Starting phenix.real_space_refine on Mon May 26 05:45:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8g_39045/05_2025/8y8g_39045.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8g_39045/05_2025/8y8g_39045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y8g_39045/05_2025/8y8g_39045.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8g_39045/05_2025/8y8g_39045.map" model { file = "/net/cci-nas-00/data/ceres_data/8y8g_39045/05_2025/8y8g_39045.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8g_39045/05_2025/8y8g_39045.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.066 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 162 5.16 5 C 17737 2.51 5 N 4508 2.21 5 O 5421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 27828 Number of models: 1 Model: "" Number of chains: 11 Chain: "C" Number of atoms: 9108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1172, 9108 Classifications: {'peptide': 1172} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1115} Chain breaks: 4 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 26 Chain: "A" Number of atoms: 9073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1170, 9073 Classifications: {'peptide': 1170} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1113} Chain breaks: 5 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 3, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 9216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1185, 9216 Classifications: {'peptide': 1185} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PCIS': 3, 'PTRANS': 53, 'TRANS': 1128} Chain breaks: 3 Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 35 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: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 16.71, per 1000 atoms: 0.60 Number of scatterers: 27828 At special positions: 0 Unit cell: (147.6, 153.34, 209.92, 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 162 16.00 O 5421 8.00 N 4508 7.00 C 17737 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=67, symmetry=0 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 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 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 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 485 " - pdb=" SG CYS B 516 " distance=2.03 Simple disulfide: pdb=" SG CYS B 504 " - pdb=" SG CYS B 518 " 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 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 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 H 1 " - " NAG H 2 " NAG-ASN " NAG A1301 " - " ASN A 188 " " NAG A1302 " - " ASN A 192 " " NAG A1303 " - " ASN A 335 " " NAG A1304 " - " ASN A 664 " " NAG A1305 " - " ASN A 793 " " NAG A1306 " - " ASN A 355 " " NAG A1307 " - " ASN A1211 " " NAG A1308 " - " ASN A 58 " " NAG B1301 " - " ASN B 192 " " NAG B1302 " - " ASN B 664 " " NAG B1303 " - " ASN B 725 " " NAG B1304 " - " ASN B 793 " " NAG C1301 " - " ASN C 192 " " NAG C1302 " - " ASN C 664 " " NAG C1303 " - " ASN C 703 " " NAG C1304 " - " ASN C 725 " " NAG C1305 " - " ASN C 793 " " NAG C1306 " - " ASN C 355 " " NAG C1307 " - " ASN C1211 " " NAG C1308 " - " ASN C 19 " " NAG D 1 " - " ASN C 188 " " NAG E 1 " - " ASN C 335 " " NAG F 1 " - " ASN C 132 " " NAG G 1 " - " ASN A 725 " " NAG H 1 " - " ASN B 132 " Time building additional restraints: 6.99 Conformation dependent library (CDL) restraints added in 4.0 seconds 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6646 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 59 sheets defined 23.4% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.13 Creating SS restraints... Processing helix chain 'C' and resid 87 through 91 removed outlier: 3.687A pdb=" N TYR C 90 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS C 91 " --> pdb=" O LEU C 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 87 through 91' Processing helix chain 'C' and resid 285 through 295 removed outlier: 3.626A pdb=" N GLU C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 290 " --> pdb=" O PHE C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 334 removed outlier: 3.794A pdb=" N TRP C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.773A pdb=" N ILE C 378 " --> pdb=" O LYS C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 568 through 570 No H-bonds generated for 'chain 'C' and resid 568 through 570' Processing helix chain 'C' and resid 696 through 704 removed outlier: 3.932A pdb=" N ASN C 702 " --> pdb=" O SER C 698 " (cutoff:3.500A) Processing helix chain 'C' and resid 813 through 818 removed outlier: 3.882A pdb=" N PHE C 817 " --> pdb=" O ASP C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 822 through 830 removed outlier: 4.000A pdb=" N LEU C 828 " --> pdb=" O ALA C 824 " (cutoff:3.500A) Processing helix chain 'C' and resid 833 through 861 removed outlier: 3.608A pdb=" N ASP C 837 " --> pdb=" O GLY C 833 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE C 839 " --> pdb=" O PHE C 835 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASN C 840 " --> pdb=" O CYS C 836 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN C 844 " --> pdb=" O ASN C 840 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 854 " --> pdb=" O LEU C 850 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 909 removed outlier: 3.891A pdb=" N LEU C 906 " --> pdb=" O PRO C 902 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU C 907 " --> pdb=" O LEU C 903 " (cutoff:3.500A) Processing helix chain 'C' and resid 916 through 924 Processing helix chain 'C' and resid 933 through 940 Processing helix chain 'C' and resid 951 through 965 Processing helix chain 'C' and resid 978 through 991 removed outlier: 4.236A pdb=" N GLN C 984 " --> pdb=" O PRO C 980 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR C 985 " --> pdb=" O LEU C 981 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU C 990 " --> pdb=" O ARG C 986 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLY C 991 " --> pdb=" O ILE C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.771A pdb=" N LEU C 997 " --> pdb=" O THR C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1000 through 1019 removed outlier: 3.519A pdb=" N ASN C1009 " --> pdb=" O ALA C1005 " (cutoff:3.500A) Processing helix chain 'C' and resid 1023 through 1045 removed outlier: 3.954A pdb=" N LYS C1028 " --> pdb=" O SER C1024 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER C1031 " --> pdb=" O ALA C1027 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N VAL C1033 " --> pdb=" O ILE C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1046 through 1049 removed outlier: 3.529A 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 1066 through 1113 removed outlier: 5.096A pdb=" N VAL C1072 " --> pdb=" O PRO C1068 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLN C1073 " --> pdb=" O GLU C1069 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C1077 " --> pdb=" O GLN C1073 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR C1097 " --> pdb=" O LEU C1093 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU C1098 " --> pdb=" O SER C1094 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 removed outlier: 3.511A pdb=" N TRP A 89 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 91 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 295 removed outlier: 3.509A pdb=" N GLU A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 334 removed outlier: 3.666A pdb=" N LEU A 333 " --> pdb=" O ILE A 329 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASN A 334 " --> pdb=" O ASP A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.692A pdb=" N LEU A 401 " --> pdb=" O ARG A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 413 Processing helix chain 'A' and resid 442 through 448 removed outlier: 3.880A pdb=" N ARG A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR A 448 " --> pdb=" O TRP A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 482 removed outlier: 3.614A pdb=" N VAL A 481 " --> pdb=" O ASP A 478 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 482 " --> pdb=" O PRO A 479 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 478 through 482' 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 814 through 819 removed outlier: 3.660A pdb=" N VAL A 818 " --> pdb=" O CYS A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 830 removed outlier: 3.562A pdb=" N HIS A 826 " --> pdb=" O TYR A 822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP A 827 " --> pdb=" O ALA A 823 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU A 828 " --> pdb=" O ALA A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 862 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 878 through 882 removed outlier: 4.003A pdb=" N ASN A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 888 removed outlier: 3.502A pdb=" N LEU A 888 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 909 removed outlier: 3.819A pdb=" N LEU A 906 " --> pdb=" O PRO A 902 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU A 907 " --> pdb=" O LEU A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 924 removed outlier: 3.871A pdb=" N VAL A 919 " --> pdb=" O ASP A 915 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 940 removed outlier: 3.655A pdb=" N VAL A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN A 938 " --> pdb=" O LEU A 934 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 939 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 965 Processing helix chain 'A' and resid 978 through 989 removed outlier: 3.724A pdb=" N GLN A 984 " --> pdb=" O PRO A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1000 