Starting phenix.real_space_refine on Sun May 3 15:47:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i5b_35193/05_2026/8i5b_35193.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i5b_35193/05_2026/8i5b_35193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i5b_35193/05_2026/8i5b_35193.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i5b_35193/05_2026/8i5b_35193.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i5b_35193/05_2026/8i5b_35193.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i5b_35193/05_2026/8i5b_35193.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.077 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: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 98 5.16 5 C 8907 2.51 5 N 2039 2.21 5 O 2384 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13440 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1272, 10251 Classifications: {'peptide': 1272} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1229} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1404 Classifications: {'peptide': 171} Link IDs: {'TRANS': 170} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 980 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} 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: "A" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 679 Unusual residues: {'LPE': 6, 'NAG': 2, 'OJ0': 1, 'PCW': 5, 'Y01': 6} Classifications: {'peptide': 1, 'undetermined': 20} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'P5S:plan-2': 1, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 9 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 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.32, per 1000 atoms: 0.25 Number of scatterers: 13440 At special positions: 0 Unit cell: (131.48, 141.86, 125.425, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 98 16.00 P 12 15.00 O 2384 8.00 N 2039 7.00 C 8907 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.01 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " 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-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG B 304 " - " ASN B 135 " " NAG C 301 " - " ASN C 66 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 580.4 milliseconds 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2966 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 66.0% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 16 through 33 Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.141A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N LYS A 85 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.630A pdb=" N HIS A 125 " --> pdb=" O LYS A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.660A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.034A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.981A pdb=" N THR A 202 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 204 " --> pdb=" O TYR A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.631A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 removed outlier: 4.167A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.346A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 244 Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.721A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.504A pdb=" N PHE A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.785A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.869A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 418 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.531A pdb=" N VAL A 746 " --> pdb=" O MET A 742 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 804 removed outlier: 3.525A pdb=" N PHE A 804 " --> pdb=" O PRO A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 832 through 836 removed outlier: 4.180A pdb=" N SER A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 832 through 836' Processing helix chain 'A' and resid 837 through 848 removed outlier: 3.555A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 863 removed outlier: 3.967A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 6.082A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 925 Processing helix chain 'A' and resid 928 through 940 Processing helix chain 'A' and resid 940 through 972 removed outlier: 3.747A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.515A pdb=" N ALA A 991 " --> pdb=" O ASN A 987 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A1005 " --> pdb=" O TYR A1001 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 3.591A pdb=" N GLU A1190 " --> pdb=" O TYR A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1210 Processing helix chain 'A' and resid 1211 through 1212 No H-bonds generated for 'chain 'A' and resid 1211 through 1212' Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 4.416A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1255 removed outlier: 3.750A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 9.690A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1285 through 1292 Processing helix chain 'A' and resid 1293 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.789A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.926A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1444 removed outlier: 3.766A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1467 Processing helix chain 'A' and resid 1475 through 1488 removed outlier: 3.921A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1514 removed outlier: 4.172A pdb=" N LEU A1511 " --> pdb=" O CYS A1507 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1534 removed outlier: 3.626A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1568 removed outlier: 3.585A pdb=" N THR A1544 " --> pdb=" O SER A1540 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A1568 " --> pdb=" O LEU A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 4.170A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1625 