Starting phenix.real_space_refine on Mon May 26 09:29:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8f_39044/05_2025/8y8f_39044.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8f_39044/05_2025/8y8f_39044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8f_39044/05_2025/8y8f_39044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8f_39044/05_2025/8y8f_39044.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8f_39044/05_2025/8y8f_39044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8f_39044/05_2025/8y8f_39044.cif" } resolution = 3.07 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= 0.002 sd= 0.034 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 166 5.16 5 C 17844 2.51 5 N 4532 2.21 5 O 5485 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 1.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 28027 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1196, 9202 Classifications: {'peptide': 1196} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1139} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 148 Unresolved non-hydrogen angles: 184 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'TRP:plan': 1, 'HIS:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 9061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1168, 9061 Classifications: {'peptide': 1168} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 52, 'TRANS': 1112} Chain breaks: 5 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "C" Number of atoms: 9193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1186, 9193 Classifications: {'peptide': 1186} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1129} Chain breaks: 2 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 61 Planarities with less than four sites: {'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "C" 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 Time building chain proxies: 17.83, per 1000 atoms: 0.64 Number of scatterers: 28027 At special positions: 0 Unit cell: (150.88, 151.7, 167.28, 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 166 16.00 O 5485 8.00 N 4532 7.00 C 17844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=69, symmetry=0 Simple disulfide: pdb=" SG CYS A 20 " - pdb=" SG CYS A 156 " distance=2.03 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 327 " - pdb=" SG CYS B 352 " 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A1301 " - " ASN A 58 " " NAG A1302 " - " ASN A 355 " " NAG A1303 " - " ASN A 703 " " NAG A1304 " - " ASN A 192 " " NAG A1305 " - " ASN A 771 " " NAG A1306 " - " ASN A 664 " " NAG A1307 " - " ASN A 793 " " NAG A1308 " - " ASN A 725 " " NAG A1309 " - " ASN A1211 " " NAG A1310 " - " ASN A 433 " " NAG A1311 " - " ASN A 19 " " 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 B1309 " - " ASN B 58 " " NAG B1310 " - " ASN B 132 " " NAG B1311 " - " ASN B 433 " " NAG B1312 " - " ASN B 454 " " NAG C1301 " - " ASN C 58 " " NAG C1302 " - " ASN C 192 " " NAG C1303 " - " ASN C 725 " " NAG C1304 " - " ASN C 188 " " NAG C1305 " - " ASN C 355 " " NAG C1306 " - " ASN C1211 " " NAG C1307 " - " ASN C 19 " " NAG C1308 " - " ASN C 171 " " NAG C1309 " - " ASN C 335 " " NAG D 1 " - " ASN A 188 " " NAG E 1 " - " ASN A 335 " " NAG F 1 " - " ASN A 132 " " NAG G 1 " - " ASN C 132 " Time building additional restraints: 7.54 Conformation dependent library (CDL) restraints added in 3.6 seconds 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6692 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 71 sheets defined 24.2% alpha, 25.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.13 Creating SS restraints... Processing helix chain 'A' and resid 88 through 91 removed outlier: 3.849A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.686A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.810A pdb=" N TRP A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 344 removed outlier: 4.034A 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 363 Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 398 through 402 removed outlier: 3.640A pdb=" N GLN A 402 " --> pdb=" O ASP A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 447 removed outlier: 3.957A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 485 Processing helix chain 'A' and resid 568 through 570 No H-bonds generated for 'chain 'A' and resid 568 through 570' Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 813 through 819 Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.722A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 862 removed outlier: 4.443A pdb=" N ILE A 839 " --> pdb=" O PHE A 835 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASN A 840 " --> pdb=" O CYS A 836 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER A 841 " --> pdb=" O ASP A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 888 removed outlier: 3.595A pdb=" N LEU A 888 " --> pdb=" O LYS A 885 " (cutoff:3.500A) No H-bonds generated for '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: 3.636A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 Processing helix chain 'A' and resid 993 through 1000 removed outlier: 3.813A pdb=" N LEU A 997 " --> pdb=" O THR A 993 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1017 Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.848A pdb=" N VAL A1033 " --> pdb=" O ILE A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1049 Processing helix chain 'A' and resid 1057 through 1065 removed outlier: 3.665A pdb=" N ILE A1061 " --> pdb=" O SER A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 5.035A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLY A1080 " --> pdb=" O ARG A1076 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.527A pdb=" N LYS B 91 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.783A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.658A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 402 " --> pdb=" O ASP B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 413 Processing helix chain 'B' and resid 442 through 448 removed outlier: 3.804A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) 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 813 through 818 removed outlier: 4.067A pdb=" N VAL B 818 " --> pdb=" O CYS B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 830 Processing helix chain 'B' and resid 831 through 833 No H-bonds generated for 'chain 'B' and resid 831 through 833' Processing helix chain 'B' and resid 836 through 862 removed outlier: 3.516A pdb=" N ILE B 842 " --> pdb=" O ASN B 838 " (cutoff:3.500A) Processing helix chain 'B' and resid 885 through 888 removed outlier: 3.687A pdb=" N LEU B 888 " --> pdb=" O LYS B 885 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 885 through 888' Processing helix chain 'B' and resid 901 through 909 Processing helix chain 'B' and resid 914 through 924 removed outlier: 4.150A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 940 removed outlier: 3.695A 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: 3.646A 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: 3.732A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1018 Processing helix chain 'B' and resid 1024 through 1046 removed outlier: 4.212A pdb=" N LYS B1028 " --> pdb=" O SER B1024 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B1029 " --> pdb=" O ALA B1025 " (cutoff:3.500A) 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 removed outlier: 3.648A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1114 removed outlier: 4.076A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B1114 " --> pdb=" O VAL B1110 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 91 removed outlier: 3.663A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 88 through 91' Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 328 through 334 Processing helix chain 'C' and resid 341 through 344 removed outlier: 4.055A pdb=" N TRP C 344 " --> pdb=" O PRO C 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 341 through 344' Processing helix chain 'C' and resid 355 through 363 removed outlier: 3.627A pdb=" N LEU C 359 " --> pdb=" O ASN C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.733A pdb=" N PHE C 379 " --> pdb=" O SER C 376 " (cutoff:3.500A) Processing helix chain 'C' and resid 442 through 447 removed outlier: 3.620A pdb=" N ARG C 446 " --> pdb=" O SER C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 478 through 483 removed outlier: 3.943A pdb=" N ASN C 483 " --> pdb=" O PRO C 479 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.751A pdb=" N THR C 532 " --> pdb=" O SER C 529 " (cutoff:3.500A) removed outlier: 3.813A 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 819 Processing helix chain 'C' and resid 822 through 830 Processing helix chain 'C' and resid 834 through 862 Processing helix chain 'C' and resid 872 through 877 removed outlier: 3.691A pdb=" N HIS C 876 " --> pdb=" O ASN C 872 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER C 877 " --> pdb=" O THR C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 872 through 877' Processing helix chain 'C' and resid 885 through 888 removed outlier: 3.525A 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 909 Processing helix chain 'C' and resid 914 through 924 removed outlier: 4.213A pdb=" N VAL C 919 " --> pdb=" O ASP C 915 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ASN C 924 " --> pdb=" O GLU C 920 " (cutoff:3.500A) Processing helix chain 'C' and resid 925 through 927 No H-bonds generated for 'chain 'C' and resid 925 through 927' Processing helix chain 'C' and resid 933 through 941 Processing helix chain 'C' and resid 951 through 965 removed outlier: 3.510A pdb=" N ILE C 955 " --> pdb=" O SER C 951 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 989 Processing helix chain 'C' and resid 993 through 999 removed outlier: 3.804A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1019 removed outlier: 3.764A pdb=" N ILE C1004 " --> pdb=" O ASN C1000 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C1005 " --> pdb=" O GLN C1001 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ASN C1006 " --> pdb=" O LYS C1002 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.947A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.552A 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 Processing helix chain 'C' and resid 1066 through 1114 removed outlier: 5.486A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C1080 " --> pdb=" O ARG C1076 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 removed outlier: 3.532A pdb=" N ASN A 26 " --> pdb=" O LEU A 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 68 removed outlier: 4.508A pdb=" N GLY A 101 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 removed outlier: 7.892A pdb=" N GLN A 265 " --> pdb=" O ASP A 281 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ASP A 281 " --> pdb=" O GLN A 265 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N LEU A 267 " --> pdb=" O ALA A 279 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N ALA A 279 " --> pdb=" O LEU A 267 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ASN A 269 " --> pdb=" O THR A 277 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 80 through 81 removed outlier: 8.134A pdb=" N THR A 241 " --> pdb=" O PRO A 159 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N THR A 161 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N TRP A 174 " --> pdb=" O CYS A 156 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 96 through 97 removed outlier: 3.565A pdb=" N SER A 96 " --> pdb=" O TYR A 235 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TYR A 235 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR A 123 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ILE A 124 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N PHE A 185 " --> pdb=" O ALA A 150 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 109 through 111 removed outlier: 3.822A pdb=" N LEU A 111 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A 118 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 302 through 