Starting phenix.real_space_refine on Sun May 3 15:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thg_41261/05_2026/8thg_41261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thg_41261/05_2026/8thg_41261.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thg_41261/05_2026/8thg_41261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thg_41261/05_2026/8thg_41261.map" model { file = "/net/cci-nas-00/data/ceres_data/8thg_41261/05_2026/8thg_41261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thg_41261/05_2026/8thg_41261.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.033 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: 6 Type Number sf(0) Gaussians P 8 5.49 5 S 98 5.16 5 C 8675 2.51 5 N 2038 2.21 5 O 2346 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 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: 13168 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 10262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 10262 Classifications: {'peptide': 1273} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 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: 389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 389 Unusual residues: {'657': 1, 'LPE': 6, 'NAG': 2, 'PCW': 1, 'Y01': 3} Classifications: {'peptide': 1, 'undetermined': 13} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.15, per 1000 atoms: 0.24 Number of scatterers: 13168 At special positions: 0 Unit cell: (132.608, 137.788, 128.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 8 15.00 F 3 9.00 O 2346 8.00 N 2038 7.00 C 8675 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=2.04 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 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=2.03 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 F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2002 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 513.0 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 8 sheets defined 66.4% alpha, 7.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 50 through 54 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 4.006A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.210A pdb=" N ASP A 84 " --> 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: 3.806A pdb=" N ILE A 118 " --> pdb=" O PRO A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 removed outlier: 4.129A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 175 Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.596A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 216 Processing helix chain 'A' and resid 218 through 228 removed outlier: 4.068A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS A 223 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.683A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 267 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 291 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.901A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.871A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 392 through 418 Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.676A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.755A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 804 Proline residue: A 800 - end of helix Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 833 through 847 removed outlier: 3.930A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.931A pdb=" N LEU A 855 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.542A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.193A 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 926 Processing helix chain 'A' and resid 929 through 940 removed outlier: 3.877A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N CYS A 935 " --> pdb=" O THR A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 974 removed outlier: 4.173A pdb=" N ASP A 974 " --> pdb=" O SER A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 977 No H-bonds generated for 'chain 'A' and resid 975 through 977' Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1190 Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 removed outlier: 3.722A pdb=" N GLU A1212 " --> pdb=" O LEU