Processing helix chain 'A' and resid 1627 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.147A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 Proline residue: A1706 - end of helix removed outlier: 3.844A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1767 removed outlier: 3.715A pdb=" N VAL A1752 " --> pdb=" O PHE A1748 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ASN A1753 " --> pdb=" O LEU A1749 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.837A pdb=" N GLU B 87 " --> pdb=" O GLU B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 190 removed outlier: 3.565A pdb=" N LYS B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS B 184 " --> pdb=" O TYR B 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.195A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.539A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.195A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.029A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.346A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 48 794 hydrogen bonds defined for protein. 2253 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: 2.55 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 2024 1.29 - 1.42: 3516 1.42 - 1.56: 8018 1.56 - 1.69: 27 1.69 - 1.83: 159 Bond restraints: 13744 Sorted by residual: bond pdb=" C06 OJ0 A2021 " pdb=" N02 OJ0 A2021 " ideal model delta sigma weight residual 1.450 1.293 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" C09 OJ0 A2021 " pdb=" N02 OJ0 A2021 " ideal model delta sigma weight residual 1.446 1.302 0.144 2.00e-02 2.50e+03 5.21e+01 bond pdb=" C04 OJ0 A2021 " pdb=" N02 OJ0 A2021 " ideal model delta sigma weight residual 1.440 1.339 0.101 2.00e-02 2.50e+03 2.57e+01 bond pdb=" C VAL A1758 " pdb=" O VAL A1758 " ideal model delta sigma weight residual 1.231 1.184 0.047 1.02e-02 9.61e+03 2.17e+01 bond pdb=" CA VAL A1758 " pdb=" C VAL A1758 " ideal model delta sigma weight residual 1.524 1.476 0.047 1.07e-02 8.73e+03 1.96e+01 ... (remaining 13739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 18075 2.04 - 4.08: 398 4.08 - 6.11: 72 6.11 - 8.15: 28 8.15 - 10.19: 4 Bond angle restraints: 18577 Sorted by residual: angle pdb=" N VAL A1758 " pdb=" CA VAL A1758 " pdb=" C VAL A1758 " ideal model delta sigma weight residual 111.81 104.25 7.56 8.60e-01 1.35e+00 7.72e+01 angle pdb=" N THR A 215 " pdb=" CA THR A 215 " pdb=" C THR A 215 " ideal model delta sigma weight residual 111.36 107.10 4.26 1.09e+00 8.42e-01 1.53e+01 angle pdb=" CA CYS A1350 " pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " ideal model delta sigma weight residual 114.40 122.21 -7.81 2.30e+00 1.89e-01 1.15e+01 angle pdb=" N ILE A1246 " pdb=" CA ILE A1246 " pdb=" C ILE A1246 " ideal model delta sigma weight residual 113.07 108.53 4.54 1.36e+00 5.41e-01 1.11e+01 angle pdb=" N GLU A 407 " pdb=" CA GLU A 407 " pdb=" C GLU A 407 " ideal model delta sigma weight residual 110.97 107.36 3.61 1.09e+00 8.42e-01 1.10e+01 ... (remaining 18572 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.70: 8132 30.70 - 61.41: 543 61.41 - 92.11: 44 92.11 - 122.81: 9 122.81 - 153.52: 3 Dihedral angle restraints: 8731 sinusoidal: 4144 harmonic: 4587 Sorted by residual: dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 40.56 52.44 1 1.00e+01 1.00e-02 3.75e+01 dihedral pdb=" CA ASN A1366 " pdb=" C ASN A1366 " pdb=" N ARG A1367 " pdb=" CA ARG A1367 " ideal model delta harmonic sigma weight residual -180.00 -150.65 -29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CB CYS A1350 " pdb=" SG CYS A1350 " pdb=" SG CYS A1370 " pdb=" CB CYS A1370 " ideal model delta sinusoidal sigma weight residual 93.00 140.91 -47.91 1 1.00e+01 1.00e-02 3.17e+01 ... (remaining 8728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1865 0.064 - 0.128: 232 0.128 - 0.192: 17 0.192 - 0.256: 1 0.256 - 0.321: 3 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 66 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C1 NAG A2001 " pdb=" ND2 ASN A1375 " pdb=" C2 NAG A2001 " pdb=" O5 NAG A2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.38e+00 ... (remaining 2115 not shown) Planarity restraints: 2213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " 0.329 2.00e-02 2.50e+03 2.79e-01 9.73e+02 pdb=" C7 NAG A2001 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " 0.178 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " -0.488 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " -0.253 2.00e-02 2.50e+03 2.14e-01 5.71e+02 pdb=" C7 NAG B 301 " 0.065 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " -0.170 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " 0.362 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 301 " 0.230 2.00e-02 2.50e+03 1.93e-01 4.66e+02 pdb=" C7 NAG C 301 " -0.060 2.00e-02 2.50e+03 pdb=" C8 NAG C 301 " 0.160 2.00e-02 2.50e+03 pdb=" N2 NAG C 301 " -0.323 2.00e-02 2.50e+03 pdb=" O7 NAG C 301 " -0.007 2.00e-02 2.50e+03 ... (remaining 2210 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 828 2.74 - 3.28: 13479 3.28 - 3.82: 22140 3.82 - 4.36: 26582 4.36 - 4.90: 45464 Nonbonded interactions: 108493 Sorted by model distance: nonbonded pdb=" O ALA A1415 " pdb=" OG SER A1418 " model vdw 2.196 3.040 nonbonded pdb=" O VAL A1758 " pdb=" ND2 ASN A1762 " model vdw 2.226 3.120 nonbonded pdb=" OD1 ASN A 278 " pdb=" OG1 THR A 329 " model vdw 2.227 3.040 nonbonded pdb=" O LEU A 184 " pdb=" NE1 TRP A 190 " model vdw 2.268 3.120 nonbonded pdb=" OG SER A1320 " pdb=" OD1 ASN A1459 " model vdw 2.270 3.040 ... (remaining 108488 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 'D' selection = chain 'E' } 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=0.00 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 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 : 0.006 0.157 13766 Z= 0.300 Angle : 0.750 10.191 18632 Z= 0.356 Chirality : 0.043 0.321 