308 removed outlier: 4.807A pdb=" N VAL A 677 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ARG A 676 " --> pdb=" O ARG A 693 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ARG A 693 " --> pdb=" O ARG A 676 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 316 through 319 Processing sheet with id=AA9, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.817A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 345 through 349 removed outlier: 3.771A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A 367 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.525A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 459 through 463 removed outlier: 3.608A pdb=" N TYR A 462 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 466 through 468 removed outlier: 4.501A pdb=" N CYS A 466 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.615A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 666 through 667 removed outlier: 3.680A pdb=" N PHE A 658 " --> pdb=" O TYR A 667 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 724 through 731 removed outlier: 6.593A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.815A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) removed outlier: 9.753A pdb=" N LEU A 726 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLY A 739 " --> pdb=" O PHE A 742 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ILE A 744 " --> pdb=" O ARG A 737 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG A 737 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 773 through 775 removed outlier: 6.230A pdb=" N SER A 773 " --> pdb=" O LEU C 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 786 through 795 removed outlier: 6.970A pdb=" N GLU A 787 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU A1157 " --> pdb=" O GLU A 787 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLN A 789 " --> pdb=" O THR A1155 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A1155 " --> pdb=" O GLN A 789 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N PHE A1153 " --> pdb=" O PRO A 791 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ASN A 793 " --> pdb=" O THR A1151 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU A1157 " --> pdb=" O LYS A1179 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LYS A1179 " --> pdb=" O LEU A1157 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE A1177 " --> pdb=" O SER A1159 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 798 through 804 removed outlier: 3.915A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 809 through 811 removed outlier: 4.229A 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 1204 removed outlier: 3.713A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A1168 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU A1162 " --> pdb=" O ILE A1170 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 54 through 55 removed outlier: 5.709A pdb=" N VAL B 55 " --> pdb=" O TYR C 649 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 60 through 67 removed outlier: 3.503A pdb=" N SER B 262 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL B 280 " --> pdb=" O LEU B 267 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN B 278 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 75 through 76 removed outlier: 3.545A pdb=" N SER B 104 " --> pdb=" O PHE B 200 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS B 201 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AD1, first strand: chain 'B' and resid 95 through 97 removed outlier: 3.650A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR B 149 " --> pdb=" O VAL B 138 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE B 148 " --> pdb=" O LYS B 187 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LYS B 187 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 155 through 160 removed outlier: 7.485A pdb=" N TRP B 174 " --> pdb=" O CYS B 156 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 302 through 305 Processing sheet with id=AD4, first strand: chain 'B' and resid 309 through 310 removed outlier: 3.601A pdb=" N GLY B 675 " --> pdb=" O PHE B 309 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 316 through 319 removed outlier: 3.738A pdb=" N TYR B 622 " --> pdb=" O GLY B 629 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY B 629 " --> pdb=" O TYR B 622 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 337 through 339 removed outlier: 6.910A pdb=" N VAL B 338 " --> pdb=" O ASN B 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.783A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS B 586 " --> pdb=" O LEU B 429 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 345 through 349 removed outlier: 3.783A pdb=" N GLU B 345 " --> pdb=" O LYS B 390 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS B 390 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AE1, first strand: chain 'B' and resid 459 through 463 removed outlier: 3.502A pdb=" N TYR B 462 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 467 through 468 removed outlier: 3.567A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 550 through 551 removed outlier: 3.546A pdb=" N GLY B 550 " --> pdb=" O LEU B 573 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 635 through 636 removed outlier: 4.393A pdb=" N THR B 666 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 657 " --> pdb=" O LEU B 648 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 724 through 731 removed outlier: 6.618A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) removed outlier: 9.749A pdb=" N LEU B 726 " --> pdb=" O THR B 766 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N PHE B 742 " --> pdb=" O MET B 738 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N LEU B 736 " --> pdb=" O ILE B 744 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 786 through 804 removed outlier: 6.952A pdb=" N GLU B 787 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N LEU B1157 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N GLN B 789 " --> pdb=" O THR B1155 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N THR B1155 " --> pdb=" O GLN B 789 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N PHE B1153 " --> pdb=" O PRO B 791 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B 793 " --> pdb=" O THR B1151 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU B1131 " --> pdb=" O PHE B1146 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N TYR B1148 " --> pdb=" O HIS B1129 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N HIS B1129 " --> pdb=" O TYR B1148 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 809 through 812 removed outlier: 4.293A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 866 through 868 removed outlier: 6.958A pdb=" N LEU B 867 " --> pdb=" O VAL C 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'B' and resid 878 through 879 removed outlier: 3.526A pdb=" N VAL B 879 " --> pdb=" O ILE B 882 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 3.627A pdb=" N GLY B1169 " --> pdb=" O MET B1205 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG B1168 " --> pdb=" O LEU B1164 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 1175 through 1179 Processing sheet with id=AF3, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AF4, first strand: chain 'C' and resid 59 through 68 removed outlier: 3.557A pdb=" N THR C 59 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 63 " --> pdb=" O TYR C 266 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP C 257 " --> pdb=" O LYS C 105 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLY C 101 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.359A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 75 through 76 removed outlier: 6.880A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 80 through 81 removed outlier: 8.294A pdb=" N THR C 241 " --> pdb=" O PRO C 159 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 9.907A pdb=" N TYR C 158 " --> pdb=" O HIS C 175 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N HIS C 175 " --> pdb=" O TYR C 158 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER C 173 " --> pdb=" O HIS C 160 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 96 through 97 removed outlier: 3.650A pdb=" N SER C 96 " --> pdb=" O TYR C 235 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N THR C 123 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE C 124 " --> pdb=" O VAL C 139 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 109 through 112 removed outlier: 3.647A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 302 through 305 Processing sheet with id=AG1, first strand: chain 'C' and resid 309 through 310 Processing sheet with id=AG2, first strand: chain 'C' and resid 316 through 319 removed outlier: 6.699A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 338 through 339 removed outlier: 5.999A pdb=" N VAL C 338 " --> pdb=" O ASN C 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'C' and resid 345 through 349 removed outlier: 3.563A pdb=" N GLU C 345 " --> pdb=" O LYS C 390 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS C 390 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER C 367 " --> pdb=" O TYR C 426 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER C 428 " --> pdb=" O VAL C 365 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N VAL C 365 " --> pdb=" O SER C 428 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.669A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'C' and resid 459 through 463 Processing sheet with id=AG7, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.973A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.531A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 556 through 557 Processing sheet with id=AH1, first strand: chain 'C' and resid 632 through 636 removed outlier: 3.636A pdb=" N VAL C 636 " --> pdb=" O THR C 666 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 690 through 693 Processing sheet with id=AH3, first strand: chain 'C' and resid 724 through 725 removed outlier: 6.639A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.736A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N PHE C 742 " --> pdb=" O MET C 738 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU C 736 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'C' and resid 786 through 804 removed outlier: 6.869A pdb=" N GLU C 787 " --> pdb=" O LEU C1157 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N LEU C1157 " --> pdb=" O GLU C 787 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N GLN C 789 " --> pdb=" O THR C1155 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N THR C1155 " --> pdb=" O GLN C 789 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N PHE C1153 " --> pdb=" O PRO C 791 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASN C 793 " --> pdb=" O THR C1151 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE C 803 " --> pdb=" O LEU C1141 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 809 through 812 removed outlier: 4.234A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'C' and resid 878 through 879 Processing sheet with id=AH7, first strand: chain 'C' and resid 1202 through 1205 removed outlier: 3.522A pdb=" N ALA C1171 " --> pdb=" O VAL C1203 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'C' and resid 1175 through 1179 964 hydrogen bonds defined for protein. 