.00081 ( 67) SS BOND : angle 0.40940 ( 134) covalent geometry : bond 0.00198 (28454) covalent geometry : angle 0.39984 (38783) *********************** 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 : 2.904 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: 1.1060 time to fit residues: 767.0865 Evaluate side-chains 281 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 274 time to evaluate : 3.037 ------------------------------------------------------------------------------- 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 298 optimal weight: 2.9990 chunk 267 optimal weight: 4.9990 chunk 148 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 180 optimal weight: 0.4980 chunk 142 optimal weight: 8.9990 chunk 276 optimal weight: 9.9990 chunk 107 optimal weight: 0.9980 chunk 168 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 320 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 954 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 C1122 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.136055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.109397 restraints weight = 36381.604| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 1.83 r_work: 0.3090 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 28546 Z= 0.149 Angle : 0.555 12.259 38992 Z= 0.292 Chirality : 0.045 0.202 4464 Planarity : 0.004 0.063 4979 Dihedral : 4.850 57.744 4347 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.44 % Allowed : 9.96 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3522 helix: 1.30 (0.20), residues: 789 sheet: 0.19 (0.19), residues: 669 loop : -1.67 (0.12), residues: 2064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.015 0.002 HIS B 465 PHE 0.020 0.002 PHE B 767 TYR 0.025 0.002 TYR B 712 ARG 0.009 0.001 ARG C 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 25) link_NAG-ASN : angle 1.26439 ( 75) hydrogen bonds : bond 0.04987 ( 1012) hydrogen bonds : angle 5.30324 ( 2931) SS BOND : bond 0.00386 ( 67) SS BOND : angle 1.23016 ( 134) covalent geometry : bond 0.00345 (28454) covalent geometry : angle 0.54872 (38783) *********************** 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: 76 poor density : 272 time to evaluate : 3.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.7118 (m-30) cc_final: 0.6911 (m-30) REVERT: A 408 PHE cc_start: 0.8794 (m-10) cc_final: 0.8484 (m-80) REVERT: A 981 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8432 (mp) REVERT: B 553 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8230 (mt-10) REVERT: B 936 CYS cc_start: 0.8063 (m) cc_final: 0.7802 (m) REVERT: C 213 TYR cc_start: 0.8660 (t80) cc_final: 0.8421 (t80) REVERT: C 711 PHE cc_start: 0.7429 (m-80) cc_final: 0.7030 (m-80) REVERT: C 780 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7325 (mp0) REVERT: C 1091 GLN cc_start: 0.8419 (tt0) cc_final: 0.8132 (mt0) REVERT: C 1149 LYS cc_start: 0.8687 (tttm) cc_final: 0.8405 (tptp) REVERT: C 1216 PRO cc_start: 0.8478 (Cg_endo) cc_final: 0.8174 (Cg_exo) outliers start: 76 outliers final: 32 residues processed: 329 average time/residue: 0.9332 time to fit residues: 388.0206 Evaluate side-chains 265 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 230 time to evaluate : 3.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 435 THR 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 981 LEU Chi-restraints excluded: chain A residue 1104 SER 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 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 1131 LEU Chi-restraints excluded: chain B residue 1174 GLN 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 177 ASP Chi-restraints excluded: chain C residue 740 SER Chi-restraints excluded: chain C residue 780 GLU 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 311 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 47 optimal weight: 0.0980 chunk 190 optimal weight: 3.9990 chunk 68 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 312 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN A 410 GLN A 583 ASN A 826 HIS A 863 GLN A1135 GLN B 621 ASN B 630 GLN B1045 GLN B1086 ASN C 583 ASN C 652 ASN C 799 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.136253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.109989 restraints weight = 36313.433| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.77 r_work: 0.3097 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 28546 Z= 0.098 Angle : 0.477 9.208 38992 Z= 0.251 Chirality : 0.042 0.255 4464 Planarity : 0.004 0.046 4979 Dihedral : 4.373 58.569 4340 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.15 % Allowed : 11.28 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3522 helix: 1.69 (0.20), residues: 792 sheet: 0.38 (0.19), residues: 656 loop : -1.46 (0.13), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 444 HIS 0.007 0.001 HIS B 201 PHE 0.014 0.001 PHE A 121 TYR 0.022 0.001 TYR B 712 ARG 0.006 0.000 ARG C 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00158 ( 25) link_NAG-ASN : angle 1.11131 ( 75) hydrogen bonds : bond 0.04545 ( 1012) hydrogen bonds : angle 4.93350 ( 2931) SS BOND : bond 0.00226 ( 67) SS BOND : angle 1.19981 ( 134) covalent geometry : bond 0.00215 (28454) covalent geometry : angle 0.47007 (38783) *********************** 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 318 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 251 time to evaluate : 3.120 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 250 ASP cc_start: 0.7050 (m-30) cc_final: 0.6790 (m-30) REVERT: A 408 PHE cc_start: 0.8823 (m-10) cc_final: 0.8473 (m-80) REVERT: A 613 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 831 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: B 848 ASP cc_start: 0.8445 (m-30) cc_final: 0.8236 (m-30) REVERT: B 853 THR cc_start: 0.9252 (OUTLIER) cc_final: 0.9024 (m) REVERT: B 936 CYS cc_start: 0.7997 (m) cc_final: 0.7725 (m) REVERT: C 711 PHE cc_start: 0.7381 (m-80) cc_final: 0.6971 (m-80) outliers start: 67 outliers final: 27 residues processed: 306 average time/residue: 0.9240 time to fit residues: 357.0380 Evaluate side-chains 259 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 2.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 213 TYR 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 831 GLU Chi-restraints excluded: chain A residue 967 MET 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 359 LEU Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 602 THR 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 1202 VAL Chi-restraints excluded: chain B residue 1220 LEU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 573 LEU Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 781 THR 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 281 optimal weight: 8.9990 chunk 302 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 346 optimal weight: 3.9990 chunk 266 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 169 optimal weight: 0.5980 chunk 88 optimal weight: 0.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 A 642 ASN A 863 GLN B 621 ASN ** B1086 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.126118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.098953 restraints weight = 36742.487| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.85 r_work: 0.2919 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 28546 Z= 0.227 Angle : 0.659 20.501 38992 Z= 0.342 Chirality : 0.048 0.189 4464 Planarity : 0.005 0.055 4979 Dihedral : 5.202 59.802 4340 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.54 % Favored : 95.43 % Rotamer: Outliers : 2.80 % Allowed : 11.28 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.14), residues: 3522 helix: 1.26 (0.20), residues: 796 sheet: 0.12 (0.19), residues: 667 loop : -1.50 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 444 HIS 0.008 0.002 HIS B 201 PHE 0.025 0.002 PHE A 592 TYR 0.022 0.002 TYR B 712 ARG 0.005 0.001 ARG C 398 Details of bonding type rmsd link_NAG-ASN : bond 0.00283 ( 25) link_NAG-ASN : angle 1.58380 ( 75) hydrogen bonds : bond 0.07032 ( 1012) hydrogen bonds : angle 5.26673 ( 2931) SS BOND : bond 0.00543 ( 67) SS BOND : angle 1.87774 ( 134) covalent geometry : bond 0.00559 (28454) covalent geometry : angle 0.64736 (38783) *********************** 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 326 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 239 time to evaluate : 3.073 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7767 (m-40) cc_final: 0.7362 (m110) REVERT: A 218 MET cc_start: 0.8897 (mtt) cc_final: 0.8387 (mtt) REVERT: A 408 PHE cc_start: 0.9110 (m-10) cc_final: 0.8894 (m-80) REVERT: A 516 CYS cc_start: 0.6800 (m) cc_final: 0.6595 (m) REVERT: A 583 ASN cc_start: 0.8078 (m-40) cc_final: 0.7468 (t0) REVERT: A 831 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: A 903 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8764 (tt) REVERT: B 776 ASN cc_start: 0.8572 (t0) cc_final: 0.8361 (t0) REVERT: B 1105 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8296 (tpp-160) REVERT: C 597 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8773 (mm) REVERT: C 711 PHE cc_start: 0.7606 (m-80) cc_final: 0.7242 (m-80) outliers start: 87 outliers final: 42 residues processed: 308 average time/residue: 0.9688 time to fit residues: 370.8149 Evaluate side-chains 259 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 3.