removed outlier: 3.803A pdb=" N ASN A 998 " --> pdb=" O MET A 994 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LYS A 999 " --> pdb=" O ASP A 995 " (cutoff:3.500A) Processing helix chain 'A' and resid 1000 through 1018 removed outlier: 3.600A pdb=" N GLN A1016 " --> pdb=" O LEU A1012 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A1018 " --> pdb=" O SER A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1045 removed outlier: 3.548A pdb=" N VAL A1032 " --> pdb=" O LYS A1028 " (cutoff:3.500A) removed outlier: 3.805A 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 1060 through 1065 Processing helix chain 'A' and resid 1066 through 1114 removed outlier: 3.518A pdb=" N GLN A1071 " --> pdb=" O PRO A1067 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N VAL A1072 " --> pdb=" O PRO A1068 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN A1073 " --> pdb=" O GLU A1069 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU A1077 " --> pdb=" O GLN A1073 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N THR A1097 " --> pdb=" O LEU A1093 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU A1098 " --> pdb=" O SER A1094 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1099 " --> pdb=" O ASP A1095 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG A1105 " --> pdb=" O ALA A1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 46 removed outlier: 3.615A pdb=" N GLY B 45 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.953A pdb=" N GLU B 289 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE B 290 " --> pdb=" O PHE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 334 removed outlier: 3.624A pdb=" N TRP B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.598A pdb=" N LEU B 401 " --> pdb=" O ARG B 398 " (cutoff:3.500A) removed outlier: 3.940A 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: 4.139A pdb=" N ARG B 446 " --> pdb=" O SER B 442 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR B 448 " --> pdb=" O TRP B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 553 through 556 removed outlier: 3.591A pdb=" N CYS B 556 " --> pdb=" O GLU B 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 553 through 556' Processing helix chain 'B' and resid 568 through 570 No H-bonds generated for 'chain 'B' and resid 568 through 570' Processing helix chain 'B' and resid 696 through 701 Processing helix chain 'B' and resid 813 through 819 removed outlier: 3.764A pdb=" N PHE B 817 " --> pdb=" O ASP B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 822 through 830 removed outlier: 3.706A pdb=" N HIS B 826 " --> pdb=" O TYR B 822 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ASP B 827 " --> pdb=" O ALA B 823 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU B 828 " --> pdb=" O ALA B 824 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU B 829 " --> pdb=" O CYS B 825 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 836 removed outlier: 3.657A pdb=" N CYS B 836 " --> pdb=" O GLY B 833 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 833 through 836' Processing helix chain 'B' and resid 837 through 862 removed outlier: 3.513A pdb=" N LEU B 843 " --> pdb=" O ILE B 839 " (cutoff:3.500A) Processing helix chain 'B' and resid 878 through 882 removed outlier: 4.116A pdb=" N ASN B 881 " --> pdb=" O ASP B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 884 through 888 Processing helix chain 'B' and resid 901 through 909 removed outlier: 3.602A pdb=" N LEU B 906 " --> pdb=" O PRO B 902 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU B 907 " --> pdb=" O LEU B 903 " (cutoff:3.500A) Processing helix chain 'B' and resid 914 through 924 removed outlier: 3.514A pdb=" N PHE B 918 " --> pdb=" O SER B 914 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL B 919 " --> pdb=" O ASP B 915 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 941 removed outlier: 4.213A 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 978 through 989 removed outlier: 3.604A pdb=" N GLN B 984 " --> pdb=" O PRO B 980 " (cutoff:3.500A) Processing helix chain 'B' and resid 993 through 1000 removed outlier: 3.841A pdb=" N LEU B 997 " --> pdb=" O THR B 993 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS B 999 " --> pdb=" O ASP B 995 " (cutoff:3.500A) Processing helix chain 'B' and resid 1000 through 1019 removed outlier: 3.593A pdb=" N ILE B1004 " --> pdb=" O ASN B1000 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN B1009 " --> pdb=" O ALA B1005 " (cutoff:3.500A) Processing helix chain 'B' and resid 1023 through 1045 removed outlier: 3.529A pdb=" N VAL B1032 " --> pdb=" O LYS B1028 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B1033 " --> pdb=" O ILE B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1046 through 1049 removed outlier: 3.719A pdb=" N ASN B1049 " --> pdb=" O GLN B1046 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1046 through 1049' Processing helix chain 'B' and resid 1057 through 1062 removed outlier: 3.625A pdb=" N ILE B1061 " --> pdb=" O SER B1057 " (cutoff:3.500A) Processing helix chain 'B' and resid 1066 through 1113 removed outlier: 3.775A pdb=" N GLN B1071 " --> pdb=" O PRO B1067 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N VAL B1072 " --> pdb=" O PRO B1068 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N GLN B1073 " --> pdb=" O GLU B1069 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ARG B1076 " --> pdb=" O VAL B1072 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU B1077 " --> pdb=" O GLN B1073 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B1080 " --> pdb=" O ARG B1076 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER B1094 " --> pdb=" O SER B1090 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR B1097 " --> pdb=" O LEU B1093 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU B1098 " --> pdb=" O SER B1094 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE B1099 " --> pdb=" O ASP B1095 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B1105 " --> pdb=" O ALA B1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 60 through 67 removed outlier: 6.584A pdb=" N ASN C 269 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 75 through 76 removed outlier: 3.773A pdb=" N TYR C 199 " --> pdb=" O ALA C 214 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA C 211 " --> pdb=" O PHE C 224 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 224 " --> pdb=" O ALA C 211 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR C 213 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE C 222 " --> pdb=" O TYR C 213 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 80 through 81 removed outlier: 6.052A pdb=" N THR C 161 " --> pdb=" O THR C 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.509A pdb=" N THR C 109 " --> pdb=" O GLU C 120 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N GLU C 120 " --> pdb=" O THR C 109 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 183 through 190 removed outlier: 3.874A pdb=" N PHE C 185 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS C 151 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL C 125 " --> pdb=" O TYR C 236 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 302 through 310 removed outlier: 4.467A pdb=" N VAL C 677 " --> pdb=" O LEU C 306 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLY C 308 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLY C 675 " --> pdb=" O GLY C 308 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N ARG C 676 " --> pdb=" O ARG C 693 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ARG C 693 " --> pdb=" O ARG C 676 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N CYS C 719 " --> pdb=" O TYR C 692 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE C 713 " --> pdb=" O VAL C 720 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 316 through 319 removed outlier: 7.514A pdb=" N VAL C 317 " --> pdb=" O ASP C 623 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL C 620 " --> pdb=" O GLY C 631 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLY C 631 " --> pdb=" O VAL C 620 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 629 " --> pdb=" O TYR C 622 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N THR C 666 " --> pdb=" O VAL C 636 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR C 667 " --> pdb=" O PHE C 658 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE C 658 " --> pdb=" O TYR C 667 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE C 656 " --> pdb=" O ILE C 669 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 657 " --> pdb=" O LEU C 648 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 337 through 338 Processing sheet with id=AA9, first strand: chain 'C' and resid 345 through 349 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 345 through 349 current: chain 'C' and resid 585 through 595 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 353 through 354 removed outlier: 3.687A pdb=" N PHE C 354 " --> pdb=" O CYS C 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 467 through 468 removed outlier: 3.742A pdb=" N LYS C 536 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 550 through 551 removed outlier: 3.859A pdb=" N GLY C 550 " --> pdb=" O LEU C 573 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU C 573 " --> pdb=" O GLY C 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 724 through 725 removed outlier: 6.744A pdb=" N VAL C 724 " --> pdb=" O PHE C 764 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N THR C 766 " --> pdb=" O VAL C 724 