2697 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: 13.37 Time building geometry restraints manager: 8.70 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: 8887 1.34 - 1.46: 7095 1.46 - 1.58: 12520 1.58 - 1.70: 0 1.70 - 1.81: 193 Bond restraints: 28695 Sorted by residual: bond pdb=" C PRO C1067 " pdb=" N PRO C1068 " ideal model delta sigma weight residual 1.333 1.371 -0.037 1.44e-02 4.82e+03 6.72e+00 bond pdb=" C1 NAG A1310 " pdb=" O5 NAG A1310 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.548 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C1 NAG C1302 " pdb=" O5 NAG C1302 " 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 C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.10e+00 ... (remaining 28690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.24: 38218 1.24 - 2.47: 692 2.47 - 3.71: 182 3.71 - 4.95: 12 4.95 - 6.19: 9 Bond angle restraints: 39113 Sorted by residual: angle pdb=" N CYS B 836 " pdb=" CA CYS B 836 " pdb=" C CYS B 836 " ideal model delta sigma weight residual 114.56 110.12 4.44 1.27e+00 6.20e-01 1.22e+01 angle pdb=" CA CYS B 836 " pdb=" C CYS B 836 " pdb=" N ASP B 837 " ideal model delta sigma weight residual 119.26 116.38 2.88 1.14e+00 7.69e-01 6.38e+00 angle pdb=" C VAL A 113 " pdb=" N ASN A 114 " pdb=" CA ASN A 114 " ideal model delta sigma weight residual 121.54 126.01 -4.47 1.91e+00 2.74e-01 5.48e+00 angle pdb=" C ASN A 872 " pdb=" N THR A 873 " pdb=" CA THR A 873 " ideal model delta sigma weight residual 121.54 125.91 -4.37 1.91e+00 2.74e-01 5.24e+00 angle pdb=" C3 BMA F 3 " pdb=" C2 BMA F 3 " pdb=" O2 BMA F 3 " ideal model delta sigma weight residual 112.95 106.78 6.17 3.00e+00 1.11e-01 4.22e+00 ... (remaining 39108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.74: 17274 21.74 - 43.48: 291 43.48 - 65.23: 47 65.23 - 86.97: 9 86.97 - 108.71: 4 Dihedral angle restraints: 17625 sinusoidal: 7213 harmonic: 10412 Sorted by residual: dihedral pdb=" O4 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 288.71 180.00 108.71 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" C3 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C5 BMA F 3 " pdb=" O5 BMA F 3 " ideal model delta sinusoidal sigma weight residual 47.62 -59.08 106.70 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" CA GLU A 930 " pdb=" C GLU A 930 " pdb=" N ILE A 931 " pdb=" CA ILE A 931 " ideal model delta harmonic sigma weight residual -180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 17622 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3826 0.054 - 0.108: 632 0.108 - 0.162: 87 0.162 - 0.216: 0 0.216 - 0.270: 1 Chirality restraints: 4546 Sorted by residual: chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 433 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 355 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 4543 not shown) Planarity restraints: 5033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " 0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B1067 " -0.059 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 3.30e-02 1.74e+00 pdb=" N PRO C1067 " -0.057 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 delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " -0.021 5.00e-02 4.00e+02 3.14e-02 1.58e+00 pdb=" N PRO A1067 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " -0.017 5.00e-02 4.00e+02 ... (remaining 5030 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2004 2.74 - 3.28: 26586 3.28 - 3.82: 43972 3.82 - 4.36: 51526 4.36 - 4.90: 91641 Nonbonded interactions: 215729 Sorted by model distance: nonbonded pdb=" OH TYR C 448 " pdb=" O PHE C 473 " model vdw 2.203 3.040 nonbonded pdb=" OG SER B 340 " pdb=" OD1 ASN B 343 " model vdw 2.212 3.040 nonbonded pdb=" OG SER A 340 " pdb=" OD1 ASN A 343 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 456 " pdb=" OD2 ASP C 459 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASN C 108 " pdb=" OG SER C 119 " model vdw 2.256 3.040 ... (remaining 215724 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 28 or (resid 34 and (name N or n \ ame CA or name C or name O or name CB )) or resid 35 through 119 or (resid 120 a \ nd (name N or name CA or name C or name O or name CB )) or resid 121 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 248 and (name N or name CA or name C or name O or nam \ e CB )) or resid 249 through 374 or (resid 375 and (name N or name CA or name C \ or name O or name CB )) or resid 376 through 390 or (resid 391 through 392 and ( \ name N or name CA or name C or name O or name CB )) or resid 393 through 396 or \ (resid 397 and (name N or name CA or name C or name O or name CB )) or resid 398 \ through 399 or (resid 400 and (name N or name CA or name C or name O or name CB \ )) or resid 401 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 5 \ 63 through 569 or (resid 570 through 571 and (name N or name CA or name C or nam \ e O or name CB )) or resid 572 through 705 or (resid 706 and (name N or name CA \ or name C or name O or name CB )) or resid 707 through 781 or (resid 782 and (na \ me N or name CA or name C or name O or name CB )) or resid 783 through 1065 or ( \ resid 1066 and (name N or name CA or name C or name O or name CB )) or resid 106 \ 7 through 1221 or resid 1301 through 1309)) selection = (chain 'B' and (resid 14 through 28 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 83 or (resid 84 and (name N or nam \ e CA or name C or name O or name CB )) or resid 85 through 113 or (resid 114 thr \ ough 116 and (name N or name CA or name C or name O or name CB )) or resid 117 t \ hrough 156 or (resid 157 and (name N or name CA or name C or name O or name CB ) \ ) or resid 158 through 165 or (resid 166 and (name N or name CA or name C or nam \ e O or name CB )) or resid 167 through 179 or (resid 180 and (name N or name CA \ or name C or name O or name CB )) or resid 181 through 185 or (resid 186 and (na \ me N or name CA or name C or name O or name CB )) or resid 187 through 374 or (r \ esid 375 and (name N or name CA or name C or name O or name CB )) or resid 376 t \ hrough 390 or (resid 391 through 392 and (name N or name CA or name C or name O \ or name CB )) or resid 393 through 396 or (resid 397 and (name N or name CA or n \ ame C or name O or name CB )) or resid 398 through 399 or (resid 400 and (name N \ or name CA or name C or name O or name CB )) or resid 401 through 533 or (resid \ 534 and (name N or name CA or name C or name O or name CB )) or resid 535 throu \ gh 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 through 563 and (name N or \ name CA or name C or name O or name CB )) or resid 564 through 929 or (resid 930 \ through 932 and (name N or name CA or name C or name O or name CB )) or resid 9 \ 33 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 and (name N or name CA or name C \ or name O or name CB )) or resid 1023 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 1 \ 199 or (resid 1200 and (name N or name CA or name C or name O or name CB )) or r \ esid 1201 through 1221 or resid 1301 through 1309)) selection = (chain 'C' 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 28 or resid 34 through 115 or (r \ esid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 o \ r (resid 118 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 19 or (resid 120 and (name N or name CA or name C or name O or name CB )) or res \ id 121 through 156 or (resid 157 and (name N or name CA or name C or name O or n \ ame CB )) or resid 158 through 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 name O or name CB )) or resid 249 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 533 or (resid 534 and (name N or name CA or name C or na \ me O or name CB )) or resid 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 (n \ ame 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 5 \ 69 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 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 name 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 9 \ 33 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 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 o \ r name CA or name C or name 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 r \ esid 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 1309)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' } 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: 4.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.200 Check model and map are aligned: 0.220 Set scattering table: 0.270 Process input model: 68.330 Find NCS groups from input model: 2.000 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 0.044 28805 Z= 0.117 Angle : 0.427 6.186 39374 Z= 0.217 Chirality : 0.041 0.270 4546 Planarity : 0.003 0.034 4997 Dihedral : 8.091 108.710 10726 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.35 % Allowed : 3.63 % Favored : 95.02 % 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: -2.12 (0.13), residues: 3526 helix: 0.17 (0.19), residues: 745 sheet: -0.97 (0.19), residues: 664 loop : -2.25 (0.12), residues: 2117 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 444 HIS 0.002 0.000 HIS A 201 PHE 0.007 0.001 PHE A 121 TYR 0.005 0.001 TYR C 153 ARG 0.001 0.000 ARG C 447 Details of bonding type rmsd link_NAG-ASN : bond 0.00171 ( 36) link_NAG-ASN : angle 0.93243 ( 108) link_BETA1-4 : bond 0.00340 ( 5) link_BETA1-4 : angle 0.90315 ( 15) hydrogen bonds : bond 0.22251 ( 945) hydrogen bonds : angle 7.40953 ( 2697) SS BOND : bond 0.00092 ( 69) SS BOND : angle 0.44411 ( 138) covalent geometry : bond 0.00231 (28695) covalent geometry : angle 0.42456 (39113) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 831 time to evaluate : 3.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.6308 (p0) cc_final: 0.5769 (p0) REVERT: A 42 VAL cc_start: 0.8333 (m) cc_final: 0.8063 (t) REVERT: A 107 LYS cc_start: 0.8786 (tttm) cc_final: 0.8363 (tttm) REVERT: A 213 TYR cc_start: 0.7901 (OUTLIER) cc_final: 0.7458 (t80) REVERT: A 236 TYR cc_start: 0.8111 (t80) cc_final: 0.7808 (t80) REVERT: A 255 GLU cc_start: 0.7650 (mt-10) cc_final: 0.7361 (mt-10) REVERT: A 292 CYS cc_start: 0.7498 (OUTLIER) cc_final: 0.7279 (m) REVERT: A 500 LYS cc_start: 0.8204 (mtpp) cc_final: 0.7942 (mtpp) REVERT: A 521 LEU cc_start: 0.8548 (mm) cc_final: 0.8340 (mm) REVERT: A 584 ASN cc_start: 0.7691 (m-40) cc_final: 0.7383 (m110) REVERT: A 652 ASN cc_start: 0.8641 (m-40) cc_final: 0.8186 (m-40) REVERT: A 696 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7578 (mmtp) REVERT: A 745 ASP cc_start: 0.7465 (t0) cc_final: 0.7250 (t0) REVERT: A 815 SER cc_start: 0.8246 (m) cc_final: 0.7756 (t) REVERT: A 946 LEU cc_start: 0.8596 (mt) cc_final: 0.8340 (mt) REVERT: A 1010 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8287 (ttmm) REVERT: A 1050 LYS cc_start: 0.8724 (mttt) cc_final: 0.8492 (mttm) REVERT: A 1060 GLU cc_start: 0.6194 (tp30) cc_final: 0.5869 (tp30) REVERT: A 1064 ARG cc_start: 0.8010 (ttp80) cc_final: 0.7723 (ttm170) REVERT: A 1071 GLN cc_start: 0.6675 (OUTLIER) cc_final: 0.6369 (mp10) REVERT: A 1189 SER cc_start: 0.7856 (p) cc_final: 0.7620 (t) REVERT: B 34 ARG cc_start: 0.5317 (ttp80) cc_final: 0.5029 (ttp80) REVERT: B 66 TYR cc_start: 0.7625 (m-80) cc_final: 0.7002 (m-80) REVERT: B 76 ASP cc_start: 0.7990 (t0) cc_final: 0.7382 (t0) REVERT: B 147 GLU cc_start: 0.5517 (mm-30) cc_final: 0.5239 (mm-30) REVERT: B 174 TRP cc_start: 0.6261 (p-90) cc_final: 0.5614 (p-90) REVERT: B 194 SER cc_start: 0.8534 (m) cc_final: 0.8155 (t) REVERT: B 282 CYS cc_start: 0.4990 (m) cc_final: 0.4613 (m) REVERT: B 418 ILE cc_start: 0.8293 (mm) cc_final: 0.7921 (mm) REVERT: B 500 LYS cc_start: 0.7748 (mttm) cc_final: 0.7356 (mttm) REVERT: B 583 ASN cc_start: 0.7288 (t0) cc_final: 0.7046 (t0) REVERT: B 634 LYS cc_start: 0.8320 (tttp) cc_final: 0.8096 (ttpp) REVERT: B 682 TYR cc_start: 0.7150 (t80) cc_final: 0.6838 (t80) REVERT: B 712 TYR cc_start: 0.8323 (p90) cc_final: 0.7995 (p90) REVERT: B 781 THR cc_start: 0.8641 (m) cc_final: 0.8403 (t) REVERT: B 832 TYR cc_start: 0.7467 (m-80) cc_final: 0.7186 (m-80) REVERT: B 879 VAL cc_start: 0.8756 (p) cc_final: 0.8494 (m) REVERT: B 955 ILE cc_start: 0.8053 (mm) cc_final: 0.7675 (mm) REVERT: B 998 ASN cc_start: 0.7838 (m-40) cc_final: 0.7635 (m-40) REVERT: B 999 LYS cc_start: 0.8504 (mttp) cc_final: 0.8219 (mttp) REVERT: B 1010 LYS cc_start: 0.8277 (ttpp) cc_final: 0.7933 (ttpp) REVERT: B 1108 GLU cc_start: 0.7129 (tt0) cc_final: 0.6887 (tt0) REVERT: B 1173 LYS cc_start: 0.8620 (ptpp) cc_final: 0.8263 (ptpp) REVERT: B 1189 SER cc_start: 0.8105 (p) cc_final: 0.7905 (t) REVERT: B 1213 THR cc_start: 0.8147 (m) cc_final: 0.7910 (m) REVERT: C 38 ASP cc_start: 0.7577 (m-30) cc_final: 0.7213 (m-30) REVERT: C 73 ASN cc_start: 0.7511 (m-40) cc_final: 0.7280 (m-40) REVERT: C 437 ASN cc_start: 0.7799 (t0) cc_final: 0.7585 (t0) REVERT: C 454 ASN cc_start: 0.7197 (t0) cc_final: 0.6782 (p0) REVERT: C 553 GLU cc_start: 0.6632 (mt-10) cc_final: 0.6274 (mt-10) REVERT: C 577 PHE cc_start: 0.7214 (p90) cc_final: 0.6841 (p90) REVERT: C 583 ASN cc_start: 0.6644 (t0) cc_final: 0.6423 (t0) REVERT: C 592 PHE cc_start: 0.8238 (m-80) cc_final: 0.7827 (m-80) REVERT: C 634 LYS cc_start: 0.8163 (tttm) cc_final: 0.7895 (tttm) REVERT: C 649 TYR cc_start: 0.8492 (m-80) cc_final: 0.8258 (m-80) REVERT: C 730 SER cc_start: 0.8300 (p) cc_final: 0.7968 (t) REVERT: C 827 ASP cc_start: 0.7450 (m-30) cc_final: 0.7219 (m-30) REVERT: C 885 LYS cc_start: 0.8189 (tptp) cc_final: 0.7874 (tptp) REVERT: C 1000 ASN cc_start: 0.8260 (m-40) cc_final: 0.8021 (m-40) REVERT: C 1149 LYS cc_start: 0.7875 (tttt) cc_final: 0.7660 (ttmm) REVERT: C 1179 LYS cc_start: 0.8397 (ttpt) cc_final: 0.8082 (ttmm) REVERT: C 1214 LYS cc_start: 0.7954 (mtpt) cc_final: 0.7663 (mtpp) outliers start: 42 outliers final: 14 residues processed: 858 average time/residue: 0.3976 time to fit residues: 538.5867 Evaluate side-chains 682 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 665 time to evaluate : 2.