A1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1209 through 1212' Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 4.380A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 removed outlier: 3.706A pdb=" N ILE A1224 " --> pdb=" O LYS A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1255 removed outlier: 3.684A pdb=" N PHE A1254 " --> pdb=" O TYR A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 3.610A pdb=" N ARG A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1301 removed outlier: 3.639A pdb=" N ALA A1294 " --> pdb=" O THR A1291 " (cutoff:3.500A) Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.604A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.684A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1377 removed outlier: 3.519A pdb=" N VAL A1376 " --> pdb=" O ALA A1372 " (cutoff:3.500A) Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.622A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (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: 3.816A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1467 Processing helix chain 'A' and resid 1475 through 1487 removed outlier: 3.773A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS A1487 " --> pdb=" O ASN A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1502 through 1513 removed outlier: 3.881A pdb=" N CYS A1507 " --> pdb=" O LYS A1503 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1534 Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 3.689A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1602 removed outlier: 3.829A pdb=" N ASP A1597 " --> pdb=" O MET A1593 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A1598 " --> pdb=" O PHE A1594 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 3.840A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.566A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.710A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix removed outlier: 3.802A pdb=" N ASN A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.019A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1706 through 1709 removed outlier: 3.735A pdb=" N ASN A1709 " --> pdb=" O PRO A1706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1706 through 1709' Processing helix chain 'A' and resid 1732 through 1768 removed outlier: 3.899A pdb=" N ILE A1744 " --> pdb=" O PHE A1740 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.545A pdb=" N HIS B 115 " --> pdb=" O THR B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 153 through 192 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 74 through 76 removed outlier: 3.583A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) 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 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.114A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA6, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.980A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 41 removed outlier: 3.624A pdb=" N ILE C 129 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 47 through 48 794 hydrogen bonds defined for protein. 2241 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: 2.25 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2014 1.32 - 1.44: 3664 1.44 - 1.57: 7611 1.57 - 1.69: 17 1.69 - 1.82: 157 Bond restraints: 13463 Sorted by residual: bond pdb=" C8 657 A2003 " pdb=" S1 657 A2003 " ideal model delta sigma weight residual 1.765 1.542 0.223 2.00e-02 2.50e+03 1.24e+02 bond pdb=" C4 657 A2003 " pdb=" S1 657 A2003 " ideal model delta sigma weight residual 1.737 1.518 0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" C3 657 A2003 " pdb=" N1 657 A2003 " ideal model delta sigma weight residual 1.370 1.574 -0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C4 657 A2003 " pdb=" C5 657 A2003 " ideal model delta sigma weight residual 1.384 1.544 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" C2 657 A2003 " pdb=" C3 657 A2003 " ideal model delta sigma weight residual 1.393 1.543 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 13458 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.86: 18134 3.86 - 7.72: 76 7.72 - 11.58: 3 11.58 - 15.44: 0 15.44 - 19.30: 1 Bond