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 773 through 775 removed outlier: 6.019A pdb=" N SER C 773 " --> pdb=" O LEU B 867 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 786 through 791 removed outlier: 4.022A pdb=" N ILE C 788 " --> pdb=" O VAL C1156 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C1156 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU C1157 " --> pdb=" O LYS C1179 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS C1179 " --> pdb=" O LEU C1157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 794 through 803 removed outlier: 3.646A pdb=" N LYS C1149 " --> pdb=" O THR C 795 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C1137 " --> pdb=" O GLY C1140 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU C1131 " --> pdb=" O PHE C1146 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N TYR C1148 " --> pdb=" O HIS C1129 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS C1129 " --> pdb=" O TYR C1148 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 809 through 811 removed outlier: 4.298A pdb=" N LYS C 809 " --> pdb=" O LEU C 946 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS C 944 " --> pdb=" O THR C 811 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 866 through 868 removed outlier: 6.589A pdb=" N LEU C 867 " --> pdb=" O VAL A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 1202 through 1204 removed outlier: 3.693A pdb=" N ARG C1168 " --> pdb=" O LEU C1164 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.508A pdb=" N VAL A 55 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU B 648 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 658 " --> pdb=" O TYR B 667 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 60 through 68 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 60 through 68 current: chain 'A' and resid 197 through 204 removed outlier: 3.508A pdb=" N TYR A 199 " --> pdb=" O ALA A 214 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N TYR A 203 " --> pdb=" O TYR A 210 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA A 211 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N PHE A 224 " --> pdb=" O ALA A 211 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N TYR A 213 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N PHE A 222 " --> pdb=" O TYR A 213 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 80 through 81 removed outlier: 3.944A pdb=" N GLY A 81 " --> pdb=" O LEU A 240 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'A' and resid 109 through 113 removed outlier: 4.102A pdb=" N THR A 109 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU A 120 " --> pdb=" O THR A 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 125 through 127 Processing sheet with id=AC7, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.536A pdb=" N PHE A 681 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 713 " --> pdb=" O VAL A 720 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 316 through 319 removed outlier: 6.942A pdb=" N VAL A 317 " --> pdb=" O ASP A 623 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A 620 " --> pdb=" O GLY A 631 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N GLY A 631 " --> pdb=" O VAL A 620 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 629 " --> pdb=" O TYR A 622 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR A 666 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ILE A 656 " --> pdb=" O ILE A 669 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY A 657 " --> pdb=" O LEU A 648 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'A' and resid 337 through 339 removed outlier: 6.734A pdb=" N VAL A 338 " --> pdb=" O ASN A 437 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'A' and resid 345 through 349 removed outlier: 4.089A pdb=" N GLU A 345 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LYS A 390 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N PHE A 383 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 597 " --> pdb=" O PHE A 383 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER A 367 " --> pdb=" O TYR A 426 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N SER A 428 " --> pdb=" O VAL A 365 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N VAL A 365 " --> pdb=" O SER A 428 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 353 through 354 removed outlier: 3.721A pdb=" N PHE A 354 " --> pdb=" O CYS A 603 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'A' and resid 467 through 468 removed outlier: 3.553A pdb=" N LYS A 536 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 550 through 551 removed outlier: 3.694A pdb=" N GLY A 550 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 573 " --> pdb=" O GLY A 550 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'A' and resid 724 through 725 removed outlier: 6.736A pdb=" N VAL A 724 " --> pdb=" O PHE A 764 " (cutoff:3.500A) removed outlier: 8.831A pdb=" N THR A 766 " --> pdb=" O VAL A 724 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 786 through 789 Processing sheet with id=AD7, first strand: chain 'A' and resid 794 through 803 removed outlier: 3.519A pdb=" N ALA A1137 " --> pdb=" O GLY A1140 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1131 " --> pdb=" O PHE A1146 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N TYR A1148 " --> pdb=" O HIS A1129 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N HIS A1129 " --> pdb=" O TYR A1148 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'A' and resid 809 through 812 removed outlier: 4.270A pdb=" N LYS A 809 " --> pdb=" O LEU A 946 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'A' and resid 866 through 868 removed outlier: 6.681A pdb=" N LEU A 867 " --> pdb=" O VAL B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'A' and resid 1162 through 1163 removed outlier: 3.863A pdb=" N CYS A1163 " --> pdb=" O THR A1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'A' and resid 1170 through 1172 removed outlier: 3.527A pdb=" N ALA A1171 " --> pdb=" O VAL A1203 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'A' and resid 1175 through 1180 Processing sheet with id=AE4, first strand: chain 'B' and resid 25 through 26 removed outlier: 3.930A pdb=" N ASN B 26 " --> pdb=" O LEU B 85 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 60 through 61 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 60 through 61 current: chain 'B' and resid 197 through 205 removed outlier: 3.727A pdb=" N TYR B 199 " --> pdb=" O ALA B 214 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE B 224 " --> pdb=" O ALA B 211 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N TYR B 213 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE B 222 " --> pdb=" O TYR B 213 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 221 through 227 current: chain 'B' and resid 280 through 281 Processing sheet with id=AE6, first strand: chain 'B' and resid 80 through 81 removed outlier: 3.810A pdb=" N GLY B 81 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR B 161 " --> pdb=" O THR B 241 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'B' and resid 96 through 97 removed outlier: 3.664A pdb=" N SER B 96 " --> pdb=" O TYR B 235 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N TYR B 235 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N THR B 123 " --> pdb=" O MET B 238 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N CYS B 151 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 189 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 185 " --> pdb=" O ALA B 150 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 109 through 113 removed outlier: 3.805A pdb=" N THR B 109 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 120 " --> pdb=" O THR B 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL B 113 " --> pdb=" O THR B 116 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 302 through 306 Processing sheet with id=AF1, first strand: chain 'B' and resid 317 through 318 removed outlier: 3.708A pdb=" N GLY B 629 " --> pdb=" O TYR B 622 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'B' and resid 337 through 339 Processing sheet with id=AF3, first strand: chain 'B' and resid 346 through 349 removed outlier: 3.661A pdb=" N ARG B 347 " --> pdb=" O VAL B 388 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER B 385 " --> pdb=" O ASN B 595 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N TYR B 427 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER B 422 " --> pdb=" O ASN B 371 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N SER B 428 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL B 365 " --> pdb=" O SER B 428 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 382 through 383 Processing sheet with id=AF5, first strand: chain 'B' and resid 459 through 462 Processing sheet with id=AF6, first strand: chain 'B' and resid 466 through 468 removed outlier: 4.567A pdb=" N CYS B 466 " --> pdb=" O VAL B 538 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 536 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'B' and resid 504 through 506 Processing sheet with id=AF8, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AF9, first strand: chain 'B' and resid 724 through 725 removed outlier: 6.668A pdb=" N VAL B 724 " --> pdb=" O PHE B 764 " (cutoff:3.500A) removed outlier: 8.783A pdb=" N THR B 766 " --> pdb=" O VAL B 724 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 786 through 791 removed outlier: 3.605A pdb=" N ILE B 788 " --> pdb=" O VAL B1156 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B1156 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU B1157 " --> pdb=" O LYS B1179 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS B1179 " --> pdb=" O LEU B1157 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE B1177 " --> pdb=" O SER B1159 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 794 through 803 removed outlier: 3.538A pdb=" N ALA B1137 " --> pdb=" O GLY B1140 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 809 through 811 removed outlier: 4.352A pdb=" N LYS B 809 " --> pdb=" O LEU B 946 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 944 " --> pdb=" O THR B 811 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 1162 through 1163 removed outlier: 3.713A pdb=" N CYS B1163 " --> pdb=" O THR B1213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'B' and resid 1169 through 1172 removed outlier: 3.843A pdb=" N GLY B1169 " --> pdb=" O MET B1205 " (cutoff:3.500A) 779 hydrogen bonds defined for protein. 