2118 Planarity : 0.011 0.279 2204 Dihedral : 18.981 153.515 5732 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.93 % Allowed : 28.58 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.22), residues: 1547 helix: 1.62 (0.17), residues: 905 sheet: 0.22 (0.48), residues: 130 loop : -0.90 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.015 0.001 TYR A1739 PHE 0.021 0.001 PHE A 100 TRP 0.013 0.001 TRP A1382 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00582 (13744) covalent geometry : angle 0.74029 (18577) SS BOND : bond 0.00732 ( 11) SS BOND : angle 1.82323 ( 22) hydrogen bonds : bond 0.15004 ( 786) hydrogen bonds : angle 6.33666 ( 2253) link_BETA1-4 : bond 0.00491 ( 2) link_BETA1-4 : angle 3.15862 ( 6) link_NAG-ASN : bond 0.00765 ( 9) link_NAG-ASN : angle 2.49950 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 222 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 LYS cc_start: 0.7317 (tppt) cc_final: 0.6863 (tmmt) REVERT: A 130 MET cc_start: 0.6473 (ttt) cc_final: 0.6030 (mpp) REVERT: A 151 TRP cc_start: 0.8072 (p-90) cc_final: 0.7779 (p-90) REVERT: A 214 ARG cc_start: 0.7423 (ttm-80) cc_final: 0.7190 (tmt170) REVERT: A 403 MET cc_start: 0.7657 (mtt) cc_final: 0.7182 (mtp) REVERT: A 781 LEU cc_start: 0.8078 (tp) cc_final: 0.7818 (mt) REVERT: A 798 MET cc_start: 0.6228 (ptt) cc_final: 0.6020 (ptm) REVERT: A 1230 ASP cc_start: 0.7742 (t0) cc_final: 0.7390 (m-30) REVERT: A 1251 LYS cc_start: 0.6083 (ttmt) cc_final: 0.5361 (ttpp) REVERT: A 1486 LYS cc_start: 0.8110 (ttpt) cc_final: 0.7684 (ttpp) REVERT: A 1543 MET cc_start: 0.7828 (mmt) cc_final: 0.7576 (mmt) REVERT: A 1561 GLU cc_start: 0.8027 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 1571 HIS cc_start: 0.7135 (p-80) cc_final: 0.6647 (p90) REVERT: B 116 SER cc_start: 0.8711 (t) cc_final: 0.8443 (p) outliers start: 13 outliers final: 10 residues processed: 234 average time/residue: 0.5259 time to fit residues: 136.1055 Evaluate side-chains 198 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1557 LEU Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 360 GLN A 861 ASN A1180 ASN A1462 GLN A1579 ASN A1709 ASN B 131 ASN C 39 ASN C 59 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.188197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.121921 restraints weight = 16095.126| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 2.20 r_work: 0.3181 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13766 Z= 0.160 Angle : 0.597 8.637 18632 Z= 0.297 Chirality : 0.043 0.287 2118 Planarity : 0.004 0.043 2204 Dihedral : 13.338 155.593 2756 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 4.49 % Allowed : 25.45 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.21), residues: 1547 helix: 1.73 (0.17), residues: 914 sheet: -0.13 (0.45), residues: 135 loop : -0.81 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 84 TYR 0.018 0.001 TYR A1739 PHE 0.026 0.002 PHE C 52 TRP 0.011 0.001 TRP A1382 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00366 (13744) covalent geometry : angle 0.58356 (18577) SS BOND : bond 0.01200 ( 11) SS BOND : angle 1.65570 ( 22) hydrogen bonds : bond 0.04507 ( 786) hydrogen bonds : angle 4.83813 ( 2253) link_BETA1-4 : bond 0.00131 ( 2) link_BETA1-4 : angle 3.78104 ( 6) link_NAG-ASN : bond 0.00988 ( 9) link_NAG-ASN : angle 2.51047 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 198 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8884 (mt) cc_final: 0.8588 (mp) REVERT: A 130 MET cc_start: 0.6469 (ttt) cc_final: 0.5880 (mpp) REVERT: A 151 TRP cc_start: 0.8051 (p-90) cc_final: 0.7728 (p-90) REVERT: A 214 ARG cc_start: 0.7569 (ttm-80) cc_final: 0.7029 (tmt170) REVERT: A 240 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8178 (mm-40) REVERT: A 403 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.6782 (mpt) REVERT: A 405 TYR cc_start: 0.7134 (t80) cc_final: 0.6441 (t80) REVERT: A 408 GLN cc_start: 0.7149 (OUTLIER) cc_final: 0.6268 (mt0) REVERT: A 781 LEU cc_start: 0.8068 (tp) cc_final: 0.7802 (mt) REVERT: A 952 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7853 (tpt) REVERT: A 1187 LYS cc_start: 0.8690 (tptt) cc_final: 0.8153 (mptt) REVERT: A 1251 LYS cc_start: 0.6113 (ttmt) cc_final: 0.5315 (ttpp) REVERT: A 1350 CYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8671 (m) REVERT: A 1366 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7184 (p0) REVERT: A 1466 LYS cc_start: 0.7429 (mmmt) cc_final: 0.7171 (ttpt) REVERT: A 1543 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7645 (mmt) REVERT: A 1561 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7594 (tm-30) REVERT: A 1571 HIS cc_start: 0.7235 (OUTLIER) cc_final: 0.6926 (p-80) REVERT: B 34 MET cc_start: 0.8541 (mmp) cc_final: 0.8129 (mmp) REVERT: B 68 VAL cc_start: 0.8142 (t) cc_final: 0.7880 (m) REVERT: B 79 GLN cc_start: 0.8614 (tt0) cc_final: 0.8306 (tt0) REVERT: B 149 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7956 (tttm) REVERT: B 154 MET cc_start: 0.6672 (tpt) cc_final: 0.6330 (tmm) REVERT: B 178 MET cc_start: 0.7789 (ttm) cc_final: 0.7503 (mtp) REVERT: C 130 MET cc_start: 0.7049 (mmm) cc_final: 0.6622 (mmt) outliers start: 63 outliers final: 22 residues processed: 243 average time/residue: 0.5094 time to fit residues: 137.4119 Evaluate side-chains 216 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 186 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1374 MET Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1571 HIS Chi-restraints excluded: chain A residue 1725 SER Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 123 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 143 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1180 ASN A1709 ASN B 131 ASN C 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.189340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.119275 restraints weight = 