angle restraints: 18214 Sorted by residual: angle pdb=" C4 657 A2003 " pdb=" S1 657 A2003 " pdb=" C8 657 A2003 " ideal model delta sigma weight residual 88.43 107.73 -19.30 3.00e+00 1.11e-01 4.14e+01 angle pdb=" N TYR A 801 " pdb=" CA TYR A 801 " pdb=" C TYR A 801 " ideal model delta sigma weight residual 111.14 106.95 4.19 1.08e+00 8.57e-01 1.51e+01 angle pdb=" C ILE A1318 " pdb=" CA ILE A1318 " pdb=" CB ILE A1318 " ideal model delta sigma weight residual 113.70 110.05 3.65 9.50e-01 1.11e+00 1.48e+01 angle pdb=" N THR A 182 " pdb=" CA THR A 182 " pdb=" C THR A 182 " ideal model delta sigma weight residual 108.34 113.16 -4.82 1.31e+00 5.83e-01 1.35e+01 angle pdb=" C ASP A1673 " pdb=" CA ASP A1673 " pdb=" CB ASP A1673 " ideal model delta sigma weight residual 117.23 112.47 4.76 1.36e+00 5.41e-01 1.22e+01 ... (remaining 18209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 7982 35.80 - 71.59: 351 71.59 - 107.39: 18 107.39 - 143.18: 7 143.18 - 178.98: 1 Dihedral angle restraints: 8359 sinusoidal: 3768 harmonic: 4591 Sorted by residual: dihedral pdb=" C41 P5S A2009 " pdb=" C42 P5S A2009 " pdb=" C43 P5S A2009 " pdb=" C44 P5S A2009 " ideal model delta sinusoidal sigma weight residual 92.81 -86.17 178.98 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C33 PCW A2008 " pdb=" C31 PCW A2008 " pdb=" C32 PCW A2008 " pdb=" O2 PCW A2008 " ideal model delta sinusoidal sigma weight residual 191.83 66.06 125.77 1 3.00e+01 1.11e-03 1.69e+01 dihedral pdb=" N PCW A2008 " pdb=" C4 PCW A2008 " pdb=" C5 PCW A2008 " pdb=" O4P PCW A2008 " ideal model delta sinusoidal sigma weight residual 293.34 169.80 123.54 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 8356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1833 0.063 - 0.126: 227 0.126 - 0.190: 27 0.190 - 0.253: 4 0.253 - 0.316: 1 Chirality restraints: 2092 Sorted by residual: chirality pdb=" C1 NAG A2001 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A2001 " pdb=" O5 NAG A2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA ILE A 122 " pdb=" N ILE A 122 " pdb=" C ILE A 122 " pdb=" CB ILE A 122 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA ILE A 120 " pdb=" N ILE A 120 " pdb=" C ILE A 120 " pdb=" CB ILE A 120 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 2089 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2008 " -0.065 2.00e-02 2.50e+03 1.25e-01 1.57e+02 pdb=" C19 PCW A2008 " 0.165 2.00e-02 2.50e+03 pdb=" C20 PCW A2008 " -0.165 2.00e-02 2.50e+03 pdb=" C21 PCW A2008 " 0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C38 PCW A2008 " -0.030 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" C39 PCW A2008 " 0.030 2.00e-02 2.50e+03 pdb=" C40 PCW A2008 " 0.029 2.00e-02 2.50e+03 pdb=" C41 PCW A2008 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.026 2.00e-02 2.50e+03 2.17e-02 5.88e+00 pdb=" C7 NAG E 1 " 0.013 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.022 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.032 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.003 2.00e-02 2.50e+03 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 167 2.67 - 3.23: 12685 3.23 - 3.79: 19806 3.79 - 4.34: 26931 4.34 - 4.90: 45389 Nonbonded interactions: 104978 Sorted by model distance: nonbonded pdb=" O ASN A 147 " pdb=" OD1 ASN A 147 " model vdw 2.116 3.040 nonbonded pdb=" OH TYR A1235 " pdb=" OG1 THR B 171 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASP A1701 " pdb=" N GLY A1702 " model vdw 2.238 3.120 nonbonded pdb=" O GLY A 8 " pdb=" OG SER A 11 " model vdw 2.263 3.040 nonbonded pdb=" O GLY A 179 " pdb=" NH2 ARG A 185 " model vdw 2.268 3.120 ... (remaining 104973 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' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 12.690 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:8.