2181 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: 12.21 Time building geometry restraints manager: 8.00 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: 8822 1.34 - 1.46: 7077 1.46 - 1.58: 12411 1.58 - 1.70: 0 1.70 - 1.81: 188 Bond restraints: 28498 Sorted by residual: bond pdb=" C1 BMA F 3 " pdb=" C2 BMA F 3 " ideal model delta sigma weight residual 1.519 1.550 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C1 NAG A1306 " pdb=" O5 NAG A1306 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C1 NAG C1307 " pdb=" O5 NAG C1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.28e+00 bond pdb=" C1 NAG A1307 " pdb=" O5 NAG A1307 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 ... (remaining 28493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 37997 1.31 - 2.63: 679 2.63 - 3.94: 138 3.94 - 5.25: 12 5.25 - 6.56: 5 Bond angle restraints: 38831 Sorted by residual: angle pdb=" N VAL A 700 " pdb=" CA VAL A 700 " pdb=" C VAL A 700 " ideal model delta sigma weight residual 113.07 109.14 3.93 1.37e+00 5.33e-01 8.25e+00 angle pdb=" C PHE A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta sigma weight residual 121.54 126.21 -4.67 1.91e+00 2.74e-01 5.97e+00 angle pdb=" N ASN B 664 " pdb=" CA ASN B 664 " pdb=" C ASN B 664 " ideal model delta sigma weight residual 108.63 112.31 -3.68 1.60e+00 3.91e-01 5.30e+00 angle pdb=" N TYR B 667 " pdb=" CA TYR B 667 " pdb=" C TYR B 667 " ideal model delta sigma weight residual 108.34 111.09 -2.75 1.31e+00 5.83e-01 4.41e+00 angle pdb=" C PHE B 130 " pdb=" N VAL B 131 " pdb=" CA VAL B 131 " ideal model delta sigma weight residual 121.97 118.21 3.76 1.80e+00 3.09e-01 4.36e+00 ... (remaining 38826 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 17003 21.78 - 43.57: 327 43.57 - 65.35: 37 65.35 - 87.14: 7 87.14 - 108.92: 4 Dihedral angle restraints: 17378 sinusoidal: 7034 harmonic: 10344 Sorted by residual: dihedral pdb=" CB CYS B 925 " pdb=" SG CYS B 925 " pdb=" SG CYS B 936 " pdb=" CB CYS B 936 " ideal model delta sinusoidal sigma weight residual 93.00 134.79 -41.79 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CA PHE A 98 " pdb=" C PHE A 98 " pdb=" N ASN A 99 " pdb=" CA ASN A 99 " ideal model delta harmonic sigma weight residual 180.00 156.14 23.86 0 5.00e+00 4.00e-02 2.28e+01 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 288.71 179.79 108.92 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 17375 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3806 0.055 - 0.109: 590 0.109 - 0.164: 74 0.164 - 0.218: 0 0.218 - 0.273: 1 Chirality restraints: 4471 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 -2.55 0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" C1 NAG A1307 " pdb=" ND2 ASN A1211 " pdb=" C2 NAG A1307 " pdb=" O5 NAG A1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" C1 NAG C1303 " pdb=" ND2 ASN C 703 " pdb=" C2 NAG C1303 " pdb=" O5 NAG C1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 4468 not shown) Planarity restraints: 4994 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A1066 " 0.030 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO A1067 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A1067 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A1067 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B1066 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.94e+00 pdb=" N PRO B1067 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B1067 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B1067 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 521 " 0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO B 522 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO B 522 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 522 " 0.023 5.00e-02 4.00e+02 ... (remaining 4991 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4650 2.77 - 3.30: 25483 3.30 - 3.83: 43500 3.83 - 4.37: 50159 4.37 - 4.90: 88280 Nonbonded interactions: 212072 Sorted by model distance: nonbonded pdb=" O VAL A 113 " pdb=" OG1 THR A 116 " model vdw 2.236 3.040 nonbonded pdb=" O PRO B 68 " pdb=" OH TYR B 266 " model vdw 2.239 3.040 nonbonded pdb=" OH TYR A 448 " pdb=" O PHE A 473 " model vdw 2.242 3.040 nonbonded pdb=" O VAL B 113 " pdb=" OG1 THR B 116 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR A 123 " pdb=" O VAL A 139 " model vdw 2.258 3.040 ... (remaining 212067 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 130 or (resid 131 and (name N or name CA or nam \ e C or name O or name CB )) or resid 132 through 163 or (resid 164 and (name N o \ r name CA or name C or name O or name CB )) or resid 165 or (resid 166 and (name \ N or name CA or name C or name O or name CB )) or resid 167 through 244 or resi \ d 254 through 363 or (resid 364 and (name N or name CA or name C or name O or na \ me CB )) or resid 365 through 373 or (resid 374 and (name N or name CA or name C \ or name O or name CB )) or resid 375 through 412 or (resid 413 and (name N or n \ ame CA or name C or name O or name CB )) or resid 414 through 446 or (resid 447 \ and (name N or name CA or name C or name O or name CB )) or resid 448 through 45 \ 4 or (resid 455 and (name N or name CA or name C or name O or name CB )) or resi \ d 456 through 491 or (resid 492 through 493 and (name N or name CA or name C or \ name O or name CB )) or resid 494 through 553 or (resid 554 and (name N or name \ CA or name C or name O or name CB )) or resid 555 through 557 or resid 563 throu \ gh 660 or (resid 661 and (name N or name CA or name C or name O or name CB )) or \ resid 662 through 1065 or (resid 1066 and (name N or name CA or name C or name \ O or name CB )) or resid 1067 through 1221 or resid 1301 through 1304)) selection = (chain 'B' and (resid 14 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 139 or (resid 140 and (name N or n \ ame CA or name C or name O or name CB )) or resid 141 through 163 or (resid 164 \ and (name N or name CA or name C or name O or name CB )) or resid 165 or (resid \ 166 and (name N or name CA or name C or name O or name CB )) or resid 167 throug \ h 185 or (resid 186 and (name N or name CA or name C or name O or name CB )) or \ resid 187 through 205 or (resid 206 and (name N or name CA or name C or name O o \ r name CB )) or resid 207 through 235 or resid 239 or (resid 240 and (name N or \ name CA or name C or name O or name CB )) or resid 241 through 373 or (resid 374 \ and (name N or name CA or name C or name O or name CB )) or resid 375 through 4 \ 46 or (resid 447 and (name N or name CA or name C or name O or name CB )) or res \ id 448 through 454 or (resid 455 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 483 or resid 490 through 501 or (resid 502 and (n \ ame N or name CA or name C or name O or name CB )) or resid 519 through 520 or ( \ resid 521 and (name N or name CA or name C or name O or name CB )) or resid 522 \ through 536 or (resid 537 and (name N or name CA or name C or name O or name CB \ )) or resid 538 through 779 or (resid 780 and (name N or name CA or name C or na \ me O or name CB )) or resid 781 through 1221 or resid 1301 through 1304)) selection = (chain 'C' and (resid 14 through 90 or (resid 91 and (name N or name CA or name \ C or name O or name CB )) or resid 92 through 130 or (resid 131 and (name N or n \ ame CA or name C or name O or name CB )) or resid 132 through 139 or (resid 140 \ and (name N or name CA or name C or name O or name CB )) or resid 141 through 18 \ 5 or (resid 186 and (name N or name CA or name C or name O or name CB )) or resi \ d 187 through 205 or (resid 206 and (name N or name CA or name C or name O or na \ me CB )) or resid 207 through 235 or resid 239 or (resid 240 and (name N or name \ CA or name C or name O or name CB )) or resid 241 through 244 or resid 254 thro \ ugh 311 or (resid 312 and (name N or name CA or name C or name O or name CB )) o \ r resid 313 through 363 or (resid 364 and (name N or name CA or name C or name O \ or name CB )) or resid 365 through 412 or (resid 413 and (name N or name CA or \ name C or name O or name CB )) or resid 414 through 491 or (resid 492 through 49 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 494 through \ 536 or (resid 537 and (name N or name CA or name C or name O or name CB )) or re \ sid 538 through 553 or (resid 554 and (name N or name CA or name C or name O or \ name CB )) or resid 555 through 660 or (resid 661 and (name N or name CA or name \ C or name O or name CB )) or resid 662 through 779 or (resid 780 and (name N or \ name CA or name C or name O or name CB )) or resid 781 through 931 or (resid 93 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 933 through \ 1065 or (resid 1066 and (name N or name CA or name C or name O or name CB )) or \ resid 1067 through 1221 or resid 1301 through 1304)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' } 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: 4.