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 180 GLU 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 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 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 B residue 88 LEU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 124 ILE 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 674 SER 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 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 163 CYS Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 597 ILE 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 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 171 optimal weight: 0.8980 chunk 302 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 271 optimal weight: 7.9990 chunk 50 optimal weight: 0.2980 chunk 236 optimal weight: 10.0000 chunk 294 optimal weight: 0.4980 chunk 274 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 273 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 A1211 ASN B 621 ASN B 838 ASN B1086 ASN B1181 ASN C 583 ASN C 684 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 = 0.3489 r_free = 0.3489 target = 0.129047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.102387 restraints weight = 36015.622| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.76 r_work: 0.2979 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28546 Z= 0.112 Angle : 0.515 10.229 38992 Z= 0.271 Chirality : 0.043 0.156 4464 Planarity : 0.004 0.045 4979 Dihedral : 4.715 58.822 4338 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.48 % Allowed : 12.12 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.14), residues: 3522 helix: 1.64 (0.20), residues: 784 sheet: 0.24 (0.19), residues: 654 loop : -1.35 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 174 HIS 0.006 0.001 HIS B 201 PHE 0.015 0.001 PHE A 121 TYR 0.017 0.001 TYR B 712 ARG 0.004 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00123 ( 25) link_NAG-ASN : angle 1.36761 ( 75) hydrogen bonds : bond 0.05491 ( 1012) hydrogen bonds : angle 4.97776 ( 2931) SS BOND : bond 0.00372 ( 67) SS BOND : angle 1.37939 ( 134) covalent geometry : bond 0.00246 (28454) covalent geometry : angle 0.50604 (38783) *********************** 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 305 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 228 time to evaluate : 2.912 Fit side-chains REVERT: A 132 ASN cc_start: 0.7633 (m-40) cc_final: 0.7266 (m110) REVERT: A 408 PHE cc_start: 0.8986 (m-10) cc_final: 0.8785 (m-80) REVERT: A 726 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 831 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 903 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8687 (tt) REVERT: B 821 ASN cc_start: 0.8043 (p0) cc_final: 0.7742 (p0) REVERT: C 305 ASP cc_start: 0.8551 (OUTLIER) cc_final: 0.8338 (m-30) REVERT: C 711 PHE cc_start: 0.7443 (m-80) cc_final: 0.7050 (m-80) REVERT: C 815 SER cc_start: 0.9273 (OUTLIER) cc_final: 0.8999 (m) outliers start: 77 outliers final: 35 residues processed: 285 average time/residue: 0.9462 time to fit residues: 339.7063 Evaluate side-chains 252 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 3.003 ------------------------------------------------------------------------------- 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 112 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 726 LEU 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 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 359 LEU Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 602 THR Chi-restraints excluded: chain B residue 674 SER 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 1096 ILE 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 177 ASP Chi-restraints excluded: chain C residue 305 ASP Chi-restraints excluded: chain C residue 521 LEU Chi-restraints excluded: chain C residue 587 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 299 optimal weight: 2.9990 chunk 274 optimal weight: 7.9990 chunk 210 optimal weight: 4.9990 chunk 188 optimal weight: 5.9990 chunk 334 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 C 323 ASN C 684 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.123609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096499 restraints weight = 36577.649| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 1.81 r_work: 0.2810 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 28546 Z= 0.264 Angle : 0.678 11.062 38992 Z= 0.352 Chirality : 0.048 0.193 4464 Planarity : 0.005 0.060 4979 Dihedral : 5.382 59.359 4338 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.21 % Allowed : 12.05 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3522 helix: 1.22 (0.19), residues: 789 sheet: 0.03 (0.19), residues: 680 loop : -1.53 (0.12), residues: 2053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 444 HIS 0.008 0.002 HIS B 201 PHE 0.026 0.002 PHE A 592 TYR 0.019 0.002 TYR B 266 ARG 0.004 0.001 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00529 ( 25) link_NAG-ASN : angle 1.70102 ( 75) hydrogen bonds : bond 0.07429 ( 1012) hydrogen bonds : angle 5.30275 ( 2931) SS BOND : bond 0.00469 ( 67) SS BOND : angle 2.11152 ( 134) covalent geometry : bond 0.00657 (28454) covalent geometry : angle 0.66450 (38783) *********************** 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 325 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 225 time to evaluate : 2.987 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7640 (m-40) cc_final: 0.7293 (m110) REVERT: A 218 MET cc_start: 0.8986 (mtt) cc_final: 0.8572 (mtt) REVERT: A 583 ASN cc_start: 0.8139 (m-40) cc_final: 0.7545 (t0) REVERT: A 726 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8524 (mp) REVERT: A 831 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: A 903 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8701 (tt) REVERT: B 912 LYS cc_start: 0.8755 (tmmt) cc_final: 0.8532 (ttpp) REVERT: C 597 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8724 (mm) REVERT: C 711 PHE cc_start: 0.7537 (m-80) cc_final: 0.7144 (m-80) REVERT: C 815 SER cc_start: 0.9265 (t) cc_final: 0.9018 (m) outliers start: 100 outliers final: 55 residues processed: 303 average time/residue: 0.8728 time to fit residues: 333.2277 Evaluate side-chains 272 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 2.965 ------------------------------------------------------------------------------- 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 180 GLU Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 406 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 732 SER 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 981 LEU Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR 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 674 SER 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 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 129 VAL Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 580 CYS Chi-restraints excluded: chain C residue 587 ASN 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 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 805 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 59 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 349 optimal weight: 1.9990 chunk 323 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 172 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 B1181 ASN C 29 ASN 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 = 0.3470 r_free = 0.3470 target = 0.127780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.100810 restraints weight = 36341.830| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.78 r_work: 0.2890 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.3457 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= 0.114 Angle : 0.528 8.333 38992 Z= 0.279 Chirality : 0.043 0.171 4464 Planarity : 0.004 0.049 4979 Dihedral : 4.848 59.445 4338 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.12 % Allowed : 13.15 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.14), residues: 3522 helix: 1.67 (0.20), residues: 778 sheet: 0.19 (0.19), residues: 665 loop : -1.36 (0.13), residues: 2079 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 444 HIS 0.006 0.001 HIS B 201 PHE 0.017 0.001 PHE A 121 TYR 0.016 0.001 TYR B 203 ARG 0.004 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00144 ( 25) link_NAG-ASN : angle 1.50904 ( 75) hydrogen bonds : bond 0.05590 ( 1012) hydrogen bonds : angle 5.00328 ( 2931) SS BOND : bond 0.00300 ( 67) SS BOND : angle 1.53656 ( 134) covalent geometry : bond 0.00251 (28454) covalent geometry : angle 0.51723 (38783) *********************** 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 281 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 215 time to evaluate : 3.034 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7577 (m-40) cc_final: 0.7232 (m110) REVERT: A 164 LYS cc_start: 0.8079 (ttmm) cc_final: 0.7749 (ttmm) REVERT: A 583 ASN cc_start: 0.8101 (m-40) cc_final: 0.7475 (t0) REVERT: B 821 ASN cc_start: 0.8371 (p0) cc_final: 0.8163 (p0) REVERT: C 711 PHE cc_start: 0.7464 (m-80) cc_final: 0.7090 (m-80) REVERT: C 815 SER cc_start: 0.9274 (OUTLIER) cc_final: 0.9010 (m) outliers start: 66 outliers final: 39 residues processed: 267 average time/residue: 0.9382 time to fit residues: 317.9879 Evaluate side-chains 242 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 3.310 ------------------------------------------------------------------------------- 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 213 TYR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 516 CYS Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 745 ASP Chi-restraints excluded: chain A residue 1015 ILE 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 119 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR 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 674 SER 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 1056 SER Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1156 VAL 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 177 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 465 HIS 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 Chi-restraints excluded: chain C residue 1014 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 138 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 156 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 73 ASN B 621 ASN C 684 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.096202 restraints weight = 36548.757| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.78 r_work: 0.2805 