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 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 : 0.007 0.223 13485 Z= 0.378 Angle : 0.759 19.296 18269 Z= 0.402 Chirality : 0.044 0.316 2092 Planarity : 0.004 0.125 2187 Dihedral : 18.299 178.979 5358 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.64 % Allowed : 23.86 % Favored : 75.50 % 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: 1.53 (0.23), residues: 1549 helix: 1.98 (0.18), residues: 892 sheet: -0.62 (0.44), residues: 143 loop : -0.13 (0.30), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 60 TYR 0.022 0.001 TYR A 367 PHE 0.022 0.001 PHE A1509 TRP 0.011 0.001 TRP A 188 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00709 (13463) covalent geometry : angle 0.75055 (18214) SS BOND : bond 0.00203 ( 11) SS BOND : angle 0.68815 ( 22) hydrogen bonds : bond 0.13230 ( 794) hydrogen bonds : angle 5.15191 ( 2241) link_BETA1-4 : bond 0.00865 ( 3) link_BETA1-4 : angle 4.02888 ( 9) link_NAG-ASN : bond 0.00422 ( 8) link_NAG-ASN : angle 2.02183 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 166 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1456 ILE cc_start: 0.6845 (tt) cc_final: 0.6615 (tt) REVERT: A 1591 VAL cc_start: 0.8075 (t) cc_final: 0.7830 (m) REVERT: C 54 SER cc_start: 0.8699 (t) cc_final: 0.8446 (t) outliers start: 9 outliers final: 4 residues processed: 174 average time/residue: 0.5558 time to fit residues: 105.8346 Evaluate side-chains 165 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0470 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 395 ASN A 408 GLN A1341 ASN A1528 ASN B 79 GLN C 104 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.187172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.123640 restraints weight = 15346.530| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.40 r_work: 0.3292 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.0904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13485 Z= 0.119 Angle : 0.527 8.316 18269 Z= 0.271 Chirality : 0.041 0.324 2092 Planarity : 0.004 0.043 2187 Dihedral : 12.897 176.386 2368 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.56 % Allowed : 20.09 % Favored : 76.35 % 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: 1.80 (0.22), residues: 1549 helix: 2.26 (0.18), residues: 890 sheet: -0.93 (0.41), residues: 143 loop : -0.01 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 30 TYR 0.019 0.001 TYR A 367 PHE 0.028 0.001 PHE A 204 TRP 0.015 0.001 TRP A1408 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00254 (13463) covalent geometry : angle 0.51532 (18214) SS BOND : bond 0.00332 ( 11) SS BOND : angle 0.99649 ( 22) hydrogen bonds : bond 0.04229 ( 794) hydrogen bonds : angle 4.11213 ( 2241) link_BETA1-4 : bond 0.00670 ( 3) link_BETA1-4 : angle 3.29100 ( 9) link_NAG-ASN : bond 0.00601 ( 8) link_NAG-ASN : angle 2.23935 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 172 time to evaluate : 0.455 Fit side-chains REVERT: A 406 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7364 (tm-30) REVERT: A 794 LYS cc_start: 0.7151 (mtpp) cc_final: 0.6877 (ttpt) REVERT: A 796 ILE cc_start: 0.6128 (OUTLIER) cc_final: 0.5817 (tp) REVERT: A 1456 ILE cc_start: 0.7746 (tt) cc_final: 0.7504 (tt) REVERT: A 1591 VAL cc_start: 0.8651 (t) cc_final: 0.8410 (m) REVERT: A 1600 GLU cc_start: 0.7459 (tt0) cc_final: 0.7211 (pp20) outliers start: 50 outliers final: 19 residues processed: 204 average time/residue: 0.4654 time to fit residues: 105.3059 Evaluate side-chains 178 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 268 MET Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1599 ILE Chi-restraints excluded: chain A residue 1608 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 1.9990 chunk 153 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 0.3980 chunk 146 optimal weight: 2.9990 chunk 122 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 360 GLN A 408 GLN A1579 ASN A1676 ASN B 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.185289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.122119 restraints weight = 15395.279| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.39 r_work: 0.3277 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13485 Z= 0.142 Angle : 0.516 8.254 18269 Z= 0.266 Chirality : 0.041 0.306 2092 Planarity : 0.004 0.042 2187 Dihedral : 11.831 177.405 2365 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.49 % Allowed : 21.44 % Favored : 75.07 % 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: 1.81 (0.22), residues: 1549 helix: 2.29 (0.17), residues: 893 sheet: -0.80 (0.40), residues: 143 loop : -0.11 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 96 TYR 0.022 0.001 TYR A 367 PHE 0.022 0.001 PHE A1509 TRP 0.010 0.001 TRP A 151 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00335 (13463) covalent geometry : angle 0.50411 (18214) SS BOND : bond 0.00293 ( 11) SS BOND : angle 0.92406 ( 22) hydrogen bonds : bond 0.04185 ( 794) hydrogen bonds : angle 3.94331 ( 2241) link_BETA1-4 : bond 0.00610 ( 3) link_BETA1-4 : angle 3.11083 ( 9) link_NAG-ASN : bond 0.00519 ( 8) link_NAG-ASN : angle 2.40310 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 0.478 Fit side-chains REVERT: A 296 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6799 (tm-30) REVERT: A 406 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7434 (tm-30) REVERT: A 796 ILE cc_start: 0.6366 (OUTLIER) cc_final: 0.6041 (tp) REVERT: A 943 MET cc_start: 0.8148 (OUTLIER) cc_final: 0.7701 (mmm) REVERT: A 1456 ILE cc_start: 0.7751 (OUTLIER) cc_final: 0.7483 (tt) REVERT: A 1595 LEU cc_start: 0.8534 (tp) cc_final: 0.8319 (tt) REVERT: A 1600 GLU cc_start: 0.7456 (tt0) cc_final: 0.7246 (pp20) REVERT: A 1760 LEU cc_start: 0.6940 (mp) cc_final: 0.6731 (tt) outliers start: 49 outliers final: 21 residues processed: 194 average time/residue: 0.4824 time to fit residues: 103.9013 Evaluate side-chains 176 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 30 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.8980 chunk 144 optimal weight: 20.0000 chunk 37 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A1341 ASN A1462 GLN A1676 ASN B 79 GLN C 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.186317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.123166 restraints weight = 15410.803| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.40 r_work: 0.3289 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13485 Z= 0.115 Angle : 0.493 9.630 18269 Z= 0.253 Chirality : 0.040 0.311 2092 Planarity : 0.004 0.048 2187 Dihedral : 11.220 178.497 2365 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.71 % Allowed : 22.01 % Favored : 75.28 % 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: 1.93 (0.22), residues: 1549 helix: 2.43 (0.17), residues: 888 sheet: -0.95 (0.39), residues: 147 loop : -0.04 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.018 0.001 TYR A 367 PHE 0.022 0.001 PHE A1509 TRP 0.012 0.001 TRP A 151 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00260 (13463) covalent geometry : angle 0.48047 (18214) SS BOND : bond 0.00295 ( 11) SS BOND : angle 0.89529 ( 22) hydrogen bonds : bond 0.03800 ( 794) hydrogen bonds : angle 3.79449 ( 2241) link_BETA1-4 : bond 0.00504 ( 3) link_BETA1-4 : angle 2.90835 ( 9) link_NAG-ASN : bond 0.00559 ( 8) link_NAG-ASN : angle 2.35451 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.389 Fit side-chains REVERT: A 189 ASN cc_start: 0.7887 (m-40) cc_final: 0.7630 (m-40) REVERT: A 296 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6795 (tm-30) REVERT: A 406 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7422 (tm-30) REVERT: A 796 ILE cc_start: 0.6353 (OUTLIER) cc_final: 0.6022 (tp) REVERT: A 844 LYS cc_start: 0.8822 (mttp) cc_final: 0.8496 (mtpt) REVERT: A 943 MET cc_start: 0.8181 (OUTLIER) cc_final: 0.7725 (mmm) REVERT: A 1456 ILE cc_start: 0.7692 (tt) cc_final: 0.7427 (tt) REVERT: A 1591 VAL cc_start: 0.8647 (t) cc_final: 0.8412 (m) REVERT: A 1595 LEU cc_start: 0.8563 (tp) cc_final: 0.8349 (tt) REVERT: A 1600 GLU cc_start: 0.7503 (tt0) cc_final: 0.7182 (pp20) outliers start: 38 outliers final: 16 residues processed: 187 average time/residue: 0.4822 time to fit residues: 99.9412 Evaluate side-chains 170 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain B residue 131 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 28 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 152 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN A1676 ASN B 79 GLN C 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.180121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117137 restraints weight = 15431.119| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.36 r_work: 0.3285 