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 1071 GLN Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1069 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 298 optimal weight: 0.0470 chunk 267 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 276 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 320 optimal weight: 4.9990 overall best weight: 1.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 424 GLN A 630 GLN A 709 GLN A 881 ASN A1001 GLN A1041 ASN A1135 GLN A1174 GLN B 115 ASN B 140 GLN B 364 HIS ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN B 630 GLN B 642 ASN B 709 GLN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 ASN B1016 GLN B1049 ASN B1071 GLN B1079 ASN B1174 GLN C 100 ASN C 351 ASN C 470 ASN C 645 GLN C 789 GLN C 847 ASN C 870 ASN C 874 ASN C 909 ASN C1030 GLN C1041 ASN C1059 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098350 restraints weight = 41684.512| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.30 r_work: 0.3112 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 28805 Z= 0.207 Angle : 0.606 12.292 39374 Z= 0.318 Chirality : 0.047 0.326 4546 Planarity : 0.004 0.042 4997 Dihedral : 6.816 83.714 4701 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.60 % Allowed : 9.09 % Favored : 88.31 % 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: -1.40 (0.13), residues: 3526 helix: 0.92 (0.20), residues: 767 sheet: -0.34 (0.19), residues: 669 loop : -1.95 (0.12), residues: 2090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 197 HIS 0.010 0.002 HIS C 201 PHE 0.028 0.002 PHE A 794 TYR 0.025 0.002 TYR C 667 ARG 0.009 0.001 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00326 ( 36) link_NAG-ASN : angle 1.56791 ( 108) link_BETA1-4 : bond 0.00141 ( 5) link_BETA1-4 : angle 2.07195 ( 15) hydrogen bonds : bond 0.05448 ( 945) hydrogen bonds : angle 5.16513 ( 2697) SS BOND : bond 0.00377 ( 69) SS BOND : angle 1.48669 ( 138) covalent geometry : bond 0.00480 (28695) covalent geometry : angle 0.59449 (39113) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 712 time to evaluate : 3.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7333 (p0) cc_final: 0.6766 (p0) REVERT: A 42 VAL cc_start: 0.8660 (m) cc_final: 0.8328 (t) REVERT: A 104 SER cc_start: 0.8452 (p) cc_final: 0.8159 (m) REVERT: A 351 ASN cc_start: 0.8286 (OUTLIER) cc_final: 0.7692 (m-40) REVERT: A 500 LYS cc_start: 0.8441 (mtpp) cc_final: 0.8233 (mtpp) REVERT: A 521 LEU cc_start: 0.8704 (mm) cc_final: 0.8488 (mm) REVERT: A 620 VAL cc_start: 0.8299 (m) cc_final: 0.8024 (p) REVERT: A 635 GLU cc_start: 0.8544 (tt0) cc_final: 0.8242 (tt0) REVERT: A 745 ASP cc_start: 0.8299 (t0) cc_final: 0.8027 (t0) REVERT: A 799 HIS cc_start: 0.7277 (m90) cc_final: 0.6876 (m90) REVERT: A 828 LEU cc_start: 0.8773 (mt) cc_final: 0.8343 (mp) REVERT: A 1010 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8582 (ttmm) REVERT: A 1069 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7638 (mm-30) REVERT: A 1149 LYS cc_start: 0.8396 (tttp) cc_final: 0.8186 (ttpp) REVERT: A 1189 SER cc_start: 0.8308 (p) cc_final: 0.8065 (t) REVERT: B 34 ARG cc_start: 0.6514 (ttp80) cc_final: 0.6001 (ttp80) REVERT: B 66 TYR cc_start: 0.8112 (m-80) cc_final: 0.7615 (m-80) REVERT: B 76 ASP cc_start: 0.8580 (t0) cc_final: 0.8101 (t0) REVERT: B 117 LEU cc_start: 0.5024 (OUTLIER) cc_final: 0.4511 (pp) REVERT: B 147 GLU cc_start: 0.6834 (mm-30) cc_final: 0.6288 (mm-30) REVERT: B 194 SER cc_start: 0.8827 (m) cc_final: 0.8463 (t) REVERT: B 205 GLU cc_start: 0.7834 (tt0) cc_final: 0.7438 (tt0) REVERT: B 218 MET cc_start: 0.8096 (mmm) cc_final: 0.7823 (mtp) REVERT: B 265 GLN cc_start: 0.8634 (tt0) cc_final: 0.8304 (tt0) REVERT: B 418 ILE cc_start: 0.8511 (mm) cc_final: 0.8208 (mm) REVERT: B 442 SER cc_start: 0.8600 (t) cc_final: 0.8390 (m) REVERT: B 500 LYS cc_start: 0.8201 (mttm) cc_final: 0.7974 (mttm) REVERT: B 583 ASN cc_start: 0.8133 (t0) cc_final: 0.7894 (t0) REVERT: B 634 LYS cc_start: 0.8693 (tttp) cc_final: 0.8439 (ttpp) REVERT: B 682 TYR cc_start: 0.7624 (t80) cc_final: 0.7337 (t80) REVERT: B 712 TYR cc_start: 0.8881 (p90) cc_final: 0.8548 (p90) REVERT: B 800 GLU cc_start: 0.7807 (pm20) cc_final: 0.7533 (pm20) REVERT: B 955 ILE cc_start: 0.8449 (mm) cc_final: 0.8184 (mm) REVERT: B 999 LYS cc_start: 0.8844 (mttp) cc_final: 0.8571 (mttp) REVERT: B 1010 LYS cc_start: 0.8584 (ttpp) cc_final: 0.8322 (ttpp) REVERT: B 1031 SER cc_start: 0.8172 (p) cc_final: 0.7873 (m) REVERT: B 1038 GLN cc_start: 0.8512 (tt0) cc_final: 0.8310 (tt0) REVERT: B 1149 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8416 (tttp) REVERT: B 1173 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8405 (ptpp) REVERT: C 38 ASP cc_start: 0.7953 (m-30) cc_final: 0.7651 (m-30) REVERT: C 73 ASN cc_start: 0.8297 (m-40) cc_final: 0.7980 (m-40) REVERT: C 328 ASP cc_start: 0.7212 (p0) cc_final: 0.7000 (p0) REVERT: C 366 ASP cc_start: 0.7880 (t70) cc_final: 0.7566 (t0) REVERT: C 437 ASN cc_start: 0.8181 (t0) cc_final: 0.7960 (t0) REVERT: C 446 ARG cc_start: 0.8126 (mtp-110) cc_final: 0.7916 (mtp85) REVERT: C 454 ASN cc_start: 0.7845 (t0) cc_final: 0.7349 (p0) REVERT: C 553 GLU cc_start: 0.7287 (mt-10) cc_final: 0.6759 (mt-10) REVERT: C 577 PHE cc_start: 0.7759 (p90) cc_final: 0.7254 (p90) REVERT: C 583 ASN cc_start: 0.7311 (t0) cc_final: 0.7103 (t0) REVERT: C 634 LYS cc_start: 0.8470 (tttm) cc_final: 0.8245 (tttm) REVERT: C 649 TYR cc_start: 0.8776 (m-80) cc_final: 0.8343 (m-80) REVERT: C 674 SER cc_start: 0.8682 (m) cc_final: 0.8430 (p) REVERT: C 827 ASP cc_start: 0.8215 (m-30) cc_final: 0.7854 (m-30) REVERT: C 831 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7611 (mm-30) REVERT: C 885 LYS cc_start: 0.8486 (tptp) cc_final: 0.8181 (tptp) REVERT: C 912 LYS cc_start: 0.8456 (ttpp) cc_final: 0.8182 (ttpp) REVERT: C 1149 LYS cc_start: 0.8316 (tttt) cc_final: 0.8051 (ttmt) REVERT: C 1179 LYS cc_start: 0.8758 (ttpt) cc_final: 0.8419 (ttmm) REVERT: C 1200 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7695 (mmmt) REVERT: C 1214 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7901 (mtpp) outliers start: 81 outliers final: 54 residues processed: 753 average time/residue: 0.3894 time to fit residues: 468.3942 Evaluate side-chains 707 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 650 time to evaluate : 3.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 258 VAL Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 953 THR Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1149 LYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 780 GLU Chi-restraints excluded: chain C residue 811 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1041 ASN Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 282 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 245 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 190 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 230 optimal weight: 3.9990 chunk 257 optimal weight: 0.1980 chunk 142 optimal weight: 0.7980 chunk 342 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN A1071 GLN B 353 ASN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1180 GLN C 160 HIS C 470 ASN C 645 GLN C 863 GLN C 870 ASN C 881 ASN C 909 ASN C1041 ASN C1059 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.116209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.098550 restraints weight = 41645.240| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.30 r_work: 0.3120 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 28805 Z= 0.122 Angle : 0.521 10.827 39374 Z= 0.273 Chirality : 0.044 0.427 4546 Planarity : 0.004 0.040 4997 Dihedral : 6.101 59.302 4698 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.57 % Allowed : 11.24 % Favored : 86.19 % 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: -1.05 (0.14), residues: 3526 helix: 1.31 (0.20), residues: 765 sheet: -0.10 (0.19), residues: 672 loop : -1.78 (0.12), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 197 HIS 0.007 0.001 HIS B 201 PHE 0.021 0.001 PHE A 794 TYR 0.026 0.001 TYR B 203 ARG 0.006 0.000 ARG B 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00175 ( 36) link_NAG-ASN : angle 1.45676 ( 108) link_BETA1-4 : bond 0.00317 ( 5) link_BETA1-4 : angle 1.67567 ( 15) hydrogen bonds : bond 0.04631 ( 945) hydrogen bonds : angle 4.87033 ( 2697) SS BOND : bond 0.00374 ( 69) SS BOND : angle 1.22178 ( 138) covalent geometry : bond 0.00281 (28695) covalent geometry : angle 0.51053 (39113) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 657 time to evaluate : 2.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7245 (p0) cc_final: 0.6646 (p0) REVERT: A 83 ILE cc_start: 0.8587 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 176 ILE cc_start: 0.8477 (mm) cc_final: 0.8186 (mm) REVERT: A 351 ASN cc_start: 0.8060 (OUTLIER) cc_final: 0.7783 (m110) REVERT: A 500 LYS cc_start: 0.8459 (mtpp) cc_final: 0.8244 (mtpp) REVERT: A 521 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8473 (mm) REVERT: A 620 VAL cc_start: 0.8324 (m) cc_final: 0.8033 (p) REVERT: A 635 GLU cc_start: 0.8563 (tt0) cc_final: 0.8241 (tt0) REVERT: A 745 ASP cc_start: 0.8272 (t0) cc_final: 0.7993 (t0) REVERT: A 763 ARG cc_start: 0.8493 (mtp85) cc_final: 0.8242 (mtp85) REVERT: A 799 HIS cc_start: 0.7100 (m90) cc_final: 0.6695 (m90) REVERT: A 828 LEU cc_start: 0.8758 (mt) cc_final: 0.8250 (mp) REVERT: A 879 VAL cc_start: 0.7849 (m) cc_final: 0.7639 (p) REVERT: A 1010 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8581 (ttmm) REVERT: A 1149 LYS cc_start: 0.8422 (tttp) cc_final: 0.8190 (ttpp) REVERT: A 1189 SER cc_start: 0.8292 (p) cc_final: 0.8047 (t) REVERT: B 34 ARG cc_start: 0.6509 (ttp80) cc_final: 0.5944 (ttp80) REVERT: B 42 VAL cc_start: 0.8788 (m) cc_final: 0.8356 (t) REVERT: B 66 TYR cc_start: 0.8150 (m-80) cc_final: 0.7694 (m-80) REVERT: B 76 ASP cc_start: 0.8535 (t0) cc_final: 0.8042 (t0) REVERT: B 147 GLU cc_start: 0.6911 (mm-30) cc_final: 0.6241 (mm-30) REVERT: B 218 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7920 (mtm) REVERT: B 265 GLN cc_start: 0.8611 (tt0) cc_final: 0.8289 (tt0) REVERT: B 418 ILE cc_start: 0.8495 (mm) cc_final: 0.8186 (mm) REVERT: B 500 LYS cc_start: 0.8181 (mttm) cc_final: 0.7939 (mttm) REVERT: B 634 LYS cc_start: 0.8689 (tttp) cc_final: 0.8437 (ttpp) REVERT: B 682 TYR cc_start: 0.7602 (t80) cc_final: 0.7354 (t80) REVERT: B 712 TYR cc_start: 0.8909 (p90) cc_final: 0.8611 (p90) REVERT: B 800 GLU cc_start: 0.7769 (pm20) cc_final: 0.7484 (pm20) REVERT: B 955 ILE cc_start: 0.8392 (mm) cc_final: 0.8114 (mm) REVERT: B 999 LYS cc_start: 0.8810 (mttp) cc_final: 0.8538 (mttp) REVERT: B 1010 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8309 (ttpp) REVERT: B 1031 SER cc_start: 0.8153 (p) cc_final: 0.7806 (m) REVERT: B 1064 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8146 (ttp-170) REVERT: B 1173 LYS