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.180 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 64.430 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 28596 Z= 0.110 Angle : 0.430 6.563 39058 Z= 0.224 Chirality : 0.041 0.273 4471 Planarity : 0.003 0.045 4969 Dihedral : 8.081 108.919 10531 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.57 % Rotamer: Outliers : 1.19 % Allowed : 5.19 % Favored : 93.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -3.23 (0.12), residues: 3497 helix: -3.19 (0.11), residues: 642 sheet: -0.90 (0.19), residues: 696 loop : -2.33 (0.11), residues: 2159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 344 HIS 0.001 0.000 HIS B 175 PHE 0.016 0.001 PHE A 98 TYR 0.006 0.001 TYR C 56 ARG 0.001 0.000 ARG B 319 Details of bonding type rmsd link_NAG-ASN : bond 0.00244 ( 25) link_NAG-ASN : angle 1.07780 ( 75) link_BETA1-4 : bond 0.00389 ( 6) link_BETA1-4 : angle 0.92590 ( 18) hydrogen bonds : bond 0.31508 ( 779) hydrogen bonds : angle 8.47897 ( 2181) SS BOND : bond 0.00085 ( 67) SS BOND : angle 0.42959 ( 134) covalent geometry : bond 0.00218 (28498) covalent geometry : angle 0.42779 (38831) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 593 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 556 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 31 THR cc_start: 0.5974 (p) cc_final: 0.5523 (p) REVERT: C 213 TYR cc_start: 0.7749 (OUTLIER) cc_final: 0.7401 (t80) REVERT: C 278 ASN cc_start: 0.8183 (m-40) cc_final: 0.7981 (m110) REVERT: C 402 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7368 (mm110) REVERT: C 464 ASP cc_start: 0.7908 (t0) cc_final: 0.7398 (t0) REVERT: C 915 ASP cc_start: 0.6923 (t70) cc_final: 0.6670 (t0) REVERT: A 52 LEU cc_start: 0.8888 (mm) cc_final: 0.8572 (mp) REVERT: A 579 SER cc_start: 0.8683 (p) cc_final: 0.8187 (m) REVERT: B 169 ILE cc_start: 0.8325 (pt) cc_final: 0.7794 (tt) REVERT: B 313 PRO cc_start: 0.5353 (Cg_endo) cc_final: 0.5081 (Cg_exo) REVERT: B 848 ASP cc_start: 0.7332 (m-30) cc_final: 0.7122 (m-30) REVERT: B 884 PHE cc_start: 0.6644 (m-10) cc_final: 0.6289 (m-80) outliers start: 37 outliers final: 14 residues processed: 585 average time/residue: 0.3771 time to fit residues: 352.9807 Evaluate side-chains 270 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 255 time to evaluate : 3.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain C residue 1163 CYS Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 697 CYS Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 934 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 8.9990 chunk 266 optimal weight: 9.9990 chunk 148 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 179 optimal weight: 1.9990 chunk 142 optimal weight: 7.9990 chunk 275 optimal weight: 30.0000 chunk 106 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 630 GLN C 847 ASN C 854 GLN C 856 GLN C 984 GLN C1001 GLN C1009 ASN C1030 GLN C1071 GLN A 26 ASN A 100 ASN A 160 HIS A 291 GLN A 353 ASN A 402 GLN ** A 413 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 445 ASN A 535 GLN A 587 ASN ** A 605 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 621 ASN ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1001 GLN A1046 GLN A1091 GLN A1126 ASN A1135 GLN B 100 ASN B 201 HIS B 243 ASN B 465 HIS B 535 GLN B 683 GLN B 804 GLN B 941 ASN B 998 ASN B1059 GLN B1091 GLN B1211 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.132045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.094461 restraints weight = 54081.498| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 3.19 r_work: 0.3180 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 28596 Z= 0.208 Angle : 0.629 10.176 39058 Z= 0.326 Chirality : 0.047 0.355 4471 Planarity : 0.004 0.048 4969 Dihedral : 6.052 59.705 4461 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.88 % Allowed : 8.69 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -2.04 (0.13), residues: 3497 helix: -0.37 (0.18), residues: 700 sheet: -0.74 (0.19), residues: 740 loop : -2.03 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.007 0.001 HIS C1145 PHE 0.027 0.002 PHE A 98 TYR 0.030 0.002 TYR C1219 ARG 0.004 0.001 ARG A 347 Details of bonding type rmsd link_NAG-ASN : bond 0.00750 ( 25) link_NAG-ASN : angle 2.23630 ( 75) link_BETA1-4 : bond 0.00575 ( 6) link_BETA1-4 : angle 1.86122 ( 18) hydrogen bonds : bond 0.06216 ( 779) hydrogen bonds : angle 5.50927 ( 2181) SS BOND : bond 0.00433 ( 67) SS BOND : angle 1.55917 ( 134) covalent geometry : bond 0.00489 (28498) covalent geometry : angle 0.61463 (38831) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 266 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7816 (mm-40) REVERT: C 431 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7651 (pp) REVERT: C 464 ASP cc_start: 0.8501 (t0) cc_final: 0.7728 (t0) REVERT: C 501 TYR cc_start: 0.8208 (m-80) cc_final: 0.7825 (m-80) REVERT: C 566 PHE cc_start: 0.7019 (t80) cc_final: 0.5896 (m-80) REVERT: C 577 PHE cc_start: 0.7561 (m-10) cc_final: 0.7259 (m-80) REVERT: C 1075 ASP cc_start: 0.8775 (t0) cc_final: 0.8571 (t0) REVERT: A 366 ASP cc_start: 0.8232 (m-30) cc_final: 0.8009 (t0) REVERT: A 453 PHE cc_start: 0.5861 (OUTLIER) cc_final: 0.4538 (p90) REVERT: A 528 TYR cc_start: 0.6667 (OUTLIER) cc_final: 0.6304 (m-80) REVERT: A 711 PHE cc_start: 0.7880 (m-80) cc_final: 0.7362 (m-80) REVERT: B 84 TYR cc_start: 0.7708 (m-80) cc_final: 0.7394 (t80) REVERT: B 318 TYR cc_start: 0.7594 (m-10) cc_final: 0.7272 (m-80) REVERT: B 322 PRO cc_start: 0.7415 (Cg_exo) cc_final: 0.7127 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8015 (t0) cc_final: 0.6899 (t0) REVERT: B 669 ILE cc_start: 0.9192 (mp) cc_final: 0.8909 (mt) REVERT: B 884 PHE cc_start: 0.7481 (m-10) cc_final: 0.7153 (m-80) REVERT: B 994 MET cc_start: 0.8672 (tpp) cc_final: 0.8355 (ttt) outliers start: 90 outliers final: 47 residues processed: 335 average time/residue: 0.3397 time to fit residues: 191.9603 Evaluate side-chains 257 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 207 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 117 LEU Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 494 ILE Chi-restraints excluded: chain C residue 539 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 732 SER Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 836 CYS Chi-restraints excluded: chain C residue 879 VAL Chi-restraints excluded: chain A residue 84 TYR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 878 ASP Chi-restraints excluded: chain B residue 890 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 89 optimal weight: 0.9990 chunk 286 optimal weight: 0.0000 chunk 252 optimal weight: 2.9990 chunk 324 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 250 optimal weight: 5.9990 chunk 208 optimal weight: 0.0570 chunk 98 optimal weight: 0.9980 chunk 163 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 321 optimal weight: 3.9990 overall best weight: 1.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 535 GLN C 584 ASN C 984 GLN C1001 GLN C1049 ASN C1071 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN B 100 ASN B 160 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.131860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.093442 restraints weight = 53432.616| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.91 r_work: 0.3219 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28596 Z= 0.111 Angle : 0.500 9.760 39058 Z= 0.262 Chirality : 0.043 0.259 4471 Planarity : 0.004 0.047 4969 Dihedral : 5.041 57.416 4452 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.47 % Allowed : 9.87 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.45 (0.14), residues: 3497 helix: 0.80 (0.20), residues: 710 sheet: -0.45 (0.19), residues: 718 loop : -1.88 (0.12), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 174 HIS 0.004 0.001 HIS C 876 PHE 0.026 0.001 PHE A 566 TYR 0.017 0.001 TYR A 458 ARG 0.009 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00336 ( 25) link_NAG-ASN : angle 1.90556 ( 75) link_BETA1-4 : bond 0.00464 ( 6) link_BETA1-4 : angle 1.38708 ( 18) hydrogen bonds : bond 0.05074 ( 779) hydrogen bonds : angle 4.98887 ( 2181) SS BOND : bond 0.00219 ( 67) SS BOND : angle 1.14101 ( 134) covalent geometry : bond 0.00247 (28498) covalent geometry : angle 0.48910 (38831) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 3.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 GLN cc_start: 0.7975 (mm-40) cc_final: 0.7692 (mm-40) REVERT: C 431 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7629 (pp) REVERT: C 464 ASP cc_start: 0.8469 (t0) cc_final: 0.7708 (t0) REVERT: C 501 TYR cc_start: 0.8315 (m-80) cc_final: 0.7862 (m-80) REVERT: C 551 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7645 (mt) REVERT: C 566 PHE cc_start: 0.6885 (t80) cc_final: 0.5826 (m-80) REVERT: C 577 PHE cc_start: 0.7577 (m-10) cc_final: 0.7373 (m-80) REVERT: A 528 TYR cc_start: 0.6623 (OUTLIER) cc_final: 0.6311 (m-80) REVERT: A 1000 ASN cc_start: 0.8618 (m-40) cc_final: 0.8407 (m110) REVERT: B 322 PRO cc_start: 0.7402 (Cg_exo) cc_final: 0.7131 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8197 (t0) cc_final: 0.7864 (t0) REVERT: B 669 ILE cc_start: 0.9146 (mp) cc_final: 0.8941 (mt) REVERT: B 1185 MET cc_start: 0.9045 (mmm) cc_final: 0.8811 (mtp) outliers start: 77 outliers final: 46 residues processed: 295 average time/residue: 0.3304 time to fit residues: 167.5366 Evaluate side-chains 258 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 209 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 875 LEU Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 100 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 69 optimal weight: 0.3980 chunk 28 optimal weight: 6.9990 chunk 240 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 305 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 300 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 180 optimal weight: 4.