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.3752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 28546 Z= 0.257 Angle : 0.663 9.642 38992 Z= 0.344 Chirality : 0.048 0.188 4464 Planarity : 0.005 0.055 4979 Dihedral : 5.391 59.728 4338 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.93 % Allowed : 12.89 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.14), residues: 3522 helix: 1.33 (0.19), residues: 782 sheet: 0.03 (0.20), residues: 647 loop : -1.48 (0.12), residues: 2093 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 444 HIS 0.008 0.002 HIS C 142 PHE 0.025 0.002 PHE A 592 TYR 0.017 0.002 TYR A 266 ARG 0.004 0.001 ARG A 737 Details of bonding type rmsd link_NAG-ASN : bond 0.00303 ( 25) link_NAG-ASN : angle 1.71353 ( 75) hydrogen bonds : bond 0.07292 ( 1012) hydrogen bonds : angle 5.25967 ( 2931) SS BOND : bond 0.00431 ( 67) SS BOND : angle 2.04143 ( 134) covalent geometry : bond 0.00638 (28454) covalent geometry : angle 0.64993 (38783) *********************** 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: 91 poor density : 215 time to evaluate : 3.331 Fit side-chains revert: symmetry clash REVERT: A 132 ASN cc_start: 0.7631 (m-40) cc_final: 0.7305 (m110) REVERT: A 218 MET cc_start: 0.9012 (mtt) cc_final: 0.8594 (mtt) REVERT: A 583 ASN cc_start: 0.8134 (m-40) cc_final: 0.7554 (t0) REVERT: C 711 PHE cc_start: 0.7564 (m-80) cc_final: 0.7191 (m-80) REVERT: C 815 SER cc_start: 0.9265 (t) cc_final: 0.9024 (m) REVERT: C 1149 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8359 (ttmm) outliers start: 91 outliers final: 46 residues processed: 286 average time/residue: 0.9156 time to fit residues: 331.7895 Evaluate side-chains 251 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 204 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 272 GLU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 387 THR Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain A residue 732 SER 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 1156 VAL Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 213 TYR 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 674 SER 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 996 VAL 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 177 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 805 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 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 344 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 208 optimal weight: 1.9990 chunk 172 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 322 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 167 optimal weight: 1.9990 chunk 195 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 353 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 = 0.3460 r_free = 0.3460 target = 0.127066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.100099 restraints weight = 36303.834| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.80 r_work: 0.2905 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3599 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= 0.115 Angle : 0.533 9.464 38992 Z= 0.280 Chirality : 0.043 0.182 4464 Planarity : 0.004 0.049 4979 Dihedral : 4.927 58.899 4338 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.77 % Allowed : 14.11 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3522 helix: 1.71 (0.20), residues: 773 sheet: 0.21 (0.19), residues: 662 loop : -1.34 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 444 HIS 0.006 0.001 HIS B 201 PHE 0.016 0.001 PHE A 121 TYR 0.016 0.001 TYR B 203 ARG 0.005 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00132 ( 25) link_NAG-ASN : angle 1.54741 ( 75) hydrogen bonds : bond 0.05646 ( 1012) hydrogen bonds : angle 5.01083 ( 2931) SS BOND : bond 0.00304 ( 67) SS BOND : angle 1.56368 ( 134) covalent geometry : bond 0.00257 (28454) covalent geometry : angle 0.52179 (38783) *********************** 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 264 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 209 time to evaluate : 3.089 Fit side-chains REVERT: A 132 ASN cc_start: 0.7640 (m-40) cc_final: 0.7269 (m110) REVERT: A 164 LYS cc_start: 0.8069 (ttmm) cc_final: 0.7755 (ttmm) REVERT: A 583 ASN cc_start: 0.8107 (m-40) cc_final: 0.7528 (t0) REVERT: A 903 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8743 (tt) REVERT: C 711 PHE cc_start: 0.7559 (m-80) cc_final: 0.7210 (m-80) REVERT: C 815 SER cc_start: 0.9276 (t) cc_final: 0.9020 (m) outliers start: 55 outliers final: 41 residues processed: 249 average time/residue: 0.9260 time to fit residues: 290.9944 Evaluate side-chains 242 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 3.