cc_start: 0.8759 (ptpp) cc_final: 0.8343 (ptpp) REVERT: C 38 ASP cc_start: 0.7944 (m-30) cc_final: 0.7649 (m-30) REVERT: C 73 ASN cc_start: 0.8366 (m-40) cc_final: 0.8098 (m-40) REVERT: C 218 MET cc_start: 0.8319 (mtp) cc_final: 0.7984 (mtp) REVERT: C 366 ASP cc_start: 0.7847 (t70) cc_final: 0.7495 (t0) REVERT: C 454 ASN cc_start: 0.7852 (t0) cc_final: 0.7354 (p0) REVERT: C 553 GLU cc_start: 0.7355 (mt-10) cc_final: 0.6822 (mt-10) REVERT: C 577 PHE cc_start: 0.7657 (p90) cc_final: 0.7162 (p90) REVERT: C 634 LYS cc_start: 0.8505 (tttm) cc_final: 0.8288 (tttm) REVERT: C 649 TYR cc_start: 0.8802 (m-80) cc_final: 0.8408 (m-80) REVERT: C 670 LEU cc_start: 0.8432 (mt) cc_final: 0.8221 (mp) REVERT: C 827 ASP cc_start: 0.8213 (m-30) cc_final: 0.7842 (m-30) REVERT: C 831 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7615 (mm-30) REVERT: C 863 GLN cc_start: 0.8317 (tt0) cc_final: 0.8016 (tm-30) REVERT: C 885 LYS cc_start: 0.8509 (tptp) cc_final: 0.8182 (tptp) REVERT: C 912 LYS cc_start: 0.8441 (ttpp) cc_final: 0.8166 (ttpp) REVERT: C 1026 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8493 (mm) REVERT: C 1030 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7927 (mm-40) REVERT: C 1149 LYS cc_start: 0.8326 (tttt) cc_final: 0.7987 (ttmm) REVERT: C 1179 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8377 (ttmm) REVERT: C 1200 LYS cc_start: 0.8075 (mmmt) cc_final: 0.7698 (mmmt) REVERT: C 1214 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7885 (mtpp) outliers start: 80 outliers final: 52 residues processed: 701 average time/residue: 0.3676 time to fit residues: 413.2808 Evaluate side-chains 699 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 641 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 218 MET Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 619 CYS Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 240 LEU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 913 LEU Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1030 GLN Chi-restraints excluded: chain C residue 1116 SER Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 297 optimal weight: 2.9990 chunk 304 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 chunk 126 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 148 optimal weight: 0.0020 chunk 259 optimal weight: 1.9990 chunk 214 optimal weight: 3.9990 chunk 237 optimal weight: 2.9990 chunk 343 optimal weight: 2.9990 overall best weight: 0.9970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN B 353 ASN B 598 ASN B 630 GLN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 998 ASN C 175 HIS C 470 ASN C 645 GLN C 881 ASN C 909 ASN C1059 GLN C1071 GLN C1181 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.114146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.096529 restraints weight = 41919.714| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.31 r_work: 0.3091 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28805 Z= 0.154 Angle : 0.537 8.944 39374 Z= 0.283 Chirality : 0.045 0.291 4546 Planarity : 0.004 0.042 4997 Dihedral : 5.801 57.045 4693 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 3.05 % Allowed : 11.73 % Favored : 85.22 % 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: -0.89 (0.14), residues: 3526 helix: 1.42 (0.20), residues: 769 sheet: 0.03 (0.19), residues: 692 loop : -1.69 (0.13), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 197 HIS 0.008 0.001 HIS B 201 PHE 0.019 0.002 PHE B 592 TYR 0.029 0.002 TYR B 203 ARG 0.004 0.000 ARG A 34 Details of bonding type rmsd link_NAG-ASN : bond 0.00260 ( 36) link_NAG-ASN : angle 1.52577 ( 108) link_BETA1-4 : bond 0.00328 ( 5) link_BETA1-4 : angle 1.60646 ( 15) hydrogen bonds : bond 0.04893 ( 945) hydrogen bonds : angle 4.75652 ( 2697) SS BOND : bond 0.00347 ( 69) SS BOND : angle 1.26348 ( 138) covalent geometry : bond 0.00362 (28695) covalent geometry : angle 0.52684 (39113) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 668 time to evaluate : 2.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7221 (p0) cc_final: 0.6611 (p0) REVERT: A 41 ASP cc_start: 0.8138 (t0) cc_final: 0.7729 (t0) REVERT: A 176 ILE cc_start: 0.8447 (mm) cc_final: 0.8139 (mm) REVERT: A 328 ASP cc_start: 0.7765 (m-30) cc_final: 0.7559 (m-30) REVERT: A 351 ASN cc_start: 0.8143 (OUTLIER) cc_final: 0.7902 (m-40) REVERT: A 443 SER cc_start: 0.8851 (p) cc_final: 0.8612 (m) REVERT: A 446 ARG cc_start: 0.8627 (mtm-85) cc_final: 0.8308 (mtm110) REVERT: A 500 LYS cc_start: 0.8488 (mtpp) cc_final: 0.8267 (mtpp) REVERT: A 521 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8446 (mm) REVERT: A 745 ASP cc_start: 0.8257 (t0) cc_final: 0.7975 (t0) REVERT: A 815 SER cc_start: 0.8640 (m) cc_final: 0.8372 (p) REVERT: A 828 LEU cc_start: 0.8759 (mt) cc_final: 0.8295 (mp) REVERT: A 1010 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8610 (ttmm) REVERT: A 1189 SER cc_start: 0.8310 (p) cc_final: 0.8066 (t) REVERT: B 34 ARG cc_start: 0.6648 (ttp80) cc_final: 0.6053 (ttp80) REVERT: B 66 TYR cc_start: 0.8154 (m-80) cc_final: 0.7279 (m-80) REVERT: B 76 ASP cc_start: 0.8571 (t0) cc_final: 0.8036 (t0) REVERT: B 147 GLU cc_start: 0.7127 (mm-30) cc_final: 0.6581 (mm-30) REVERT: B 205 GLU cc_start: 0.7863 (tt0) cc_final: 0.7155 (tt0) REVERT: B 265 GLN cc_start: 0.8593 (tt0) cc_final: 0.8320 (tt0) REVERT: B 418 ILE cc_start: 0.8519 (mm) cc_final: 0.8189 (mm) REVERT: B 442 SER cc_start: 0.8729 (t) cc_final: 0.8512 (m) REVERT: B 500 LYS cc_start: 0.8124 (mttm) cc_final: 0.7885 (mttm) REVERT: B 634 LYS cc_start: 0.8700 (tttp) cc_final: 0.8450 (ttpp) REVERT: B 682 TYR cc_start: 0.7596 (t80) cc_final: 0.7298 (t80) REVERT: B 712 TYR cc_start: 0.8934 (p90) cc_final: 0.8623 (p90) REVERT: B 800 GLU cc_start: 0.7763 (pm20) cc_final: 0.7472 (pm20) REVERT: B 830 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8298 (t) REVERT: B 845 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6853 (pp20) REVERT: B 848 ASP cc_start: 0.7721 (m-30) cc_final: 0.7290 (m-30) REVERT: B 955 ILE cc_start: 0.8424 (mm) cc_final: 0.8132 (mm) REVERT: B 999 LYS cc_start: 0.8817 (mttp) cc_final: 0.8565 (mttp) REVERT: B 1010 LYS cc_start: 0.8583 (ttpp) cc_final: 0.8278 (ttpp) REVERT: B 1031 SER cc_start: 0.8225 (p) cc_final: 0.7899 (m) REVERT: B 1064 ARG cc_start: 0.8395 (ttp80) cc_final: 0.8188 (ttp-170) REVERT: B 1165 SER cc_start: 0.8282 (p) cc_final: 0.7932 (m) REVERT: B 1173 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8342 (ptpp) REVERT: C 366 ASP cc_start: 0.7880 (t70) cc_final: 0.7509 (t0) REVERT: C 402 GLN cc_start: 0.7966 (mm-40) cc_final: 0.7717 (mm-40) REVERT: C 454 ASN cc_start: 0.7848 (t0) cc_final: 0.7372 (p0) REVERT: C 553 GLU cc_start: 0.7336 (mt-10) cc_final: 0.6805 (mt-10) REVERT: C 577 PHE cc_start: 0.7619 (p90) cc_final: 0.7125 (p90) REVERT: C 634 LYS cc_start: 0.8555 (tttm) cc_final: 0.8344 (tttm) REVERT: C 649 TYR cc_start: 0.8848 (m-80) cc_final: 0.8501 (m-80) REVERT: C 827 ASP cc_start: 0.8229 (m-30) cc_final: 0.7831 (m-30) REVERT: C 831 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7664 (mm-30) REVERT: C 885 LYS cc_start: 0.8548 (tptp) cc_final: 0.8174 (tptp) REVERT: C 912 LYS cc_start: 0.8493 (ttpp) cc_final: 0.8205 (ttpp) REVERT: C 998 ASN cc_start: 0.8409 (t0) cc_final: 0.8045 (t0) REVERT: C 1149 LYS cc_start: 0.8375 (tttt) cc_final: 0.8052 (tttm) REVERT: C 1179 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8379 (ttmm) REVERT: C 1200 LYS cc_start: 0.8121 (mmmt) cc_final: 0.7814 (mmmt) REVERT: C 1214 LYS cc_start: 0.8224 (mtpt) cc_final: 0.7943 (mtpp) outliers start: 95 outliers final: 71 residues processed: 712 average time/residue: 0.3907 time to fit residues: 443.2159 Evaluate side-chains 717 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 642 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 88 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 630 GLN Chi-restraints excluded: chain B residue 830 SER Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 290 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 279 optimal weight: 0.6980 chunk 227 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 190 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 146 optimal weight: 0.5980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A1071 GLN A1111 ASN B 353 ASN B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1045 GLN B1180 GLN C 470 ASN C 645 GLN C 881 ASN C 909 ASN C1059 GLN C1181 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.112988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.095658 restraints weight = 41589.419| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.28 r_work: 0.3080 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28805 Z= 0.175 Angle : 0.555 8.265 39374 Z= 0.292 Chirality : 0.045 0.415 4546 Planarity : 0.004 0.044 4997 Dihedral : 5.797 59.055 4693 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.31 % Allowed : 12.17 % Favored : 84.52 % 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: -0.83 (0.14), residues: 3526 helix: 1.46 (0.20), residues: 769 sheet: 0.02 (0.19), residues: 714 loop : -1.64 (0.13), residues: 2043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 197 HIS 0.008 0.001 HIS B 201 PHE 0.025 0.002 PHE C1186 TYR 0.024 0.002 TYR B 203 ARG 0.006 0.000 ARG B 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00239 ( 36) link_NAG-ASN : angle 1.66985 ( 108) link_BETA1-4 : bond 0.00247 ( 5) link_BETA1-4 : angle 1.50014 ( 15) hydrogen bonds : bond 0.05086 ( 945) hydrogen bonds : angle 4.73913 ( 2697) SS BOND : bond 0.00369 ( 69) SS BOND : angle 1.36903 ( 138) covalent geometry : bond 0.00413 (28695) covalent geometry : angle 0.54293 (39113) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 646 time to evaluate : 2.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7202 (p0) cc_final: 0.6561 (p0) REVERT: A 41 ASP cc_start: 0.8108 (t0) cc_final: 0.7684 (t0) REVERT: A 83 ILE cc_start: 0.8632 (OUTLIER) cc_final: 0.8424 (mm) REVERT: A 176 ILE cc_start: 0.8444 (mm) cc_final: 0.8145 (mm) REVERT: A 351 ASN cc_start: 0.8175 (OUTLIER) cc_final: 0.7906 (m-40) REVERT: A 443 SER cc_start: 0.8852 (p) cc_final: 0.8625 (m) REVERT: A 454 ASN cc_start: 0.8619 (t0) cc_final: 0.8214 (t0) REVERT: A 500 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8285 (mtpp) REVERT: A 521 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8386 (mm) REVERT: A 635 GLU cc_start: 0.8563 (tt0) cc_final: 0.8158 (tt0) REVERT: A 745 ASP cc_start: 0.8244 (t0) cc_final: 0.8006 (t0) REVERT: A 815 SER cc_start: 0.8611 (m) cc_final: 0.8278 (p) REVERT: A 828 LEU cc_start: 0.8795 (mt) cc_final: 0.8394 (mp) REVERT: A 1010 LYS cc_start: 0.8843 (ttmm) cc_final: 0.8615 (ttmm) REVERT: A 1189 SER cc_start: 0.8327 (p) cc_final: 0.8110 (t) REVERT: B 34 ARG cc_start: 0.6671 (ttp80) cc_final: 0.6102 (ttp80) REVERT: B 42 VAL cc_start: 0.8755 (m) cc_final: 0.8324 (t) REVERT: B 66 TYR cc_start: 0.8120 (m-80) cc_final: 0.7587 (m-80) REVERT: B 76 ASP cc_start: 0.8566 (t0) cc_final: 0.7940 (t0) REVERT: B 147 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6576 (mm-30) REVERT: B 265 GLN cc_start: 0.8583 (tt0) cc_final: 0.8344 (tt0) REVERT: B 280 VAL cc_start: 0.8702 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 418 ILE cc_start: 0.8515 (mm) cc_final: 0.8164 (mm) REVERT: B 442 SER cc_start: 0.8719 (t) cc_final: 0.8515 (m) REVERT: B 634 LYS cc_start: 0.8681 (tttp) cc_final: 0.8439 (ttpp) REVERT: B 673 TYR cc_start: 0.8571 (t80) cc_final: 0.8315 (t80) REVERT: B 682 TYR cc_start: 0.7612 (t80) cc_final: 0.7335 (t80) REVERT: B 712 TYR cc_start: 0.8923 (p90) cc_final: 0.8605 (p90) REVERT: B 800 GLU cc_start: 0.7758 (pm20) cc_final: 0.7462 (pm20) REVERT: B 830 SER cc_start: 0.8546 (m) cc_final: 0.8332 (t) REVERT: B 845 GLU cc_start: 0.7270 (OUTLIER) cc_final: 0.6803 (pp20) REVERT: B 848 ASP cc_start: 0.7740 (m-30) cc_final: 0.7360 (m-30) REVERT: B 955 ILE cc_start: 0.8433 (mm) cc_final: 0.8149 (mm) REVERT: B 999 LYS cc_start: 0.8828 (mttp) cc_final: 0.8582 (mttp) REVERT: B 1010 LYS cc_start: 0.8596 (ttpp) cc_final: 0.8330 (ttpp) REVERT: B 1031 SER cc_start: 0.8252 (p) cc_final: 0.7932 (m) REVERT: B 1064 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8205 (ttp-170) REVERT: B 1112 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8267 (mt-10) REVERT: B 1165 SER cc_start: 0.8285 (p) cc_final: 0.7952 (m) REVERT: B 1173 LYS cc_start: 0.8748 (ptpp) cc_final: 0.8323 (ptpp) REVERT: C 69 LYS cc_start: 0.8745 (tttm) cc_final: 0.8540 (ttpp) REVERT: C 366 ASP cc_start: 0.7921 (t70) cc_final: 0.7551 (t0) REVERT: C 402 GLN cc_start: 0.7989 (mm-40) cc_final: 0.7748 (mm-40) REVERT: C 454 ASN cc_start: 0.7911 (t0) cc_final: 0.7438 (p0) REVERT: C 553 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6832 (mt-10) REVERT: C 577 PHE cc_start: 0.7581 (p90) cc_final: 0.7090 (p90) REVERT: C 649 TYR cc_start: 0.8846 (m-80) cc_final: 0.8492 (m-80) REVERT: C 827 ASP cc_start: 0.8236 (m-30) cc_final: 0.7853 (m-30) REVERT: C 831 GLU cc_start: 0.7921 (mm-30) cc_final: 0.7644 (mm-30) REVERT: C 885 LYS cc_start: 0.8500 (tptp) cc_final: 0.8263 (tptp) REVERT: C 998 ASN cc_start: 0.8425 (t0) cc_final: 0.8024 (t0) REVERT: C 1112 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7752 (mt-10) REVERT: C 1149 LYS cc_start: 0.8379 (tttt) cc_final: 0.8060 (tttm) REVERT: C 1168 ARG cc_start: 0.8055 (mtm110) cc_final: 0.7815 (mtm180) REVERT: C 1179 LYS cc_start: 0.8795 (ttpt) cc_final: 0.8428 (ttmm) REVERT: C 1200 LYS cc_start: 0.8172 (mmmt) cc_final: 0.7904 (mmmt) REVERT: C 1214 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7994 (mtpp) outliers start: 103 outliers final: 76 residues processed: 688 average time/residue: 0.3660 time to fit residues: 401.7180 Evaluate side-chains 709 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 628 time to evaluate : 2.