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 876 HIS C 984 GLN C1001 GLN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1126 ASN B 100 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.132866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.094361 restraints weight = 54265.478| |-----------------------------------------------------------------------------| r_work (start): 0.3323 rms_B_bonded: 2.92 r_work: 0.3218 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 28596 Z= 0.096 Angle : 0.479 8.366 39058 Z= 0.248 Chirality : 0.043 0.255 4471 Planarity : 0.004 0.051 4969 Dihedral : 4.667 56.971 4451 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.56 % Allowed : 10.00 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.20 (0.14), residues: 3497 helix: 1.18 (0.21), residues: 719 sheet: -0.35 (0.19), residues: 727 loop : -1.78 (0.13), residues: 2051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 174 HIS 0.003 0.001 HIS C 201 PHE 0.025 0.001 PHE C 18 TYR 0.017 0.001 TYR A 235 ARG 0.008 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00245 ( 25) link_NAG-ASN : angle 1.81538 ( 75) link_BETA1-4 : bond 0.00495 ( 6) link_BETA1-4 : angle 1.22298 ( 18) hydrogen bonds : bond 0.04271 ( 779) hydrogen bonds : angle 4.70667 ( 2181) SS BOND : bond 0.00179 ( 67) SS BOND : angle 1.08546 ( 134) covalent geometry : bond 0.00215 (28498) covalent geometry : angle 0.46861 (38831) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 222 time to evaluate : 3.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 402 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7714 (mm-40) REVERT: C 431 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7593 (pp) REVERT: C 464 ASP cc_start: 0.8465 (t0) cc_final: 0.7657 (t0) REVERT: C 551 ILE cc_start: 0.7872 (OUTLIER) cc_final: 0.7507 (mt) REVERT: C 566 PHE cc_start: 0.6755 (t80) cc_final: 0.5750 (m-80) REVERT: C 577 PHE cc_start: 0.7649 (m-10) cc_final: 0.7439 (m-80) REVERT: C 1091 GLN cc_start: 0.8529 (tt0) cc_final: 0.8306 (tt0) REVERT: C 1185 MET cc_start: 0.8913 (mmm) cc_final: 0.8693 (mtp) REVERT: C 1205 MET cc_start: 0.8047 (OUTLIER) cc_final: 0.6912 (mpp) REVERT: A 453 PHE cc_start: 0.5990 (OUTLIER) cc_final: 0.4862 (p90) REVERT: A 528 TYR cc_start: 0.6630 (OUTLIER) cc_final: 0.6328 (m-80) REVERT: B 34 ARG cc_start: 0.7571 (mmm160) cc_final: 0.7117 (mmp-170) REVERT: B 84 TYR cc_start: 0.7280 (m-80) cc_final: 0.6973 (t80) REVERT: B 87 THR cc_start: 0.8322 (t) cc_final: 0.8096 (t) REVERT: B 97 ASP cc_start: 0.8336 (t70) cc_final: 0.8017 (t0) REVERT: B 322 PRO cc_start: 0.7465 (Cg_exo) cc_final: 0.7196 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8212 (t0) cc_final: 0.7839 (t0) outliers start: 80 outliers final: 48 residues processed: 283 average time/residue: 0.3171 time to fit residues: 155.6187 Evaluate side-chains 255 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 202 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 121 PHE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 255 GLU Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 528 TYR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1126 ASN Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 800 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 226 optimal weight: 5.9990 chunk 160 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 158 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 189 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 194 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 630 GLN C 984 GLN C1129 HIS A 160 HIS A 847 ASN ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1041 ASN B 552 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.127747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.088561 restraints weight = 53955.367| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.94 r_work: 0.3107 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 28596 Z= 0.212 Angle : 0.595 10.139 39058 Z= 0.308 Chirality : 0.046 0.254 4471 Planarity : 0.004 0.056 4969 Dihedral : 5.097 57.161 4451 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.33 % Allowed : 9.74 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.30 (0.14), residues: 3497 helix: 0.98 (0.20), residues: 728 sheet: -0.46 (0.19), residues: 768 loop : -1.80 (0.13), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 575 HIS 0.008 0.002 HIS C1145 PHE 0.027 0.002 PHE A 566 TYR 0.022 0.002 TYR A 682 ARG 0.004 0.001 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00337 ( 25) link_NAG-ASN : angle 2.07543 ( 75) link_BETA1-4 : bond 0.00474 ( 6) link_BETA1-4 : angle 1.16688 ( 18) hydrogen bonds : bond 0.05364 ( 779) hydrogen bonds : angle 4.85310 ( 2181) SS BOND : bond 0.00740 ( 67) SS BOND : angle 1.65508 ( 134) covalent geometry : bond 0.00508 (28498) covalent geometry : angle 0.58120 (38831) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 218 time to evaluate : 3.078 Fit side-chains revert: symmetry clash REVERT: C 402 GLN cc_start: 0.8137 (mm-40) cc_final: 0.7853 (mm-40) REVERT: C 431 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7606 (pp) REVERT: C 464 ASP cc_start: 0.8715 (t0) cc_final: 0.7806 (t0) REVERT: C 501 TYR cc_start: 0.8302 (m-80) cc_final: 0.7937 (m-80) REVERT: C 544 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: C 551 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7823 (mt) REVERT: C 577 PHE cc_start: 0.7901 (m-10) cc_final: 0.7599 (m-80) REVERT: C 800 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.8120 (pm20) REVERT: C 981 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9104 (tt) REVERT: C 1069 GLU cc_start: 0.8514 (tp30) cc_final: 0.8079 (mt-10) REVERT: C 1075 ASP cc_start: 0.8966 (t70) cc_final: 0.8702 (t0) REVERT: C 1205 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7141 (mpp) REVERT: A 153 TYR cc_start: 0.7694 (m-10) cc_final: 0.7400 (m-80) REVERT: A 453 PHE cc_start: 0.6488 (OUTLIER) cc_final: 0.5794 (p90) REVERT: A 1162 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8701 (pp) REVERT: B 84 TYR cc_start: 0.7457 (m-80) cc_final: 0.7077 (t80) REVERT: B 318 TYR cc_start: 0.7954 (m-10) cc_final: 0.7431 (m-80) REVERT: B 322 PRO cc_start: 0.7564 (Cg_exo) cc_final: 0.7250 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8521 (t0) cc_final: 0.7345 (t0) REVERT: B 777 ASP cc_start: 0.8236 (m-30) cc_final: 0.8006 (m-30) REVERT: B 863 GLN cc_start: 0.8251 (tp40) cc_final: 0.8009 (tm-30) outliers start: 104 outliers final: 63 residues processed: 298 average time/residue: 0.3129 time to fit residues: 161.9752 Evaluate side-chains 268 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 197 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 618 VAL Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 880 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 289 GLU Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 800 GLU Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 17 optimal weight: 2.9990 chunk 231 optimal weight: 3.9990 chunk 232 optimal weight: 1.9990 chunk 220 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 185 optimal weight: 0.2980 chunk 78 optimal weight: 0.9990 chunk 226 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 335 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN A 998 ASN B 535 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.129834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.090918 restraints weight = 53831.438| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.92 r_work: 0.3159 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.071 28596 Z= 0.107 Angle : 0.510 10.777 39058 Z= 0.264 Chirality : 0.043 0.265 4471 Planarity : 0.004 0.054 4969 Dihedral : 4.752 56.582 4451 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer: Outliers : 2.76 % Allowed : 10.61 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.10 (0.14), residues: 3497 helix: 1.18 (0.21), residues: 737 sheet: -0.37 (0.19), residues: 753 loop : -1.68 (0.13), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.004 0.001 HIS C 201 PHE 0.030 0.001 PHE C 18 TYR 0.020 0.001 TYR A 235 ARG 0.006 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00256 ( 25) link_NAG-ASN : angle 1.80030 ( 75) link_BETA1-4 : bond 0.00475 ( 6) link_BETA1-4 : angle 1.07226 ( 18) hydrogen bonds : bond 0.04276 ( 779) hydrogen bonds : angle 4.60750 ( 2181) SS BOND : bond 0.00203 ( 67) SS BOND : angle 1.49978 ( 134) covalent geometry : bond 0.00248 (28498) covalent geometry : angle 0.49671 (38831) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 218 time to evaluate : 3.027 Fit side-chains revert: symmetry clash REVERT: C 218 MET cc_start: 0.8464 (mtt) cc_final: 0.7975 (mtp) REVERT: C 377 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: C 402 GLN cc_start: 0.8076 (mm-40) cc_final: 0.7834 (mm-40) REVERT: C 431 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7653 (pp) REVERT: C 464 ASP cc_start: 0.8653 (t0) cc_final: 0.7739 (t0) REVERT: C 501 TYR cc_start: 0.8250 (m-80) cc_final: 