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 387 THR 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 903 LEU Chi-restraints excluded: chain A residue 1173 LYS Chi-restraints excluded: chain A residue 1202 VAL Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR 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 674 SER 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 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 87 THR Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 805 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 325 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 83 optimal weight: 7.9990 chunk 216 optimal weight: 2.9990 chunk 208 optimal weight: 0.3980 chunk 130 optimal weight: 4.9990 chunk 203 optimal weight: 0.6980 chunk 129 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 73 ASN B 621 ASN C 684 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.100154 restraints weight = 36343.759| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.76 r_work: 0.2891 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28546 Z= 0.127 Angle : 0.536 10.491 38992 Z= 0.281 Chirality : 0.043 0.165 4464 Planarity : 0.004 0.050 4979 Dihedral : 4.801 58.114 4338 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.83 % Allowed : 14.11 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.14), residues: 3522 helix: 1.78 (0.20), residues: 773 sheet: 0.30 (0.20), residues: 654 loop : -1.30 (0.13), residues: 2095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.001 HIS B 201 PHE 0.014 0.001 PHE A 592 TYR 0.015 0.001 TYR B 203 ARG 0.004 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00128 ( 25) link_NAG-ASN : angle 1.52919 ( 75) hydrogen bonds : bond 0.05600 ( 1012) hydrogen bonds : angle 4.94182 ( 2931) SS BOND : bond 0.00341 ( 67) SS BOND : angle 1.71314 ( 134) covalent geometry : bond 0.00295 (28454) covalent geometry : angle 0.52332 (38783) ********************** 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 261 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 204 time to evaluate : 2.962 Fit side-chains REVERT: A 132 ASN cc_start: 0.7626 (m-40) cc_final: 0.7247 (m110) REVERT: A 164 LYS cc_start: 0.8059 (ttmm) cc_final: 0.7751 (ttmm) REVERT: A 583 ASN cc_start: 0.8081 (m-40) cc_final: 0.7500 (t0) REVERT: A 903 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8779 (tt) REVERT: B 400 ASP cc_start: 0.8763 (m-30) cc_final: 0.8558 (m-30) REVERT: B 880 ASP cc_start: 0.8181 (t70) cc_final: 0.7736 (t0) REVERT: C 711 PHE cc_start: 0.7585 (m-80) cc_final: 0.7232 (m-80) REVERT: C 815 SER cc_start: 0.9279 (t) cc_final: 0.9005 (m) outliers start: 57 outliers final: 48 residues processed: 253 average time/residue: 0.8828 time to fit residues: 283.6309 Evaluate side-chains 252 residues out of total 3177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 203 time to evaluate : 3.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL 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 387 THR 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 903 LEU 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 119 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 374 ASP 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 674 SER 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 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 177 ASP Chi-restraints excluded: chain C residue 221 THR Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 465 HIS Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 580 CYS Chi-restraints excluded: chain C residue 587 ASN Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 772 VAL Chi-restraints excluded: chain C residue 788 ILE Chi-restraints excluded: chain C residue 799 HIS Chi-restraints excluded: chain C residue 805 THR 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 220 optimal weight: 0.7980 chunk 157 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 162 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 245 optimal weight: 1.9990 chunk 347 optimal weight: 0.5980 chunk 297 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 248 ASN B 621 ASN B 821 ASN B1136 ASN C 684 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.099884 restraints weight = 36404.654| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.78 r_work: 0.2908 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 28546 Z= 0.132 Angle : 0.542 10.414 38992 Z= 0.284 Chirality : 0.044 0.166 4464 Planarity : 0.004 0.049 4979 Dihedral : 4.817 57.967 4338 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.96 % Allowed : 13.85 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.14), residues: 3522 helix: 1.81 (0.20), residues: 773 sheet: 0.32 (0.19), residues: 665 loop : -1.28 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 174 HIS 0.006 0.001 HIS B 201 PHE 0.016 0.001 PHE C 577 TYR 0.015 0.001 TYR B 203 ARG 0.004 0.000 ARG C1105 Details of bonding type rmsd link_NAG-ASN : bond 0.00135 ( 25) link_NAG-ASN : angle 1.52320 ( 75) hydrogen bonds : bond 0.05624 ( 1012) hydrogen bonds : angle 4.93965 ( 2931) SS BOND : bond 0.00337 ( 67) SS BOND : angle 1.77732 ( 134) covalent geometry : bond 0.00311 (28454) covalent geometry : angle 0.52933 (38783) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17041.67 seconds wall clock time: 294 minutes 44.90 seconds (17684.90 seconds total)