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 628 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 885 LYS Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1026 LEU Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 999 LYS Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 208 optimal weight: 0.0370 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 337 optimal weight: 0.7980 chunk 129 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 chunk 238 optimal weight: 2.9990 chunk 224 optimal weight: 0.6980 chunk 170 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A1071 GLN A1111 ASN B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 470 ASN C 645 GLN C 881 ASN C 909 ASN C1181 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.096626 restraints weight = 41555.992| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.29 r_work: 0.3094 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 28805 Z= 0.118 Angle : 0.522 8.746 39374 Z= 0.273 Chirality : 0.044 0.321 4546 Planarity : 0.004 0.042 4997 Dihedral : 5.588 59.226 4692 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.02 % Allowed : 13.49 % Favored : 83.49 % 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: -0.69 (0.14), residues: 3526 helix: 1.57 (0.20), residues: 773 sheet: 0.14 (0.19), residues: 697 loop : -1.56 (0.13), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 197 HIS 0.007 0.001 HIS B 201 PHE 0.022 0.001 PHE C1186 TYR 0.029 0.001 TYR B 203 ARG 0.005 0.000 ARG B 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 36) link_NAG-ASN : angle 1.50113 ( 108) link_BETA1-4 : bond 0.00300 ( 5) link_BETA1-4 : angle 1.38934 ( 15) hydrogen bonds : bond 0.04509 ( 945) hydrogen bonds : angle 4.63790 ( 2697) SS BOND : bond 0.00290 ( 69) SS BOND : angle 1.17863 ( 138) covalent geometry : bond 0.00270 (28695) covalent geometry : angle 0.51240 (39113) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 644 time to evaluate : 2.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7135 (p0) cc_final: 0.6494 (p0) REVERT: A 41 ASP cc_start: 0.8100 (t0) cc_final: 0.7675 (t0) REVERT: A 83 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8408 (mm) REVERT: A 176 ILE cc_start: 0.8394 (mm) cc_final: 0.8085 (mm) REVERT: A 351 ASN cc_start: 0.8121 (OUTLIER) cc_final: 0.7883 (m-40) REVERT: A 454 ASN cc_start: 0.8603 (t0) cc_final: 0.8191 (t0) REVERT: A 500 LYS cc_start: 0.8512 (mtpp) cc_final: 0.8274 (mtpp) REVERT: A 521 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8363 (mm) REVERT: A 635 GLU cc_start: 0.8542 (tt0) cc_final: 0.8133 (tt0) REVERT: A 745 ASP cc_start: 0.8229 (t0) cc_final: 0.8002 (t0) REVERT: A 813 ASP cc_start: 0.8053 (t0) cc_final: 0.7840 (t0) REVERT: A 815 SER cc_start: 0.8624 (m) cc_final: 0.8255 (p) REVERT: A 828 LEU cc_start: 0.8782 (mt) cc_final: 0.8275 (mp) REVERT: A 1010 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8601 (ttmm) REVERT: A 1189 SER cc_start: 0.8298 (p) cc_final: 0.8091 (t) REVERT: B 34 ARG cc_start: 0.6677 (ttp80) cc_final: 0.6200 (ttp80) REVERT: B 66 TYR cc_start: 0.8101 (m-80) cc_final: 0.7553 (m-80) REVERT: B 76 ASP cc_start: 0.8556 (t0) cc_final: 0.7878 (t0) REVERT: B 147 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6594 (mm-30) REVERT: B 265 GLN cc_start: 0.8586 (tt0) cc_final: 0.8344 (tt0) REVERT: B 280 VAL cc_start: 0.8679 (m) cc_final: 0.8411 (p) REVERT: B 418 ILE cc_start: 0.8505 (mm) cc_final: 0.8151 (mm) REVERT: B 634 LYS cc_start: 0.8684 (tttp) cc_final: 0.8440 (ttpp) REVERT: B 682 TYR cc_start: 0.7574 (t80) cc_final: 0.7302 (t80) REVERT: B 712 TYR cc_start: 0.8926 (p90) cc_final: 0.8614 (p90) REVERT: B 800 GLU cc_start: 0.7739 (pm20) cc_final: 0.7445 (pm20) REVERT: B 845 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6812 (pp20) REVERT: B 848 ASP cc_start: 0.7755 (m-30) cc_final: 0.7375 (m-30) REVERT: B 955 ILE cc_start: 0.8418 (mm) cc_final: 0.8126 (mm) REVERT: B 999 LYS cc_start: 0.8814 (mttp) cc_final: 0.8557 (mttp) REVERT: B 1010 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8321 (ttpp) REVERT: B 1031 SER cc_start: 0.8203 (p) cc_final: 0.7844 (m) REVERT: B 1045 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8119 (mp10) REVERT: B 1064 ARG cc_start: 0.8394 (ttp80) cc_final: 0.8158 (ttp-170) REVERT: B 1126 ASN cc_start: 0.8670 (p0) cc_final: 0.8441 (p0) REVERT: B 1165 SER cc_start: 0.8263 (p) cc_final: 0.7915 (m) REVERT: B 1173 LYS cc_start: 0.8727 (ptpp) cc_final: 0.8330 (ptpp) REVERT: C 69 LYS cc_start: 0.8731 (tttm) cc_final: 0.8528 (ttpp) REVERT: C 366 ASP cc_start: 0.7938 (t70) cc_final: 0.7555 (t0) REVERT: C 402 GLN cc_start: 0.7953 (mm-40) cc_final: 0.7713 (mm-40) REVERT: C 454 ASN cc_start: 0.7888 (t0) cc_final: 0.7422 (p0) REVERT: C 553 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6835 (mt-10) REVERT: C 649 TYR cc_start: 0.8824 (m-80) cc_final: 0.8466 (m-80) REVERT: C 827 ASP cc_start: 0.8222 (m-30) cc_final: 0.7842 (m-30) REVERT: C 831 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7650 (mm-30) REVERT: C 885 LYS cc_start: 0.8557 (tptp) cc_final: 0.8210 (tptp) REVERT: C 916 VAL cc_start: 0.8706 (m) cc_final: 0.8442 (t) REVERT: C 998 ASN cc_start: 0.8399 (t0) cc_final: 0.8001 (t0) REVERT: C 1112 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7726 (mt-10) REVERT: C 1149 LYS cc_start: 0.8366 (tttt) cc_final: 0.8046 (tttm) REVERT: C 1179 LYS cc_start: 0.8794 (ttpt) cc_final: 0.8477 (ttmm) REVERT: C 1200 LYS cc_start: 0.8147 (mmmt) cc_final: 0.7871 (mmmt) REVERT: C 1214 LYS cc_start: 0.8270 (mtpt) cc_final: 0.7977 (mtpp) outliers start: 94 outliers final: 70 residues processed: 686 average time/residue: 0.3693 time to fit residues: 406.9080 Evaluate side-chains 706 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 631 time to evaluate : 2.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1131 LEU Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 999 LYS Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 146 optimal weight: 0.0470 chunk 292 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 336 optimal weight: 0.0070 chunk 155 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 122 optimal weight: 0.3980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A1071 GLN A1111 ASN B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 ASN C 384 ASN C 645 GLN C 881 ASN C 909 ASN C1059 GLN C1181 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.114011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.096628 restraints weight = 41512.617| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.29 r_work: 0.3095 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28805 Z= 0.121 Angle : 0.520 7.270 39374 Z= 0.271 Chirality : 0.044 0.280 4546 Planarity : 0.004 0.041 4997 Dihedral : 5.493 56.494 4692 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.05 % Allowed : 13.75 % Favored : 83.20 % 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: -0.59 (0.14), residues: 3526 helix: 1.65 (0.20), residues: 772 sheet: 0.19 (0.19), residues: 700 loop : -1.49 (0.13), residues: 2054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 197 HIS 0.007 0.001 HIS B 201 PHE 0.021 0.001 PHE C1186 TYR 0.027 0.001 TYR B 203 ARG 0.005 0.000 ARG B 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 36) link_NAG-ASN : angle 1.47706 ( 108) link_BETA1-4 : bond 0.00346 ( 5) link_BETA1-4 : angle 1.37955 ( 15) hydrogen bonds : bond 0.04419 ( 945) hydrogen bonds : angle 4.56398 ( 2697) SS BOND : bond 0.00392 ( 69) SS BOND : angle 1.14025 ( 138) covalent geometry : bond 0.00279 (28695) covalent geometry : angle 0.51068 (39113) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 644 time to evaluate : 3.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 ASP cc_start: 0.7113 (p0) cc_final: 0.6488 (p0) REVERT: A 41 ASP cc_start: 0.8091 (t0) cc_final: 0.7675 (t0) REVERT: A 80 LYS cc_start: 0.8508 (tptp) cc_final: 0.8205 (tptp) REVERT: A 83 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8422 (mm) REVERT: A 176 ILE cc_start: 0.8363 (mm) cc_final: 0.8053 (mm) REVERT: A 351 ASN cc_start: 0.8109 (OUTLIER) cc_final: 0.7885 (m-40) REVERT: A 454 ASN cc_start: 0.8613 (t0) cc_final: 0.8215 (t0) REVERT: A 500 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8274 (mtpp) REVERT: A 521 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8354 (mm) REVERT: A 544 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7919 (mt-10) REVERT: A 635 GLU cc_start: 0.8541 (tt0) cc_final: 0.8117 (tt0) REVERT: A 745 ASP cc_start: 0.8241 (t0) cc_final: 0.8011 (t0) REVERT: A 813 ASP cc_start: 0.8071 (t0) cc_final: 0.7860 (t0) REVERT: A 815 SER cc_start: 0.8652 (m) cc_final: 0.8268 (p) REVERT: A 828 LEU cc_start: 0.8787 (mt) cc_final: 0.8280 (mp) REVERT: A 993 THR cc_start: 0.8661 (OUTLIER) cc_final: 0.8302 (p) REVERT: A 1010 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8604 (ttmm) REVERT: A 1189 SER cc_start: 0.8303 (p) cc_final: 0.8097 (t) REVERT: B 34 ARG cc_start: 0.6681 (ttp80) cc_final: 0.6275 (ttp80) REVERT: B 42 VAL cc_start: 0.8696 (m) cc_final: 0.8287 (t) REVERT: B 66 TYR cc_start: 0.8087 (m-80) cc_final: 0.7555 (m-80) REVERT: B 76 ASP cc_start: 0.8559 (t0) cc_final: 0.7923 (t0) REVERT: B 147 GLU cc_start: 0.7232 (mm-30) cc_final: 0.6613 (mm-30) REVERT: B 265 GLN cc_start: 0.8581 (tt0) cc_final: 0.8342 (tt0) REVERT: B 280 VAL cc_start: 0.8657 (OUTLIER) cc_final: 0.8380 (p) REVERT: B 418 ILE cc_start: 0.8498 (mm) cc_final: 0.8134 (mm) REVERT: B 634 LYS cc_start: 0.8675 (tttp) cc_final: 0.8432 (ttpp) REVERT: B 682 TYR cc_start: 0.7578 (t80) cc_final: 0.7315 (t80) REVERT: B 712 TYR cc_start: 0.8926 (p90) cc_final: 0.8613 (p90) REVERT: B 800 GLU cc_start: 0.7723 (pm20) cc_final: 0.7421 (pm20) REVERT: B 821 ASN cc_start: 0.8540 (t0) cc_final: 0.8292 (t0) REVERT: B 845 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6834 (pp20) REVERT: B 848 ASP cc_start: 0.7727 (m-30) cc_final: 0.7352 (m-30) REVERT: B 955 ILE cc_start: 0.8424 (mm) cc_final: 0.8128 (mm) REVERT: B 999 LYS cc_start: 0.8816 (mttp) cc_final: 0.8561 (mttp) REVERT: B 1010 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8300 (ttpp) REVERT: B 1031 SER cc_start: 0.8195 (p) cc_final: 0.7825 (m) REVERT: B 1064 ARG cc_start: 0.8440 (ttp80) cc_final: 0.8183 (ttp-170) REVERT: B 1126 ASN cc_start: 0.8670 (p0) cc_final: 0.8430 (p0) REVERT: B 1173 LYS cc_start: 0.8728 (ptpp) cc_final: 0.8350 (ptpp) REVERT: C 366 ASP cc_start: 0.7940 (t70) cc_final: 0.7560 (t0) REVERT: C 376 SER cc_start: 0.8873 (m) cc_final: 0.8485 (p) REVERT: C 402 GLN cc_start: 0.7948 (mm-40) cc_final: 0.7714 (mm-40) REVERT: C 454 ASN cc_start: 0.7854 (t0) cc_final: 0.7401 (p0) REVERT: C 553 GLU cc_start: 0.7362 (mt-10) cc_final: 0.6829 (mt-10) REVERT: C 649 TYR cc_start: 0.8841 (m-80) cc_final: 0.8477 (m-80) REVERT: C 827 ASP cc_start: 0.8228 (m-30) cc_final: 0.7846 (m-30) REVERT: C 831 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7639 (mm-30) REVERT: C 885 LYS cc_start: 0.8495 (tptp) cc_final: 0.8233 (tptp) REVERT: C 916 VAL cc_start: 0.8709 (m) cc_final: 0.8438 (t) REVERT: C 998 ASN cc_start: 0.8391 (t0) cc_final: 0.7984 (t0) REVERT: C 1112 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7731 (mt-10) REVERT: C 1149 LYS cc_start: 0.8372 (tttt) cc_final: 0.8048 (tttm) REVERT: C 1179 LYS cc_start: 0.8792 (ttpt) cc_final: 0.8474 (ttmm) REVERT: C 1200 LYS cc_start: 0.8162 (mmmt) cc_final: 0.7884 (mmmt) REVERT: C 1214 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7988 (mtpp) outliers start: 95 outliers final: 70 residues processed: 685 average time/residue: 0.3784 time to fit residues: 415.1344 Evaluate side-chains 712 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 636 time to evaluate : 2.