15983.904| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.91 r_work: 0.3252 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13766 Z= 0.129 Angle : 0.549 8.706 18632 Z= 0.274 Chirality : 0.041 0.297 2118 Planarity : 0.004 0.042 2204 Dihedral : 12.661 154.869 2743 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 5.27 % Allowed : 25.23 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.21), residues: 1547 helix: 1.87 (0.17), residues: 914 sheet: -0.02 (0.44), residues: 135 loop : -0.79 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.017 0.001 TYR A1739 PHE 0.028 0.001 PHE C 52 TRP 0.010 0.001 TRP A1382 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00294 (13744) covalent geometry : angle 0.53669 (18577) SS BOND : bond 0.00517 ( 11) SS BOND : angle 1.49581 ( 22) hydrogen bonds : bond 0.03992 ( 786) hydrogen bonds : angle 4.60440 ( 2253) link_BETA1-4 : bond 0.00267 ( 2) link_BETA1-4 : angle 3.59321 ( 6) link_NAG-ASN : bond 0.00939 ( 9) link_NAG-ASN : angle 2.27481 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 195 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 ILE cc_start: 0.8883 (mt) cc_final: 0.8574 (mp) REVERT: A 130 MET cc_start: 0.6549 (ttt) cc_final: 0.5926 (mpp) REVERT: A 151 TRP cc_start: 0.8057 (p-90) cc_final: 0.7753 (p-90) REVERT: A 214 ARG cc_start: 0.7492 (ttm-80) cc_final: 0.7013 (tmt170) REVERT: A 240 GLN cc_start: 0.8427 (mm-40) cc_final: 0.8158 (mm-40) REVERT: A 405 TYR cc_start: 0.7070 (t80) cc_final: 0.6397 (t80) REVERT: A 408 GLN cc_start: 0.7201 (OUTLIER) cc_final: 0.6847 (tp40) REVERT: A 781 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7763 (mt) REVERT: A 952 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7833 (tpt) REVERT: A 1187 LYS cc_start: 0.8642 (tptt) cc_final: 0.8076 (mptt) REVERT: A 1251 LYS cc_start: 0.6131 (ttmt) cc_final: 0.5344 (ttpp) REVERT: A 1308 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.6142 (ttm-80) REVERT: A 1350 CYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8530 (m) REVERT: A 1366 ASN cc_start: 0.7604 (OUTLIER) cc_final: 0.7208 (p0) REVERT: A 1543 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7772 (mmt) REVERT: A 1561 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: A 1571 HIS cc_start: 0.7409 (p-80) cc_final: 0.7152 (p-80) REVERT: A 1754 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7547 (mtt) REVERT: B 34 MET cc_start: 0.8494 (mmp) cc_final: 0.8096 (mmp) REVERT: B 45 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.6915 (ttt180) REVERT: B 112 THR cc_start: 0.8004 (OUTLIER) cc_final: 0.7674 (p) REVERT: B 149 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7906 (tttm) REVERT: B 154 MET cc_start: 0.6640 (tpt) cc_final: 0.6328 (tmm) REVERT: B 178 MET cc_start: 0.7608 (ttm) cc_final: 0.7365 (mtp) REVERT: C 130 MET cc_start: 0.7015 (mmm) cc_final: 0.6752 (mmt) outliers start: 74 outliers final: 25 residues processed: 251 average time/residue: 0.5482 time to fit residues: 152.0070 Evaluate side-chains 226 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 189 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1308 ARG Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain A residue 1725 SER Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 64 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 115 optimal weight: 0.7980 chunk 117 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 6.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1180 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.188426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.119295 restraints weight = 16150.909| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.24 r_work: 0.3200 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13766 Z= 0.127 Angle : 0.552 9.496 18632 Z= 0.273 Chirality : 0.040 0.304 2118 Planarity : 0.004 0.040 2204 Dihedral : 12.286 155.991 2743 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.92 % Allowed : 25.87 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.22), residues: 1547 helix: 1.93 (0.17), residues: 914 sheet: 0.14 (0.45), residues: 135 loop : -0.79 (0.28), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.017 0.001 TYR A1739 PHE 0.031 0.001 PHE C 52 TRP 0.010 0.001 TRP A 188 HIS 0.008 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00287 (13744) covalent geometry : angle 0.53823 (18577) SS BOND : bond 0.00397 ( 11) SS BOND : angle 1.66951 ( 22) hydrogen bonds : bond 0.03818 ( 786) hydrogen bonds : angle 4.48015 ( 2253) link_BETA1-4 : bond 0.00221 ( 2) link_BETA1-4 : angle 3.50106 ( 6) link_NAG-ASN : bond 0.00934 ( 9) link_NAG-ASN : angle 2.39011 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 191 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6534 (ttt) cc_final: 0.5915 (mpp) REVERT: A 151 TRP cc_start: 0.8052 (p-90) cc_final: 0.7749 (p-90) REVERT: A 214 ARG cc_start: 0.7551 (ttm-80) cc_final: 0.7123 (mtp180) REVERT: A 220 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7972 (mtt180) REVERT: A 240 GLN cc_start: 0.8392 (mm-40) cc_final: 0.8151 (mm-40) REVERT: A 405 TYR cc_start: 0.7087 (t80) cc_final: 0.6387 (t80) REVERT: A 408 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6832 (tp40) REVERT: A 781 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7786 (mt) REVERT: A 952 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7856 (tpt) REVERT: A 1187 LYS cc_start: 0.8625 (tptt) cc_final: 0.8032 (mptt) REVERT: A 1251 LYS cc_start: 0.6168 (ttmt) cc_final: 0.5399 (ttpp) REVERT: A 1350 CYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8582 (m) REVERT: A 1366 ASN cc_start: 0.7642 (OUTLIER) cc_final: 0.7262 (p0) REVERT: A 1543 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7753 (mmt) REVERT: A 1561 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 1571 HIS cc_start: 0.7345 (p-80) cc_final: 0.7093 (p-80) REVERT: A 1754 MET cc_start: 0.8121 (OUTLIER) cc_final: 0.7644 (mtt) REVERT: B 45 ARG cc_start: 0.8502 (OUTLIER) cc_final: 0.6941 (ttt180) REVERT: B 112 THR cc_start: 0.7981 (OUTLIER) cc_final: 0.7625 (p) REVERT: B 140 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8240 (mtpt) REVERT: B 149 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7881 (tttm) REVERT: B 153 ASP cc_start: 0.6975 (p0) cc_final: 0.6264 (p0) REVERT: B 154 MET cc_start: 0.6566 (tpt) cc_final: 0.6308 (tmm) REVERT: C 130 MET cc_start: 0.6981 (mmm) cc_final: 0.6655 (mmt) outliers start: 69 outliers final: 27 residues processed: 241 average time/residue: 0.5475 time to fit residues: 145.8536 Evaluate side-chains 227 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 187 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1725 SER Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 149 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 110 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 12 optimal weight: 0.1980 chunk 75 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1180 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.189603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124472 restraints weight = 16106.954| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.24 r_work: 0.3209 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 13766 Z= 0.112 Angle : 0.535 9.259 18632 Z= 0.264 Chirality : 0.039 0.307 2118 Planarity : 0.003 0.040 2204 Dihedral : 11.850 157.938 2742 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.78 % Allowed : 25.87 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.22), residues: 1547 helix: 2.02 (0.17), residues: 914 sheet: 0.25 (0.45), residues: 129 loop : -0.74 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.020 0.001 TYR B 32 PHE 0.031 0.001 PHE C 52 TRP 0.010 0.001 TRP A 188 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00246 (13744) covalent geometry : angle 0.52156 (18577) SS BOND : bond 0.00392 ( 11) SS BOND : angle 1.39274 ( 22) hydrogen bonds : bond 0.03540 ( 786) hydrogen bonds : angle 4.33041 ( 2253) link_BETA1-4 : bond 0.00419 ( 2) link_BETA1-4 : angle 3.26149 ( 6) link_NAG-ASN : bond 0.00929 ( 9) link_NAG-ASN : angle 2.46348 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 194 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7126 (p90) cc_final: 0.6468 (p90) REVERT: A 130 MET cc_start: 0.6530 (ttt) cc_final: 0.5919 (mpp) REVERT: A 151 TRP cc_start: 0.8060 (p-90) cc_final: 0.7762 (p-90) REVERT: A 214 ARG cc_start: 0.7547 (ttm-80) cc_final: 0.7146 (mtp180) REVERT: A 220 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7924 (mtt180) REVERT: A 403 MET cc_start: 0.7664 (mtt) cc_final: 0.6818 (mpt) REVERT: A 405 TYR cc_start: 0.7013 (t80) cc_final: 0.6342 (t80) REVERT: A 408 GLN cc_start: 0.7133 (OUTLIER) cc_final: 0.6794 (tp40) REVERT: A 781 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 1187 LYS cc_start: 0.8590 (tptt) cc_final: 0.7966 (mptt) REVERT: A 1251 LYS cc_start: 0.6237 (ttmt) cc_final: 0.5520 (ttpp) REVERT: A 1350 CYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8557 (m) REVERT: A 1366 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7239 (p0) REVERT: A 1543 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7748 (mmt) REVERT: A 1561 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7693 (tm-30) REVERT: A 1571 HIS cc_start: 0.7364 (p-80) cc_final: 0.7100 (p-80) REVERT: A 1754 MET cc_start: 0.8075 (OUTLIER) cc_final: 0.7599 (mtt) REVERT: B 34 MET cc_start: 0.8508 (mmp) cc_final: 0.8259 (mmm) REVERT: B 45 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7099 (ttt180) REVERT: B 79 GLN cc_start: 0.8572 (tt0) cc_final: 0.7953 (tm-30) REVERT: B 112 THR cc_start: 0.7952 (OUTLIER) cc_final: 0.7652 (p) REVERT: B 149 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7872 (tttm) REVERT: B 154 MET cc_start: 0.6499 (tpt) cc_final: 0.6243 (tmm) REVERT: C 130 MET cc_start: 0.6945 (mmm) cc_final: 0.6516 (mmt) outliers start: 67 outliers final: 26 residues processed: 241 average time/residue: 0.5405 time to fit residues: 143.9067 Evaluate side-chains 225 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1512 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 0.8980 chunk 108 optimal weight: 4.9990 chunk 98 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN A1180 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.188113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.118251 restraints weight = 16033.005| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.87 r_work: 0.3180 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13766 Z= 0.152 Angle : 0.581 9.763 18632 Z= 0.285 Chirality : 0.041 0.310 2118 Planarity : 0.004 0.040 2204 Dihedral : 11.831 158.592 2740 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.63 % Allowed : 25.94 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.22), residues: 1547 helix: 1.94 (0.17), residues: 916 sheet: 0.26 (0.45), residues: 129 loop : -0.74 (0.28), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.017 0.001 TYR A 367 PHE 0.033 0.002 PHE C 52 TRP 0.012 0.001 TRP A1382 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00355 (13744) covalent geometry : angle 0.56453 (18577) SS BOND : bond 0.00450 ( 11) SS BOND : angle 1.80845 ( 22) hydrogen bonds : bond 0.03845 ( 786) hydrogen bonds : angle 4.37615 ( 2253) link_BETA1-4 : bond 0.00238 ( 2) link_BETA1-4 : angle 3.39076 ( 6) link_NAG-ASN : bond 0.01046 ( 9) link_NAG-ASN : angle 2.96401 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 197 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7115 (p90) cc_final: 0.6378 (p90) REVERT: A 130 MET cc_start: 0.6548 (ttt) cc_final: 0.5942 (mpp) REVERT: A 151 TRP cc_start: 0.8084 (p-90) cc_final: 0.7789 (p-90) REVERT: A 214 ARG cc_start: 0.7516 (ttm-80) cc_final: 0.7059 (mtp180) REVERT: A 403 MET cc_start: 0.7634 (mtt) cc_final: 0.6740 (mpt) REVERT: A 405 TYR cc_start: 0.7023 (t80) cc_final: 