0.7889 (m-80) REVERT: C 551 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7626 (mt) REVERT: C 566 PHE cc_start: 0.7291 (t80) cc_final: 0.6134 (m-80) REVERT: C 577 PHE cc_start: 0.7849 (m-10) cc_final: 0.7632 (m-80) REVERT: C 800 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: C 1069 GLU cc_start: 0.8480 (tp30) cc_final: 0.8073 (mt-10) REVERT: C 1205 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: A 118 TYR cc_start: 0.6212 (m-80) cc_final: 0.5745 (m-80) REVERT: A 153 TYR cc_start: 0.7623 (m-10) cc_final: 0.7401 (m-80) REVERT: A 453 PHE cc_start: 0.6451 (OUTLIER) cc_final: 0.5759 (p90) REVERT: A 1126 ASN cc_start: 0.8814 (p0) cc_final: 0.8578 (p0) REVERT: B 34 ARG cc_start: 0.7632 (mmm160) cc_final: 0.7188 (mmp-170) REVERT: B 84 TYR cc_start: 0.7375 (m-80) cc_final: 0.7037 (t80) REVERT: B 318 TYR cc_start: 0.7842 (m-10) cc_final: 0.7323 (m-80) REVERT: B 322 PRO cc_start: 0.7416 (Cg_exo) cc_final: 0.7180 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8473 (t0) cc_final: 0.7302 (t0) REVERT: B 777 ASP cc_start: 0.8221 (m-30) cc_final: 0.7970 (m-30) REVERT: B 863 GLN cc_start: 0.8069 (tp40) cc_final: 0.7828 (tm-30) outliers start: 86 outliers final: 58 residues processed: 284 average time/residue: 0.3229 time to fit residues: 158.9313 Evaluate side-chains 265 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 201 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1185 MET Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 869 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 206 optimal weight: 3.9990 chunk 289 optimal weight: 20.0000 chunk 322 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 58 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C1030 GLN A 160 HIS A 998 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.126893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088092 restraints weight = 53926.369| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 2.86 r_work: 0.3088 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 28596 Z= 0.193 Angle : 0.578 11.929 39058 Z= 0.298 Chirality : 0.045 0.272 4471 Planarity : 0.004 0.058 4969 Dihedral : 5.066 56.766 4449 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.98 % Favored : 93.99 % Rotamer: Outliers : 2.92 % Allowed : 10.87 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.18 (0.14), residues: 3497 helix: 1.07 (0.20), residues: 731 sheet: -0.47 (0.19), residues: 749 loop : -1.68 (0.13), residues: 2017 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 575 HIS 0.006 0.001 HIS C1145 PHE 0.021 0.002 PHE B 713 TYR 0.021 0.002 TYR A 235 ARG 0.007 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00297 ( 25) link_NAG-ASN : angle 2.00083 ( 75) link_BETA1-4 : bond 0.00530 ( 6) link_BETA1-4 : angle 1.15476 ( 18) hydrogen bonds : bond 0.05001 ( 779) hydrogen bonds : angle 4.73139 ( 2181) SS BOND : bond 0.00356 ( 67) SS BOND : angle 1.77365 ( 134) covalent geometry : bond 0.00469 (28498) covalent geometry : angle 0.56293 (38831) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 201 time to evaluate : 2.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 176 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8473 (tt) REVERT: C 402 GLN cc_start: 0.8109 (mm-40) cc_final: 0.7822 (mm-40) REVERT: C 431 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7635 (pp) REVERT: C 453 PHE cc_start: 0.6235 (t80) cc_final: 0.5729 (t80) REVERT: C 464 ASP cc_start: 0.8673 (t0) cc_final: 0.7736 (t0) REVERT: C 501 TYR cc_start: 0.8345 (m-80) cc_final: 0.7990 (m-80) REVERT: C 551 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7838 (mt) REVERT: C 566 PHE cc_start: 0.7474 (t80) cc_final: 0.6170 (m-80) REVERT: C 577 PHE cc_start: 0.7928 (m-10) cc_final: 0.7685 (m-80) REVERT: C 800 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8077 (pm20) REVERT: C 1069 GLU cc_start: 0.8586 (tp30) cc_final: 0.8119 (mt-10) REVERT: C 1205 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7428 (mpp) REVERT: A 118 TYR cc_start: 0.6452 (m-80) cc_final: 0.5955 (m-80) REVERT: A 235 TYR cc_start: 0.6112 (p90) cc_final: 0.5908 (p90) REVERT: A 453 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6183 (p90) REVERT: A 1126 ASN cc_start: 0.8871 (p0) cc_final: 0.8549 (p0) REVERT: A 1162 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8787 (pp) REVERT: B 84 TYR cc_start: 0.7478 (m-80) cc_final: 0.7109 (t80) REVERT: B 318 TYR cc_start: 0.7996 (m-10) cc_final: 0.7400 (m-80) REVERT: B 322 PRO cc_start: 0.7499 (Cg_exo) cc_final: 0.7265 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8561 (t0) cc_final: 0.7538 (t0) REVERT: B 863 GLN cc_start: 0.8233 (tp40) cc_final: 0.8023 (tm-30) outliers start: 91 outliers final: 65 residues processed: 268 average time/residue: 0.3322 time to fit residues: 154.8504 Evaluate side-chains 261 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 189 time to evaluate : 2.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 453 PHE Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 271 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 228 optimal weight: 5.9990 chunk 216 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 165 optimal weight: 7.9990 chunk 181 optimal weight: 3.9990 chunk 283 optimal weight: 40.0000 chunk 314 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 876 HIS C1049 ASN A 160 HIS B 838 ASN ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.126153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.087530 restraints weight = 53945.898| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.88 r_work: 0.3091 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 28596 Z= 0.219 Angle : 0.612 12.678 39058 Z= 0.317 Chirality : 0.046 0.269 4471 Planarity : 0.004 0.057 4969 Dihedral : 5.417 56.674 4449 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.09 % Favored : 93.88 % Rotamer: Outliers : 2.92 % Allowed : 11.57 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % 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: -1.34 (0.14), residues: 3497 helix: 0.85 (0.20), residues: 743 sheet: -0.60 (0.19), residues: 765 loop : -1.76 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 332 HIS 0.007 0.001 HIS C1145 PHE 0.023 0.002 PHE C 24 TYR 0.021 0.002 TYR A 235 ARG 0.009 0.001 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00353 ( 25) link_NAG-ASN : angle 2.18871 ( 75) link_BETA1-4 : bond 0.00525 ( 6) link_BETA1-4 : angle 1.20300 ( 18) hydrogen bonds : bond 0.05187 ( 779) hydrogen bonds : angle 4.81926 ( 2181) SS BOND : bond 0.00353 ( 67) SS BOND : angle 1.83737 ( 134) covalent geometry : bond 0.00530 (28498) covalent geometry : angle 0.59645 (38831) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 197 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 218 MET cc_start: 0.8594 (mtt) cc_final: 0.8199 (mtp) REVERT: C 402 GLN cc_start: 0.8135 (mm-40) cc_final: 0.7847 (mm-40) REVERT: C 408 PHE cc_start: 0.8372 (m-80) cc_final: 0.8066 (m-80) REVERT: C 431 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7715 (pp) REVERT: C 453 PHE cc_start: 0.6603 (t80) cc_final: 0.6038 (t80) REVERT: C 464 ASP cc_start: 0.8761 (t0) cc_final: 0.7873 (t70) REVERT: C 551 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7793 (mt) REVERT: C 566 PHE cc_start: 0.7626 (t80) cc_final: 0.6512 (m-80) REVERT: C 800 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8073 (pm20) REVERT: C 1069 GLU cc_start: 0.8633 (tp30) cc_final: 0.8179 (mt-10) REVERT: C 1075 ASP cc_start: 0.8977 (t70) cc_final: 0.8721 (t0) REVERT: C 1205 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7557 (mpp) REVERT: A 118 TYR cc_start: 0.6664 (m-80) cc_final: 0.6177 (m-80) REVERT: A 1162 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.8900 (pp) REVERT: B 84 TYR cc_start: 0.7533 (m-80) cc_final: 0.7167 (t80) REVERT: B 318 TYR cc_start: 0.8023 (m-10) cc_final: 0.7409 (m-80) REVERT: B 322 PRO cc_start: 0.7573 (Cg_exo) cc_final: 0.7337 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8702 (t0) cc_final: 0.7649 (t0) outliers start: 91 outliers final: 67 residues processed: 267 average time/residue: 0.3183 time to fit residues: 147.4252 Evaluate side-chains 247 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 175 time to evaluate : 2.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 112 TYR Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 431 LEU Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 461 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 781 THR Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 662 LEU Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 884 PHE Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain A residue 1210 VAL Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 806 SER Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 815 SER Chi-restraints excluded: chain B residue 834 THR Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 328 optimal weight: 0.5980 chunk 23 optimal weight: 0.0980 chunk 170 optimal weight: 4.9990 chunk 105 optimal weight: 0.7980 chunk 144 optimal weight: 1.9990 chunk 225 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 139 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 31 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: C 323 ASN C 470 ASN C 584 ASN C 863 GLN C1049 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1017 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.128754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089861 restraints weight = 53798.271| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 2.91 r_work: 0.3155 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 28596 Z= 0.103 Angle : 0.524 12.943 39058 Z= 0.272 Chirality : 0.043 0.287 4471 Planarity : 0.004 0.053 4969 Dihedral : 4.936 55.454 4448 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.29 % Favored : 94.68 % Rotamer: Outliers : 1.92 % Allowed : 12.44 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3497 helix: 1.21 (0.21), residues: 744 sheet: -0.47 (0.19), residues: 740 loop : -1.63 (0.13), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 344 HIS 0.025 0.001 HIS C 876 PHE 0.018 0.001 PHE C 24 TYR 0.018 0.001 TYR A 235 ARG 0.006 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00301 ( 25) link_NAG-ASN : angle 1.91448 ( 75) link_BETA1-4 : bond 0.00484 ( 6) link_BETA1-4 : angle 1.12908 ( 18) hydrogen bonds : bond 0.04082 ( 779) hydrogen bonds : angle 4.57828 ( 2181) SS BOND : bond 0.00184 ( 67) SS BOND : angle 1.38755 ( 134) covalent geometry : bond 0.00234 (28498) covalent geometry : angle 0.51169 (38831) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 196 time to evaluate : 3.