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 34 ARG Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 351 ASN Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 726 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 913 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 528 TYR Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 967 MET Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 672 CYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 733 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 204 optimal weight: 0.0980 chunk 200 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 229 optimal weight: 0.5980 chunk 160 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 38 optimal weight: 0.0770 chunk 58 optimal weight: 6.9990 chunk 242 optimal weight: 0.0070 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A1071 GLN A1111 ASN B 353 ASN B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 ASN C 583 ASN C 645 GLN C 909 ASN C1059 GLN C1181 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.115421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.098026 restraints weight = 41591.813| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.30 r_work: 0.3119 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 28805 Z= 0.094 Angle : 0.502 8.693 39374 Z= 0.261 Chirality : 0.043 0.258 4546 Planarity : 0.004 0.042 4997 Dihedral : 5.303 55.250 4691 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.70 % Allowed : 14.49 % Favored : 82.81 % 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: -0.48 (0.14), residues: 3526 helix: 1.72 (0.20), residues: 779 sheet: 0.27 (0.19), residues: 711 loop : -1.43 (0.13), residues: 2036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 197 HIS 0.007 0.001 HIS B 201 PHE 0.018 0.001 PHE C1186 TYR 0.026 0.001 TYR B 203 ARG 0.005 0.000 ARG A 446 Details of bonding type rmsd link_NAG-ASN : bond 0.00207 ( 36) link_NAG-ASN : angle 1.37531 ( 108) link_BETA1-4 : bond 0.00371 ( 5) link_BETA1-4 : angle 1.28336 ( 15) hydrogen bonds : bond 0.03861 ( 945) hydrogen bonds : angle 4.42374 ( 2697) SS BOND : bond 0.00289 ( 69) SS BOND : angle 1.02439 ( 138) covalent geometry : bond 0.00206 (28695) covalent geometry : angle 0.49371 (39113) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 650 time to evaluate : 3.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 PHE cc_start: 0.8644 (t80) cc_final: 0.8199 (t80) REVERT: A 41 ASP cc_start: 0.8074 (t0) cc_final: 0.7637 (t0) REVERT: A 80 LYS cc_start: 0.8458 (tptp) cc_final: 0.8181 (tptp) REVERT: A 83 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8395 (mm) REVERT: A 176 ILE cc_start: 0.8335 (mm) cc_final: 0.8034 (mm) REVERT: A 446 ARG cc_start: 0.8581 (mtm-85) cc_final: 0.8127 (mtm110) REVERT: A 454 ASN cc_start: 0.8611 (t0) cc_final: 0.8213 (t0) REVERT: A 500 LYS cc_start: 0.8525 (mtpp) cc_final: 0.8295 (mtpp) REVERT: A 521 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8339 (mm) REVERT: A 544 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7951 (mt-10) REVERT: A 635 GLU cc_start: 0.8529 (tt0) cc_final: 0.8111 (tt0) REVERT: A 745 ASP cc_start: 0.8248 (t0) cc_final: 0.8002 (t0) REVERT: A 799 HIS cc_start: 0.7062 (m90) cc_final: 0.6740 (m90) REVERT: A 813 ASP cc_start: 0.8072 (t0) cc_final: 0.7869 (t0) REVERT: A 815 SER cc_start: 0.8652 (m) cc_final: 0.8274 (p) REVERT: A 828 LEU cc_start: 0.8779 (mt) cc_final: 0.8263 (mp) REVERT: A 874 ASN cc_start: 0.7646 (p0) cc_final: 0.7290 (p0) REVERT: A 993 THR cc_start: 0.8628 (OUTLIER) cc_final: 0.8288 (p) REVERT: A 1010 LYS cc_start: 0.8811 (ttmm) cc_final: 0.8601 (ttmm) REVERT: A 1189 SER cc_start: 0.8262 (p) cc_final: 0.8059 (t) REVERT: B 34 ARG cc_start: 0.6675 (ttp80) cc_final: 0.6433 (ttp80) REVERT: B 66 TYR cc_start: 0.8040 (m-80) cc_final: 0.7546 (m-80) REVERT: B 147 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6671 (mm-30) REVERT: B 209 PHE cc_start: 0.8099 (t80) cc_final: 0.7750 (t80) REVERT: B 265 GLN cc_start: 0.8566 (tt0) cc_final: 0.8303 (tt0) REVERT: B 280 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8311 (p) REVERT: B 418 ILE cc_start: 0.8491 (mm) cc_final: 0.8120 (mm) REVERT: B 634 LYS cc_start: 0.8633 (tttp) cc_final: 0.8394 (ttpp) REVERT: B 682 TYR cc_start: 0.7545 (t80) cc_final: 0.7285 (t80) REVERT: B 712 TYR cc_start: 0.8915 (p90) cc_final: 0.8619 (p90) REVERT: B 800 GLU cc_start: 0.7719 (pm20) cc_final: 0.7431 (pm20) REVERT: B 821 ASN cc_start: 0.8527 (t0) cc_final: 0.8255 (t0) REVERT: B 845 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6923 (pp20) REVERT: B 955 ILE cc_start: 0.8397 (mm) cc_final: 0.8109 (mm) REVERT: B 999 LYS cc_start: 0.8793 (mttp) cc_final: 0.8531 (mttp) REVERT: B 1010 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8299 (ttpp) REVERT: B 1031 SER cc_start: 0.8116 (p) cc_final: 0.7713 (m) REVERT: B 1064 ARG cc_start: 0.8375 (ttp80) cc_final: 0.8138 (ttp-170) REVERT: B 1112 GLU cc_start: 0.8369 (mt-10) cc_final: 0.8142 (mt-10) REVERT: B 1126 ASN cc_start: 0.8656 (p0) cc_final: 0.8416 (p0) REVERT: B 1173 LYS cc_start: 0.8742 (ptpp) cc_final: 0.8375 (ptpp) REVERT: C 250 ASP cc_start: 0.7819 (m-30) cc_final: 0.7475 (m-30) REVERT: C 366 ASP cc_start: 0.7952 (t70) cc_final: 0.7577 (t0) REVERT: C 376 SER cc_start: 0.8849 (m) cc_final: 0.8463 (p) REVERT: C 402 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7706 (mm-40) REVERT: C 435 THR cc_start: 0.7946 (m) cc_final: 0.7683 (t) REVERT: C 454 ASN cc_start: 0.7814 (t0) cc_final: 0.7370 (p0) REVERT: C 553 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6799 (mt-10) REVERT: C 649 TYR cc_start: 0.8817 (m-80) cc_final: 0.8449 (m-80) REVERT: C 827 ASP cc_start: 0.8212 (m-30) cc_final: 0.7815 (m-30) REVERT: C 831 GLU cc_start: 0.7952 (mm-30) cc_final: 0.7675 (mm-30) REVERT: C 885 LYS cc_start: 0.8471 (tptp) cc_final: 0.8213 (tptp) REVERT: C 916 VAL cc_start: 0.8615 (m) cc_final: 0.8332 (t) REVERT: C 1149 LYS cc_start: 0.8374 (tttt) cc_final: 0.8040 (tttm) REVERT: C 1179 LYS cc_start: 0.8769 (ttpt) cc_final: 0.8456 (ttmm) REVERT: C 1200 LYS cc_start: 0.8130 (mmmt) cc_final: 0.7851 (mmmt) REVERT: C 1214 LYS cc_start: 0.8273 (mtpt) cc_final: 0.7994 (mtpp) outliers start: 84 outliers final: 60 residues processed: 688 average time/residue: 0.3808 time to fit residues: 421.4813 Evaluate side-chains 699 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 634 time to evaluate : 3.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 164 LYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1060 GLU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain A residue 1094 SER Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 215 ASP Chi-restraints excluded: chain C residue 216 VAL Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 540 VAL Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 634 LYS Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 891 LEU Chi-restraints excluded: chain C residue 1010 LYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1069 GLU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 327 optimal weight: 2.9990 chunk 272 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 332 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 145 optimal weight: 0.0030 chunk 10 optimal weight: 1.9990 chunk 345 optimal weight: 0.8980 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 ASN ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 598 ASN B 941 ASN C 384 ASN C 445 ASN C 645 GLN C 838 ASN C 909 ASN C1059 GLN C1181 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.093751 restraints weight = 41791.254| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.29 r_work: 0.3046 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 28805 Z= 0.255 Angle : 0.632 10.793 39374 Z= 0.330 Chirality : 0.048 0.302 4546 Planarity : 0.004 0.050 4997 Dihedral : 5.858 57.408 4691 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.76 % Allowed : 14.62 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.69 (0.14), residues: 3526 helix: 1.51 (0.20), residues: 760 sheet: 0.14 (0.19), residues: 703 loop : -1.52 (0.13), residues: 2063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 197 HIS 0.008 0.002 HIS A 503 PHE 0.027 0.002 PHE B 592 TYR 0.026 0.002 TYR A 49 ARG 0.005 0.001 ARG C1168 Details of bonding type rmsd link_NAG-ASN : bond 0.00373 ( 36) link_NAG-ASN : angle 1.73844 ( 108) link_BETA1-4 : bond 0.00353 ( 5) link_BETA1-4 : angle 1.60215 ( 15) hydrogen bonds : bond 0.05810 ( 945) hydrogen bonds : angle 4.77695 ( 2697) SS BOND : bond 0.00427 ( 69) SS BOND : angle 1.69686 ( 138) covalent geometry : bond 0.00602 (28695) covalent geometry : angle 0.61809 (39113) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 652 time to evaluate : 2.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8151 (t0) cc_final: 0.7743 (t0) REVERT: A 83 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8449 (mm) REVERT: A 176 ILE cc_start: 0.8390 (mm) cc_final: 0.8072 (mm) REVERT: A 454 ASN cc_start: 0.8655 (t0) cc_final: 0.8276 (t0) REVERT: A 500 LYS cc_start: 0.8513 (mtpp) cc_final: 0.8287 (mtpp) REVERT: A 521 LEU cc_start: 0.8569 (mm) cc_final: 0.8257 (mm) REVERT: A 544 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7955 (mt-10) REVERT: A 613 GLU cc_start: 0.7835 (pm20) cc_final: 0.7405 (pm20) REVERT: A 635 GLU cc_start: 0.8598 (tt0) cc_final: 0.8270 (tt0) REVERT: A 745 ASP cc_start: 0.8248 (t0) cc_final: 0.8029 (t0) REVERT: A 815 SER cc_start: 0.8665 (m) cc_final: 0.8377 (p) REVERT: A 828 LEU cc_start: 0.8790 (mt) cc_final: 0.8417 (mp) REVERT: A 874 ASN cc_start: 0.7693 (p0) cc_final: 0.7334 (p0) REVERT: A 884 PHE cc_start: 0.7669 (m-10) cc_final: 0.7439 (m-10) REVERT: A 913 LEU cc_start: 0.8543 (mm) cc_final: 0.8265 (mt) REVERT: A 993 THR cc_start: 0.8654 (OUTLIER) cc_final: 0.8309 (p) REVERT: A 1010 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8631 (ttmm) REVERT: B 66 TYR cc_start: 0.8055 (m-80) cc_final: 0.7644 (m-80) REVERT: B 147 GLU cc_start: 0.7438 (mm-30) cc_final: 0.6793 (mm-30) REVERT: B 205 GLU cc_start: 0.7932 (tt0) cc_final: 0.6894 (tt0) REVERT: B 265 GLN cc_start: 0.8584 (tt0) cc_final: 0.8321 (tt0) REVERT: B 277 THR cc_start: 0.8812 (m) cc_final: 0.8588 (m) REVERT: B 280 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8468 (p) REVERT: B 418 ILE cc_start: 0.8531 (mm) cc_final: 0.8278 (mm) REVERT: B 634 LYS cc_start: 0.8695 (tttp) cc_final: 0.8460 (ttpp) REVERT: B 682 TYR cc_start: 0.7666 (t80) cc_final: 0.7412 (t80) REVERT: B 712 TYR cc_start: 0.8928 (p90) cc_final: 0.8598 (p90) REVERT: B 821 ASN cc_start: 0.8643 (t0) cc_final: 0.8387 (t0) REVERT: B 845 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7140 (pp20) REVERT: B 955 ILE cc_start: 0.8469 (mm) cc_final: 0.8157 (mm) REVERT: B 999 LYS cc_start: 0.8801 (mttp) cc_final: 0.8541 (mttp) REVERT: B 1010 LYS cc_start: 0.8621 (ttpp) cc_final: 0.8356 (ttpp) REVERT: B 1031 SER cc_start: 0.8390 (p) cc_final: 0.8120 (m) REVERT: B 1064 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8229 (ttp-170) REVERT: B 1126 ASN cc_start: 0.8740 (p0) cc_final: 0.8538 (p0) REVERT: B 1165 SER cc_start: 0.8294 (p) cc_final: 0.7991 (m) REVERT: B 1173 LYS cc_start: 0.8763 (ptpp) cc_final: 0.8398 (ptpp) REVERT: C 250 ASP cc_start: 0.7826 (m-30) cc_final: 0.7487 (m-30) REVERT: C 402 GLN cc_start: 0.7994 (mm-40) cc_final: 0.7728 (mm-40) REVERT: C 454 ASN cc_start: 0.7890 (t0) cc_final: 0.7455 (p0) REVERT: C 553 GLU cc_start: 0.7335 (mt-10) cc_final: 0.6781 (mt-10) REVERT: C 649 TYR cc_start: 0.8815 (m-80) cc_final: 0.8470 (m-80) REVERT: C 827 ASP cc_start: 0.8270 (m-30) cc_final: 0.7894 (m-30) REVERT: C 885 LYS cc_start: 0.8559 (tptp) cc_final: 0.8075 (tptp) REVERT: C 912 LYS cc_start: 0.8595 (ttpp) cc_final: 0.8187 (ttpp) REVERT: C 916 VAL cc_start: 0.8726 (m) cc_final: 0.8421 (t) REVERT: C 1126 ASN cc_start: 0.8431 (p0) cc_final: 0.8133 (p0) REVERT: C 1149 LYS cc_start: 0.8384 (tttt) cc_final: 0.8067 (tttm) REVERT: C 1179 LYS cc_start: 0.8802 (ttpt) cc_final: 0.8406 (ttmm) REVERT: C 1200 LYS cc_start: 0.8197 (mmmt) cc_final: 0.7958 (mmmt) REVERT: C 1214 LYS cc_start: 0.8296 (mtpt) cc_final: 0.8010 (mtpp) outliers start: 86 outliers final: 66 residues processed: 695 average time/residue: 0.3616 time to fit residues: 401.7981 Evaluate side-chains 700 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 630 time to evaluate : 3.