0.6310 (t80) REVERT: A 408 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6797 (tp40) REVERT: A 781 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7756 (mt) REVERT: A 1251 LYS cc_start: 0.6358 (ttmt) cc_final: 0.5636 (ttpp) REVERT: A 1350 CYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8528 (m) REVERT: A 1366 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7314 (p0) REVERT: A 1543 MET cc_start: 0.7988 (OUTLIER) cc_final: 0.7762 (mmt) REVERT: A 1561 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: A 1571 HIS cc_start: 0.7309 (p-80) cc_final: 0.7058 (p-80) REVERT: A 1754 MET cc_start: 0.8160 (OUTLIER) cc_final: 0.7714 (mtt) REVERT: B 34 MET cc_start: 0.8494 (mmp) cc_final: 0.8224 (mmm) REVERT: B 45 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.7051 (ttt180) REVERT: B 79 GLN cc_start: 0.8561 (tt0) cc_final: 0.7948 (tm-30) REVERT: B 112 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7620 (p) REVERT: B 140 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8217 (mtpt) REVERT: B 149 LYS cc_start: 0.8115 (OUTLIER) cc_final: 0.7865 (tttm) REVERT: B 154 MET cc_start: 0.6508 (OUTLIER) cc_final: 0.6268 (tmm) REVERT: C 130 MET cc_start: 0.6845 (mmm) cc_final: 0.6525 (mmt) outliers start: 65 outliers final: 26 residues processed: 240 average time/residue: 0.5379 time to fit residues: 142.4631 Evaluate side-chains 227 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 154 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 30 optimal weight: 0.5980 chunk 102 optimal weight: 0.6980 chunk 121 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN A1709 ASN A1762 ASN B 131 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.189198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.120031 restraints weight = 16041.398| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.87 r_work: 0.3216 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13766 Z= 0.121 Angle : 0.574 10.016 18632 Z= 0.283 Chirality : 0.040 0.309 2118 Planarity : 0.003 0.039 2204 Dihedral : 11.571 159.967 2738 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.28 % Allowed : 26.37 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.22), residues: 1547 helix: 1.97 (0.17), residues: 915 sheet: 0.31 (0.45), residues: 129 loop : -0.77 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.016 0.001 TYR A1739 PHE 0.035 0.001 PHE C 52 TRP 0.012 0.001 TRP A 188 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00274 (13744) covalent geometry : angle 0.55809 (18577) SS BOND : bond 0.00478 ( 11) SS BOND : angle 2.17192 ( 22) hydrogen bonds : bond 0.03605 ( 786) hydrogen bonds : angle 4.33073 ( 2253) link_BETA1-4 : bond 0.00279 ( 2) link_BETA1-4 : angle 3.27798 ( 6) link_NAG-ASN : bond 0.00944 ( 9) link_NAG-ASN : angle 2.68743 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7110 (p90) cc_final: 0.6330 (p90) REVERT: A 130 MET cc_start: 0.6548 (ttt) cc_final: 0.5943 (mpp) REVERT: A 151 TRP cc_start: 0.8070 (p-90) cc_final: 0.7759 (p-90) REVERT: A 214 ARG cc_start: 0.7565 (ttm-80) cc_final: 0.7046 (tmt170) REVERT: A 403 MET cc_start: 0.7686 (OUTLIER) cc_final: 0.6771 (mpt) REVERT: A 405 TYR cc_start: 0.6999 (t80) cc_final: 0.6321 (t80) REVERT: A 408 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.6812 (tp40) REVERT: A 781 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7761 (mt) REVERT: A 1230 ASP cc_start: 0.7992 (t0) cc_final: 0.7659 (m-30) REVERT: A 1251 LYS cc_start: 0.6305 (ttmt) cc_final: 0.5608 (ttpp) REVERT: A 1350 CYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8474 (m) REVERT: A 1366 ASN cc_start: 0.7586 (OUTLIER) cc_final: 0.7266 (p0) REVERT: A 1543 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7740 (mmt) REVERT: A 1561 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7689 (tm-30) REVERT: A 1571 HIS cc_start: 0.7318 (p-80) cc_final: 0.7079 (p-80) REVERT: A 1709 ASN cc_start: 0.7939 (OUTLIER) cc_final: 0.7671 (p0) REVERT: A 1754 MET cc_start: 0.8105 (OUTLIER) cc_final: 0.7652 (mtt) REVERT: B 34 MET cc_start: 0.8506 (mmp) cc_final: 0.8257 (mmm) REVERT: B 45 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7058 (ttt180) REVERT: B 79 GLN cc_start: 0.8571 (tt0) cc_final: 0.7957 (tm-30) REVERT: B 112 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7608 (p) REVERT: B 140 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8194 (mtpt) REVERT: B 149 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7885 (tttt) REVERT: B 153 ASP cc_start: 0.7011 (p0) cc_final: 0.6388 (p0) REVERT: B 154 MET cc_start: 0.6669 (OUTLIER) cc_final: 0.6432 (tmm) REVERT: B 178 MET cc_start: 0.7426 (mtp) cc_final: 0.7035 (mtm) REVERT: C 130 MET cc_start: 0.6878 (mmm) cc_final: 0.6543 (mmt) outliers start: 60 outliers final: 27 residues processed: 232 average time/residue: 0.5068 time to fit residues: 130.6518 Evaluate side-chains 227 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 186 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 154 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 49 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 85 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.187713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.120519 restraints weight = 15826.848| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.37 r_work: 0.3185 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13766 Z= 0.178 Angle : 0.608 10.772 18632 Z= 0.300 Chirality : 0.042 0.311 2118 Planarity : 0.004 0.039 2204 Dihedral : 11.768 161.052 2738 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.49 % Allowed : 25.87 % Favored : 69.