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13485 Z= 0.174 Angle : 0.544 9.790 18269 Z= 0.278 Chirality : 0.041 0.300 2092 Planarity : 0.004 0.045 2187 Dihedral : 11.108 169.580 2363 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.20 % Allowed : 20.80 % Favored : 75.00 % 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: 1.75 (0.22), residues: 1549 helix: 2.30 (0.17), residues: 889 sheet: -1.04 (0.38), residues: 152 loop : -0.13 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1616 TYR 0.025 0.002 TYR A 367 PHE 0.017 0.002 PHE A1509 TRP 0.011 0.001 TRP A 151 HIS 0.004 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00424 (13463) covalent geometry : angle 0.53249 (18214) SS BOND : bond 0.00323 ( 11) SS BOND : angle 0.96768 ( 22) hydrogen bonds : bond 0.04318 ( 794) hydrogen bonds : angle 3.87338 ( 2241) link_BETA1-4 : bond 0.00582 ( 3) link_BETA1-4 : angle 3.07911 ( 9) link_NAG-ASN : bond 0.00553 ( 8) link_NAG-ASN : angle 2.46183 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6902 (tpt) cc_final: 0.5462 (mtt) REVERT: A 296 GLU cc_start: 0.7060 (OUTLIER) cc_final: 0.6633 (tm-30) REVERT: A 406 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: A 796 ILE cc_start: 0.6323 (OUTLIER) cc_final: 0.6001 (tp) REVERT: A 844 LYS cc_start: 0.8719 (mttp) cc_final: 0.8299 (mtpt) REVERT: A 890 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7857 (mmtp) REVERT: A 943 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7482 (mmm) REVERT: A 982 ASP cc_start: 0.0979 (OUTLIER) cc_final: 0.0289 (t0) REVERT: A 1283 LEU cc_start: 0.6144 (OUTLIER) cc_final: 0.5864 (tp) REVERT: A 1325 LEU cc_start: 0.7780 (OUTLIER) cc_final: 0.7561 (tp) REVERT: A 1367 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7497 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7603 (OUTLIER) cc_final: 0.7364 (tt) REVERT: A 1485 MET cc_start: 0.5933 (mtt) cc_final: 0.5571 (mtp) REVERT: A 1595 LEU cc_start: 0.8428 (tp) cc_final: 0.8212 (tt) REVERT: A 1600 GLU cc_start: 0.7485 (tt0) cc_final: 0.7123 (pp20) outliers start: 59 outliers final: 23 residues processed: 211 average time/residue: 0.4802 time to fit residues: 112.0434 Evaluate side-chains 186 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 796 ILE Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1367 ARG Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 87 optimal weight: 0.7980 chunk 145 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 111 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1676 ASN B 79 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.117990 restraints weight = 15286.677| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.34 r_work: 0.3297 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13485 Z= 0.141 Angle : 0.526 10.097 18269 Z= 0.267 Chirality : 0.040 0.301 2092 Planarity : 0.004 0.045 2187 Dihedral : 10.833 163.856 2363 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.42 % Allowed : 22.01 % Favored : 74.57 % 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: 1.79 (0.22), residues: 1549 helix: 2.34 (0.17), residues: 890 sheet: -1.01 (0.39), residues: 152 loop : -0.13 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 907 TYR 0.021 0.001 TYR A 367 PHE 0.016 0.001 PHE A1509 TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00333 (13463) covalent geometry : angle 0.51456 (18214) SS BOND : bond 0.00297 ( 11) SS BOND : angle 0.91510 ( 22) hydrogen bonds : bond 0.04086 ( 794) hydrogen bonds : angle 3.82239 ( 2241) link_BETA1-4 : bond 0.00506 ( 3) link_BETA1-4 : angle 3.00086 ( 9) link_NAG-ASN : bond 0.00528 ( 8) link_NAG-ASN : angle 2.37396 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 159 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6896 (tpt) cc_final: 0.5462 (mtt) REVERT: A 296 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6643 (tm-30) REVERT: A 406 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: A 798 MET cc_start: 0.6670 (ptm) cc_final: 0.6431 (ppp) REVERT: A 844 LYS cc_start: 0.8717 (mttp) cc_final: 0.8298 (mtpt) REVERT: A 890 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7829 (mmtp) REVERT: A 943 MET cc_start: 0.7928 (OUTLIER) cc_final: 0.7461 (mmm) REVERT: A 982 ASP cc_start: 0.0995 (OUTLIER) cc_final: 0.0291 (t0) REVERT: A 1283 LEU cc_start: 0.6148 (OUTLIER) cc_final: 0.5868 (tp) REVERT: A 1325 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7552 (tp) REVERT: A 1456 ILE cc_start: 0.7654 (OUTLIER) cc_final: 0.7418 (tt) REVERT: A 1485 MET cc_start: 0.5978 (mtt) cc_final: 0.5636 (mtp) REVERT: A 1595 LEU cc_start: 0.8388 (tp) cc_final: 0.8171 (tt) REVERT: A 1600 GLU cc_start: 0.7442 (tt0) cc_final: 0.7067 (pp20) outliers start: 48 outliers final: 23 residues processed: 194 average time/residue: 0.4749 time to fit residues: 102.3004 Evaluate side-chains 184 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1187 LYS Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 8.9990 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 115 optimal weight: 0.6980 chunk 41 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 0.1980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A1462 GLN A1676 ASN B 79 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.182690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.119830 restraints weight = 15364.556| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.36 r_work: 0.3328 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13485 Z= 0.106 Angle : 0.500 11.448 18269 Z= 0.255 Chirality : 0.039 0.305 2092 Planarity : 0.003 0.043 2187 Dihedral : 10.386 158.580 2363 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.78 % Allowed : 23.15 % Favored : 74.07 % 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: 1.95 (0.22), residues: 1549 helix: 2.46 (0.17), residues: 888 sheet: -0.90 (0.39), residues: 152 loop : -0.06 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.016 0.001 TYR A 367 PHE 0.016 0.001 PHE A1509 TRP 0.014 0.001 TRP A 190 HIS 0.002 0.001 HIS A 125 Details of bonding type rmsd covalent geometry : bond 0.00234 (13463) covalent geometry : angle 0.48847 (18214) SS BOND : bond 0.00275 ( 11) SS BOND : angle 0.84703 ( 22) hydrogen bonds : bond 0.03675 ( 794) hydrogen bonds : angle 3.73468 ( 2241) link_BETA1-4 : bond 0.00625 ( 3) link_BETA1-4 : angle 2.80131 ( 9) link_NAG-ASN : bond 0.00538 ( 8) link_NAG-ASN : angle 2.32945 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 157 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6876 (tpt) cc_final: 0.5436 (mtt) REVERT: A 296 GLU cc_start: 0.7035 (OUTLIER) cc_final: 0.6623 (tm-30) REVERT: A 406 GLU cc_start: 0.7382 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: A 798 MET cc_start: 0.6771 (ptm) cc_final: 0.6483 (ppp) REVERT: A 844 LYS cc_start: 0.8712 (mttp) cc_final: 0.8346 (mtpt) REVERT: A 890 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7788 (mmtp) REVERT: A 943 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7441 (mmm) REVERT: A 982 ASP cc_start: 0.1006 (OUTLIER) cc_final: 0.0293 (t0) REVERT: A 1283 LEU cc_start: 0.6125 (OUTLIER) cc_final: 0.5872 (tp) REVERT: A 1367 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7409 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7408 (tt) REVERT: A 1533 MET cc_start: 0.8694 (mtp) cc_final: 0.8381 (mtp) REVERT: A 1566 LEU cc_start: 0.6284 (mm) cc_final: 0.6026 (mm) REVERT: A 1595 LEU cc_start: 0.8417 (tp) cc_final: 0.8190 (tt) REVERT: A 1600 GLU cc_start: 0.7399 (tt0) cc_final: 0.7044 (pp20) REVERT: B 96 ARG cc_start: 0.8652 (mtt90) cc_final: 0.8432 (mtt90) outliers start: 39 outliers final: 20 residues processed: 187 average time/residue: 0.4890 time to fit residues: 100.9960 Evaluate side-chains 180 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1367 ARG Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 0.0770 chunk 103 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 56 optimal weight: 0.0570 chunk 45 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 overall best weight: 0.5856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A1462 GLN A1676 ASN B 79 GLN C 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.183712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120972 restraints weight = 15289.231| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.36 r_work: 0.3337 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13485 Z= 0.100 Angle : 