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 772 VAL Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 540 VAL Chi-restraints excluded: chain B residue 573 LEU Chi-restraints excluded: chain B residue 618 VAL Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 863 GLN Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1159 SER Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 610 SER Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 903 LEU Chi-restraints excluded: chain C residue 999 LYS Chi-restraints excluded: chain C residue 1002 LYS Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1156 VAL Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 94 optimal weight: 0.1980 chunk 149 optimal weight: 0.0670 chunk 73 optimal weight: 0.9990 chunk 283 optimal weight: 9.9990 chunk 144 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 338 optimal weight: 1.9990 chunk 92 optimal weight: 0.0770 chunk 176 optimal weight: 3.9990 chunk 120 optimal weight: 0.0870 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A 988 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 ASN B1045 GLN B1059 GLN B1086 ASN C 583 ASN C 642 ASN C 645 GLN C 838 ASN C 909 ASN C 982 ASN C1059 GLN C1181 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.114277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.096808 restraints weight = 41458.627| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.32 r_work: 0.3099 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 28805 Z= 0.103 Angle : 0.531 9.332 39374 Z= 0.278 Chirality : 0.044 0.277 4546 Planarity : 0.004 0.044 4997 Dihedral : 5.442 55.282 4689 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.06 % Allowed : 15.42 % Favored : 82.52 % 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: -0.50 (0.14), residues: 3526 helix: 1.66 (0.20), residues: 780 sheet: 0.26 (0.19), residues: 707 loop : -1.42 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 197 HIS 0.008 0.001 HIS B 201 PHE 0.016 0.001 PHE C1186 TYR 0.029 0.001 TYR B 203 ARG 0.007 0.000 ARG B 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00247 ( 36) link_NAG-ASN : angle 1.46235 ( 108) link_BETA1-4 : bond 0.00438 ( 5) link_BETA1-4 : angle 1.33886 ( 15) hydrogen bonds : bond 0.04159 ( 945) hydrogen bonds : angle 4.52596 ( 2697) SS BOND : bond 0.00440 ( 69) SS BOND : angle 1.39655 ( 138) covalent geometry : bond 0.00228 (28695) covalent geometry : angle 0.52036 (39113) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7052 Ramachandran restraints generated. 3526 Oldfield, 0 Emsley, 3526 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 631 time to evaluate : 2.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ASP cc_start: 0.8132 (t0) cc_final: 0.7694 (t0) REVERT: A 80 LYS cc_start: 0.8525 (tptp) cc_final: 0.8251 (tptp) REVERT: A 83 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8416 (mm) REVERT: A 176 ILE cc_start: 0.8384 (mm) cc_final: 0.8047 (mm) REVERT: A 454 ASN cc_start: 0.8626 (t0) cc_final: 0.8246 (t0) REVERT: A 500 LYS cc_start: 0.8567 (mtpp) cc_final: 0.8338 (mtpp) REVERT: A 521 LEU cc_start: 0.8539 (mm) cc_final: 0.8197 (mm) REVERT: A 544 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7970 (mt-10) REVERT: A 613 GLU cc_start: 0.7819 (pm20) cc_final: 0.7387 (pm20) REVERT: A 635 GLU cc_start: 0.8546 (tt0) cc_final: 0.8329 (tt0) REVERT: A 636 VAL cc_start: 0.8704 (p) cc_final: 0.8443 (m) REVERT: A 745 ASP cc_start: 0.8262 (t0) cc_final: 0.8060 (t0) REVERT: A 799 HIS cc_start: 0.7066 (m90) cc_final: 0.6737 (m90) REVERT: A 815 SER cc_start: 0.8646 (m) cc_final: 0.8369 (p) REVERT: A 874 ASN cc_start: 0.7677 (p0) cc_final: 0.7317 (p0) REVERT: A 913 LEU cc_start: 0.8462 (mm) cc_final: 0.8211 (mt) REVERT: A 993 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8252 (p) REVERT: A 1010 LYS cc_start: 0.8782 (ttmm) cc_final: 0.8565 (ttmm) REVERT: B 66 TYR cc_start: 0.8060 (m-80) cc_final: 0.7759 (m-80) REVERT: B 75 ARG cc_start: 0.8445 (mtm-85) cc_final: 0.8070 (mtp-110) REVERT: B 147 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6759 (mm-30) REVERT: B 205 GLU cc_start: 0.7797 (tt0) cc_final: 0.7014 (tt0) REVERT: B 265 GLN cc_start: 0.8560 (tt0) cc_final: 0.8240 (tt0) REVERT: B 266 TYR cc_start: 0.8238 (m-80) cc_final: 0.7979 (m-10) REVERT: B 277 THR cc_start: 0.8780 (m) cc_final: 0.8554 (m) REVERT: B 280 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8353 (p) REVERT: B 289 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7481 (mt-10) REVERT: B 418 ILE cc_start: 0.8491 (mm) cc_final: 0.8229 (mm) REVERT: B 634 LYS cc_start: 0.8689 (tttp) cc_final: 0.8450 (ttpp) REVERT: B 682 TYR cc_start: 0.7581 (t80) cc_final: 0.7368 (t80) REVERT: B 712 TYR cc_start: 0.8903 (p90) cc_final: 0.8596 (p90) REVERT: B 821 ASN cc_start: 0.8573 (t0) cc_final: 0.8359 (t0) REVERT: B 845 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6795 (pp20) REVERT: B 848 ASP cc_start: 0.7797 (m-30) cc_final: 0.7432 (m-30) REVERT: B 955 ILE cc_start: 0.8406 (mm) cc_final: 0.8102 (mm) REVERT: B 999 LYS cc_start: 0.8741 (mttp) cc_final: 0.8459 (mttp) REVERT: B 1010 LYS cc_start: 0.8592 (ttpp) cc_final: 0.8335 (ttpp) REVERT: B 1031 SER cc_start: 0.8167 (p) cc_final: 0.7787 (m) REVERT: B 1064 ARG cc_start: 0.8428 (ttp80) cc_final: 0.8154 (ttp-170) REVERT: B 1126 ASN cc_start: 0.8674 (p0) cc_final: 0.8433 (p0) REVERT: B 1173 LYS cc_start: 0.8744 (ptpp) cc_final: 0.8478 (ptpp) REVERT: C 250 ASP cc_start: 0.7806 (m-30) cc_final: 0.7458 (m-30) REVERT: C 366 ASP cc_start: 0.7965 (t70) cc_final: 0.7578 (t0) REVERT: C 376 SER cc_start: 0.8864 (m) cc_final: 0.8481 (p) REVERT: C 402 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7715 (mm-40) REVERT: C 454 ASN cc_start: 0.7818 (t0) cc_final: 0.7406 (p0) REVERT: C 553 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6785 (mt-10) REVERT: C 649 TYR cc_start: 0.8789 (m-80) cc_final: 0.8391 (m-80) REVERT: C 827 ASP cc_start: 0.8212 (m-30) cc_final: 0.7815 (m-30) REVERT: C 831 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7685 (mm-30) REVERT: C 885 LYS cc_start: 0.8446 (tptp) cc_final: 0.8000 (tptp) REVERT: C 912 LYS cc_start: 0.8540 (ttpp) cc_final: 0.8128 (ttpp) REVERT: C 1126 ASN cc_start: 0.8403 (p0) cc_final: 0.8084 (p0) REVERT: C 1149 LYS cc_start: 0.8353 (tttt) cc_final: 0.8025 (tttm) REVERT: C 1179 LYS cc_start: 0.8778 (ttpt) cc_final: 0.8460 (ttmm) REVERT: C 1200 LYS cc_start: 0.8148 (mmmt) cc_final: 0.7892 (mmmt) REVERT: C 1214 LYS cc_start: 0.8293 (mtpt) cc_final: 0.8031 (mtpp) outliers start: 64 outliers final: 52 residues processed: 664 average time/residue: 0.3721 time to fit residues: 396.5524 Evaluate side-chains 678 residues out of total 3179 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 622 time to evaluate : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 161 THR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 292 CYS Chi-restraints excluded: chain A residue 601 THR Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 743 CYS Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 835 PHE Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 996 VAL Chi-restraints excluded: chain A residue 997 LEU Chi-restraints excluded: chain A residue 1093 LEU Chi-restraints excluded: chain B residue 20 CYS Chi-restraints excluded: chain B residue 186 LYS Chi-restraints excluded: chain B residue 213 TYR Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 483 ASN Chi-restraints excluded: chain B residue 799 HIS Chi-restraints excluded: chain B residue 845 GLU Chi-restraints excluded: chain B residue 920 GLU Chi-restraints excluded: chain B residue 1045 GLN Chi-restraints excluded: chain B residue 1086 ASN Chi-restraints excluded: chain B residue 1091 GLN Chi-restraints excluded: chain B residue 1099 ILE Chi-restraints excluded: chain B residue 1163 CYS Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 272 GLU Chi-restraints excluded: chain C residue 335 ASN Chi-restraints excluded: chain C residue 481 VAL Chi-restraints excluded: chain C residue 527 THR Chi-restraints excluded: chain C residue 601 THR Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 677 VAL Chi-restraints excluded: chain C residue 690 LEU Chi-restraints excluded: chain C residue 730 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 830 SER Chi-restraints excluded: chain C residue 999 LYS Chi-restraints excluded: chain C residue 1026 LEU Chi-restraints excluded: chain C residue 1131 LEU Chi-restraints excluded: chain C residue 1218 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 353 random chunks: chunk 246 optimal weight: 3.9990 chunk 129 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 0.0470 chunk 248 optimal weight: 2.9990 chunk 278 optimal weight: 0.8980 chunk 165 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 309 optimal weight: 2.9990 chunk 215 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.7478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 GLN A1016 GLN ** A1071 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1111 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 ASN B 598 ASN ** B 863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 941 ASN B1045 GLN B1059 GLN B1079 ASN B1086 ASN C 645 GLN C 838 ASN C 909 ASN C1059 GLN C1181 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097027 restraints weight = 41672.317| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.29 r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.199 28805 Z= 0.167 Angle : 0.777 59.200 39374 Z= 0.458 Chirality : 0.044 0.540 4546 Planarity : 0.004 0.057 4997 Dihedral : 5.446 55.293 4689 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.99 % Allowed : 15.42 % Favored : 82.59 % Cbeta Deviations : 0.06 % 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: -0.51 (0.14), residues: 3526 helix: 1.62 (0.20), residues: 780 sheet: 0.26 (0.19), residues: 707 loop : -1.41 (0.13), residues: 2039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 197 HIS 0.008 0.001 HIS B 201 PHE 0.023 0.001 PHE A 884 TYR 0.027 0.001 TYR B 203 ARG 0.006 0.000 ARG B 361 Details of bonding type rmsd link_NAG-ASN : bond 0.00238 ( 36) link_NAG-ASN : angle 1.46604 ( 108) link_BETA1-4 : bond 0.00333 ( 5) link_BETA1-4 : angle 1.33735 ( 15) hydrogen bonds : bond 0.04252 ( 945) hydrogen bonds : angle 4.52835 ( 2697) SS BOND : bond 0.00631 ( 69) SS BOND : angle 1.61484 ( 138) covalent geometry : bond 0.00355 (28695) covalent geometry : angle 0.76904 (39113) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15745.19 seconds wall clock time: 273 minutes 2.94 seconds (16382.94 seconds total)