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.21), residues: 1547 helix: 1.85 (0.17), residues: 910 sheet: 0.29 (0.45), residues: 129 loop : -0.80 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.018 0.002 TYR A 367 PHE 0.035 0.002 PHE C 52 TRP 0.012 0.001 TRP A1382 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00423 (13744) covalent geometry : angle 0.59352 (18577) SS BOND : bond 0.00542 ( 11) SS BOND : angle 1.86935 ( 22) hydrogen bonds : bond 0.04062 ( 786) hydrogen bonds : angle 4.43544 ( 2253) link_BETA1-4 : bond 0.00135 ( 2) link_BETA1-4 : angle 3.45877 ( 6) link_NAG-ASN : bond 0.00993 ( 9) link_NAG-ASN : angle 2.72647 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 192 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7131 (p90) cc_final: 0.6270 (p90) REVERT: A 130 MET cc_start: 0.6554 (ttt) cc_final: 0.5909 (mpp) REVERT: A 151 TRP cc_start: 0.8111 (p-90) cc_final: 0.7796 (p-90) REVERT: A 214 ARG cc_start: 0.7567 (ttm-80) cc_final: 0.7136 (tmt170) REVERT: A 403 MET cc_start: 0.7754 (OUTLIER) cc_final: 0.6837 (mpt) REVERT: A 405 TYR cc_start: 0.7110 (t80) cc_final: 0.6387 (t80) REVERT: A 781 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7799 (mt) REVERT: A 1251 LYS cc_start: 0.6455 (ttmt) cc_final: 0.5720 (ttpp) REVERT: A 1350 CYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8614 (m) REVERT: A 1366 ASN cc_start: 0.7801 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 1543 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.7927 (mmt) REVERT: A 1561 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7676 (tm-30) REVERT: A 1571 HIS cc_start: 0.7334 (p-80) cc_final: 0.7098 (p-80) REVERT: A 1709 ASN cc_start: 0.7865 (OUTLIER) cc_final: 0.7591 (p0) REVERT: A 1754 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7788 (mtt) REVERT: B 34 MET cc_start: 0.8541 (mmp) cc_final: 0.8313 (mmm) REVERT: B 45 ARG cc_start: 0.8517 (OUTLIER) cc_final: 0.7118 (ttt180) REVERT: B 112 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7619 (p) REVERT: B 140 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8246 (mtpt) REVERT: B 149 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7929 (tttm) REVERT: B 154 MET cc_start: 0.6637 (OUTLIER) cc_final: 0.6343 (tmm) REVERT: B 178 MET cc_start: 0.7507 (mtp) cc_final: 0.7058 (mtm) REVERT: C 130 MET cc_start: 0.6840 (mmm) cc_final: 0.6543 (mmt) outliers start: 63 outliers final: 31 residues processed: 233 average time/residue: 0.4673 time to fit residues: 121.2470 Evaluate side-chains 230 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 85 LYS Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1252 THR Chi-restraints excluded: chain A residue 1266 VAL Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1291 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1640 SER Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 149 LYS Chi-restraints excluded: chain B residue 154 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 147 optimal weight: 8.9990 chunk 66 optimal weight: 8.9990 chunk 123 optimal weight: 0.0870 chunk 84 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 150 optimal weight: 0.0670 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 58 optimal weight: 0.4980 chunk 3 optimal weight: 6.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.190103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.123604 restraints weight = 15723.919| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.16 r_work: 0.3190 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13766 Z= 0.109 Angle : 0.576 11.615 18632 Z= 0.281 Chirality : 0.040 0.303 2118 Planarity : 0.003 0.040 2204 Dihedral : 11.342 162.798 2738 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.99 % Allowed : 27.73 % Favored : 69.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.22), residues: 1547 helix: 2.04 (0.17), residues: 908 sheet: 0.36 (0.45), residues: 129 loop : -0.79 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 84 TYR 0.015 0.001 TYR A1739 PHE 0.035 0.001 PHE C 52 TRP 0.015 0.001 TRP A 188 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00237 (13744) covalent geometry : angle 0.55919 (18577) SS BOND : bond 0.00404 ( 11) SS BOND : angle 1.46919 ( 22) hydrogen bonds : bond 0.03434 ( 786) hydrogen bonds : angle 4.25779 ( 2253) link_BETA1-4 : bond 0.00422 ( 2) link_BETA1-4 : angle 3.19105 ( 6) link_NAG-ASN : bond 0.00921 ( 9) link_NAG-ASN : angle 3.16417 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 196 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7134 (p90) cc_final: 0.6287 (p90) REVERT: A 130 MET cc_start: 0.6772 (ttt) cc_final: 0.6176 (mpp) REVERT: A 151 TRP cc_start: 0.8099 (p-90) cc_final: 0.7827 (p-90) REVERT: A 214 ARG cc_start: 0.7607 (ttm-80) cc_final: 0.7260 (tmt170) REVERT: A 403 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7252 (mpt) REVERT: A 405 TYR cc_start: 0.7289 (t80) cc_final: 0.6576 (t80) REVERT: A 408 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.6899 (tp40) REVERT: A 781 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7783 (mt) REVERT: A 1230 ASP cc_start: 0.8161 (t0) cc_final: 0.7886 (m-30) REVERT: A 1251 LYS cc_start: 0.6541 (ttmt) cc_final: 0.5885 (ttpp) REVERT: A 1350 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8379 (m) REVERT: A 1366 ASN cc_start: 0.7685 (OUTLIER) cc_final: 0.7476 (p0) REVERT: A 1543 MET cc_start: 0.8214 (OUTLIER) cc_final: 0.7993 (mmt) REVERT: A 1561 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7797 (tm-30) REVERT: A 1571 HIS cc_start: 0.7328 (p-80) cc_final: 0.7001 (p90) REVERT: A 1709 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7491 (p0) REVERT: B 45 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.7219 (ttt180) REVERT: B 79 GLN cc_start: 0.8642 (tt0) cc_final: 0.8199 (tm-30) REVERT: B 112 THR cc_start: 0.8200 (OUTLIER) cc_final: 0.7838 (p) REVERT: B 140 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8183 (mtpt) REVERT: B 149 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8039 (tttt) REVERT: B 154 MET cc_start: 0.6845 (tpt) cc_final: 0.6608 (tmm) REVERT: B 178 MET cc_start: 0.7440 (mtp) cc_final: 0.7099 (mtm) REVERT: C 130 MET cc_start: 0.6907 (mmm) cc_final: 0.6594 (mmt) outliers start: 42 outliers final: 21 residues processed: 227 average time/residue: 0.5036 time to fit residues: 126.8182 Evaluate side-chains 225 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 192 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1563 VAL Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 149 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 62 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 147 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 67 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.187789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.118253 restraints weight = 15605.935| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.22 r_work: 0.3139 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13766 Z= 0.163 Angle : 0.612 12.201 18632 Z= 0.299 Chirality : 0.042 0.306 2118 Planarity : 0.004 0.040 2204 Dihedral : 11.507 163.076 2738 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.42 % Allowed : 28.23 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.21), residues: 1547 helix: 1.93 (0.17), residues: 909 sheet: 0.34 (0.45), residues: 129 loop : -0.80 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.018 0.001 TYR A 367 PHE 0.034 0.002 PHE C 52 TRP 0.011 0.001 TRP A1382 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00387 (13744) covalent geometry : angle 0.59634 (18577) SS BOND : bond 0.00536 ( 11) SS BOND : angle 1.71910 ( 22) hydrogen bonds : bond 0.03897 ( 786) hydrogen bonds : angle 4.35947 ( 2253) link_BETA1-4 : bond 0.00142 ( 2) link_BETA1-4 : angle 3.39126 ( 6) link_NAG-ASN : bond 0.00968 ( 9) link_NAG-ASN : angle 3.00676 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3094 Ramachandran restraints generated. 1547 Oldfield, 0 Emsley, 1547 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 PHE cc_start: 0.7119 (p90) cc_final: 0.6280 (p90) REVERT: A 130 MET cc_start: 0.6763 (ttt) cc_final: 0.6130 (mpp) REVERT: A 151 TRP cc_start: 0.8143 (p-90) cc_final: 0.7860 (p-90) REVERT: A 214 ARG cc_start: 0.7579 (ttm-80) cc_final: 0.7213 (tmt170) REVERT: A 403 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7174 (mpt) REVERT: A 405 TYR cc_start: 0.7335 (t80) cc_final: 0.6578 (t80) REVERT: A 408 GLN cc_start: 0.7358 (OUTLIER) cc_final: 0.6989 (tp40) REVERT: A 781 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7820 (mt) REVERT: A 1251 LYS cc_start: 0.6630 (ttmt) cc_final: 0.5928 (ttpp) REVERT: A 1350 CYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8511 (m) REVERT: A 1366 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7605 (p0) REVERT: A 1543 MET cc_start: 0.8336 (OUTLIER) cc_final: 0.8129 (mmt) REVERT: A 1561 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7827 (tm-30) REVERT: A 1571 HIS cc_start: 0.7329 (p-80) cc_final: 0.7065 (p-80) REVERT: A 1709 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7572 (p0) REVERT: B 45 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.7197 (ttt180) REVERT: B 79 GLN cc_start: 0.8701 (tt0) cc_final: 0.8254 (tm-30) REVERT: B 112 THR cc_start: 0.8228 (OUTLIER) cc_final: 0.7799 (p) REVERT: B 140 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8225 (mtpt) REVERT: B 149 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8089 (tttm) REVERT: B 154 MET cc_start: 0.6904 (tpt) cc_final: 0.6642 (tmm) REVERT: B 178 MET cc_start: 0.7488 (mtp) cc_final: 0.7116 (mtm) REVERT: C 130 MET cc_start: 0.6923 (mmm) cc_final: 0.6622 (mmt) outliers start: 34 outliers final: 22 residues processed: 214 average time/residue: 0.5273 time to fit residues: 124.6798 Evaluate side-chains 219 residues out of total 1404 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 182 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 408 GLN Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 776 LEU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 861 ASN Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1350 CYS Chi-restraints excluded: chain A residue 1366 ASN Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1709 ASN Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 112 THR Chi-restraints excluded: chain B residue 116 SER Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 140 LYS Chi-restraints excluded: chain B residue 149 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 121 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.0270 chunk 89 optimal weight: 0.5980 chunk 144 optimal weight: 10.0000 chunk 20 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 99 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 ASN A1709 ASN B 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.189795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.121055 restraints weight = 15746.915| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.22 r_work: 0.3186 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13766 Z= 0.111 Angle : 0.575 12.314 18632 Z= 0.281 Chirality : 0.040 0.301 2118 Planarity : 0.003 0.040 2204 Dihedral : 11.235 163.806 2738 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.35 % Allowed : 28.23 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.22), residues: 1547 helix: 2.07 (0.17), residues: 906 sheet: 0.36 (0.45), residues: 129 loop : -0.78 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 84 TYR 0.015 0.001 TYR B 32 PHE 0.032 0.001 PHE C 52 TRP 0.015 0.001 TRP A 188 HIS 0.009 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00245 (13744) covalent geometry : angle 0.56087 (18577) SS BOND : bond 0.00413 ( 11) SS BOND : angle 1.47555 ( 22) hydrogen bonds : bond 0.03425 ( 786) hydrogen bonds : angle 4.22137 ( 2253) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 3.19417 ( 6) link_NAG-ASN : bond 0.00918 ( 9) link_NAG-ASN : angle 2.71614 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6679.03 seconds wall clock time: 114 minutes 9.17 seconds (6849.17 seconds total)