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 218 MET cc_start: 0.8410 (mtt) cc_final: 0.8016 (mtp) REVERT: C 402 GLN cc_start: 0.8091 (mm-40) cc_final: 0.7828 (mm-40) REVERT: C 408 PHE cc_start: 0.8234 (m-80) cc_final: 0.7945 (m-80) REVERT: C 453 PHE cc_start: 0.6474 (t80) cc_final: 0.5935 (t80) REVERT: C 464 ASP cc_start: 0.8633 (t0) cc_final: 0.7416 (t0) REVERT: C 465 HIS cc_start: 0.8068 (m-70) cc_final: 0.7182 (m-70) REVERT: C 501 TYR cc_start: 0.8264 (m-80) cc_final: 0.8009 (m-80) REVERT: C 551 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7774 (mt) REVERT: C 566 PHE cc_start: 0.7521 (t80) cc_final: 0.6302 (m-80) REVERT: C 800 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: C 1069 GLU cc_start: 0.8572 (tp30) cc_final: 0.8144 (mt-10) REVERT: C 1205 MET cc_start: 0.8023 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: A 118 TYR cc_start: 0.6687 (m-80) cc_final: 0.6186 (m-80) REVERT: A 309 PHE cc_start: 0.4127 (m-10) cc_final: 0.3655 (m-80) REVERT: A 1162 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8888 (pp) REVERT: B 84 TYR cc_start: 0.7461 (m-80) cc_final: 0.7113 (t80) REVERT: B 318 TYR cc_start: 0.7973 (m-10) cc_final: 0.7354 (m-80) REVERT: B 322 PRO cc_start: 0.7486 (Cg_exo) cc_final: 0.7265 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8598 (t0) cc_final: 0.7676 (t0) outliers start: 60 outliers final: 51 residues processed: 243 average time/residue: 0.3415 time to fit residues: 145.0467 Evaluate side-chains 238 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 183 time to evaluate : 3.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 176 ILE Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 814 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 35 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 23 optimal weight: 0.0270 chunk 288 optimal weight: 30.0000 chunk 244 optimal weight: 5.9990 chunk 348 optimal weight: 5.9990 chunk 208 optimal weight: 6.9990 chunk 347 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 335 optimal weight: 4.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 876 HIS C1049 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.125289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087034 restraints weight = 54003.797| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.81 r_work: 0.3075 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 28596 Z= 0.249 Angle : 0.641 13.093 39058 Z= 0.331 Chirality : 0.047 0.308 4471 Planarity : 0.004 0.058 4969 Dihedral : 5.411 57.758 4446 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.03 % Favored : 92.94 % Rotamer: Outliers : 2.15 % Allowed : 12.53 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.14), residues: 3497 helix: 0.95 (0.20), residues: 738 sheet: -0.61 (0.19), residues: 768 loop : -1.77 (0.13), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 575 HIS 0.009 0.002 HIS C 876 PHE 0.025 0.002 PHE B 713 TYR 0.022 0.002 TYR A 235 ARG 0.007 0.001 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00357 ( 25) link_NAG-ASN : angle 2.22359 ( 75) link_BETA1-4 : bond 0.00491 ( 6) link_BETA1-4 : angle 1.26121 ( 18) hydrogen bonds : bond 0.05380 ( 779) hydrogen bonds : angle 4.85505 ( 2181) SS BOND : bond 0.00396 ( 67) SS BOND : angle 1.96816 ( 134) covalent geometry : bond 0.00607 (28498) covalent geometry : angle 0.62430 (38831) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6994 Ramachandran restraints generated. 3497 Oldfield, 0 Emsley, 3497 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 402 GLN cc_start: 0.8140 (mm-40) cc_final: 0.7850 (mm-40) REVERT: C 464 ASP cc_start: 0.8769 (t0) cc_final: 0.8167 (t70) REVERT: C 465 HIS cc_start: 0.8110 (m-70) cc_final: 0.7719 (m-70) REVERT: C 501 TYR cc_start: 0.8324 (m-80) cc_final: 0.8073 (m-80) REVERT: C 551 ILE cc_start: 0.8243 (OUTLIER) cc_final: 0.7894 (mt) REVERT: C 566 PHE cc_start: 0.7684 (t80) cc_final: 0.6622 (m-80) REVERT: C 800 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8040 (pm20) REVERT: C 1069 GLU cc_start: 0.8652 (tp30) cc_final: 0.8240 (mt-10) REVERT: C 1205 MET cc_start: 0.8095 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: A 118 TYR cc_start: 0.6782 (m-80) cc_final: 0.6264 (m-80) REVERT: A 1162 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8892 (pp) REVERT: B 84 TYR cc_start: 0.7532 (m-80) cc_final: 0.7157 (t80) REVERT: B 318 TYR cc_start: 0.8046 (m-10) cc_final: 0.7438 (m-80) REVERT: B 322 PRO cc_start: 0.7754 (Cg_exo) cc_final: 0.7523 (Cg_endo) REVERT: B 623 ASP cc_start: 0.8725 (t0) cc_final: 0.7647 (t0) outliers start: 67 outliers final: 56 residues processed: 238 average time/residue: 0.3244 time to fit residues: 134.7845 Evaluate side-chains 241 residues out of total 3157 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 181 time to evaluate : 3.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 139 VAL Chi-restraints excluded: chain C residue 213 TYR Chi-restraints excluded: chain C residue 292 CYS Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 393 ILE Chi-restraints excluded: chain C residue 432 VAL Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 551 ILE Chi-restraints excluded: chain C residue 708 SER Chi-restraints excluded: chain C residue 800 GLU Chi-restraints excluded: chain C residue 819 CYS Chi-restraints excluded: chain C residue 876 HIS Chi-restraints excluded: chain C residue 1019 PHE Chi-restraints excluded: chain C residue 1205 MET Chi-restraints excluded: chain C residue 1212 PHE Chi-restraints excluded: chain C residue 1213 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 THR Chi-restraints excluded: chain A residue 213 TYR Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 577 PHE Chi-restraints excluded: chain A residue 612 THR Chi-restraints excluded: chain A residue 618 VAL Chi-restraints excluded: chain A residue 655 ILE Chi-restraints excluded: chain A residue 707 ILE Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 821 ASN Chi-restraints excluded: chain A residue 834 THR Chi-restraints excluded: chain A residue 876 HIS Chi-restraints excluded: chain A residue 964 VAL Chi-restraints excluded: chain A residue 972 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1128 ASN Chi-restraints excluded: chain A residue 1162 LEU Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 128 SER Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 280 VAL Chi-restraints excluded: chain B residue 296 SER Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 369 SER Chi-restraints excluded: chain B residue 387 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 625 TYR Chi-restraints excluded: chain B residue 713 PHE Chi-restraints excluded: chain B residue 814 CYS Chi-restraints excluded: chain B residue 878 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 333 optimal weight: 2.9990 chunk 263 optimal weight: 20.0000 chunk 51 optimal weight: 10.0000 chunk 235 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 246 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 244 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 584 ASN C 876 HIS ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS ** B 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.127455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.088844 restraints weight = 53981.980| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 2.89 r_work: 0.3122 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.4460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28596 Z= 0.124 Angle : 0.549 13.357 39058 Z= 0.285 Chirality : 0.044 0.260 4471 Planarity : 0.004 0.054 4969 Dihedral : 5.064 56.420 4444 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.66 % Favored : 94.31 % Rotamer: Outliers : 1.92 % Allowed : 12.92 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3497 helix: 1.15 (0.21), residues: 744 sheet: -0.48 (0.19), residues: 734 loop : -1.69 (0.13), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 575 HIS 0.014 0.001 HIS C 876 PHE 0.018 0.001 PHE A 589 TYR 0.016 0.001 TYR A 235 ARG 0.006 0.000 ARG A1064 Details of bonding type rmsd link_NAG-ASN : bond 0.00277 ( 25) link_NAG-ASN : angle 2.00195 ( 75) link_BETA1-4 : bond 0.00512 ( 6) link_BETA1-4 : angle 1.18639 ( 18) hydrogen bonds : bond 0.04460 ( 779) hydrogen bonds : angle 4.64937 ( 2181) SS BOND : bond 0.00226 ( 67) SS BOND : angle 1.52536 ( 134) covalent geometry : bond 0.00294 (28498) covalent geometry : angle 0.53544 (38831) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16702.34 seconds wall clock time: 288 minutes 52.07 seconds (17332.07 seconds total)