0.496 11.104 18269 Z= 0.251 Chirality : 0.039 0.305 2092 Planarity : 0.003 0.043 2187 Dihedral : 9.946 151.179 2363 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.48 % Rotamer: Outliers : 2.71 % Allowed : 23.22 % Favored : 74.07 % 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: 1.99 (0.22), residues: 1549 helix: 2.47 (0.17), residues: 894 sheet: -0.82 (0.39), residues: 147 loop : -0.07 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.024 0.001 TYR A1482 PHE 0.021 0.001 PHE A1583 TRP 0.019 0.001 TRP A 151 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00217 (13463) covalent geometry : angle 0.48497 (18214) SS BOND : bond 0.00266 ( 11) SS BOND : angle 0.83826 ( 22) hydrogen bonds : bond 0.03463 ( 794) hydrogen bonds : angle 3.66712 ( 2241) link_BETA1-4 : bond 0.00628 ( 3) link_BETA1-4 : angle 2.66415 ( 9) link_NAG-ASN : bond 0.00538 ( 8) link_NAG-ASN : angle 2.30092 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6808 (tpt) cc_final: 0.5399 (mtt) REVERT: A 406 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7090 (tm-30) REVERT: A 844 LYS cc_start: 0.8688 (mttp) cc_final: 0.8337 (mtpt) REVERT: A 890 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7791 (mmtp) REVERT: A 943 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7456 (mmm) REVERT: A 982 ASP cc_start: 0.1160 (OUTLIER) cc_final: 0.0409 (t0) REVERT: A 1283 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5821 (OUTLIER) REVERT: A 1367 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7366 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7624 (OUTLIER) cc_final: 0.7387 (tt) REVERT: A 1485 MET cc_start: 0.5784 (mtt) cc_final: 0.5476 (mtp) REVERT: A 1533 MET cc_start: 0.8659 (mtp) cc_final: 0.8365 (mtp) REVERT: A 1566 LEU cc_start: 0.6156 (mm) cc_final: 0.5901 (mm) REVERT: A 1600 GLU cc_start: 0.7384 (tt0) cc_final: 0.7011 (pp20) REVERT: B 96 ARG cc_start: 0.8671 (mtt90) cc_final: 0.8469 (mtt90) REVERT: B 130 GLU cc_start: 0.8104 (tt0) cc_final: 0.7762 (tm-30) outliers start: 38 outliers final: 21 residues processed: 192 average time/residue: 0.5018 time to fit residues: 106.5989 Evaluate side-chains 183 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1367 ARG Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 0.8980 chunk 142 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 408 GLN A1312 ASN A1462 GLN A1676 ASN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.182650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.120373 restraints weight = 15445.819| |-----------------------------------------------------------------------------| r_work (start): 0.3456 rms_B_bonded: 2.35 r_work: 0.3326 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3192 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13485 Z= 0.114 Angle : 0.500 11.079 18269 Z= 0.255 Chirality : 0.039 0.296 2092 Planarity : 0.003 0.041 2187 Dihedral : 9.827 145.184 2363 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 2.56 % Allowed : 23.65 % Favored : 73.79 % 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: 1.97 (0.22), residues: 1549 helix: 2.47 (0.17), residues: 894 sheet: -0.85 (0.39), residues: 152 loop : -0.09 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.020 0.001 TYR A1482 PHE 0.020 0.001 PHE A1583 TRP 0.020 0.001 TRP A 151 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00260 (13463) covalent geometry : angle 0.48907 (18214) SS BOND : bond 0.00258 ( 11) SS BOND : angle 1.12672 ( 22) hydrogen bonds : bond 0.03590 ( 794) hydrogen bonds : angle 3.68324 ( 2241) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 2.65863 ( 9) link_NAG-ASN : bond 0.00522 ( 8) link_NAG-ASN : angle 2.20256 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6796 (tpt) cc_final: 0.5413 (mtt) REVERT: A 406 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7012 (tm-30) REVERT: A 844 LYS cc_start: 0.8702 (mttp) cc_final: 0.8349 (mtpt) REVERT: A 890 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7801 (mmtp) REVERT: A 902 ASP cc_start: 0.8134 (m-30) cc_final: 0.7868 (m-30) REVERT: A 943 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7478 (mmm) REVERT: A 982 ASP cc_start: 0.1185 (OUTLIER) cc_final: 0.0417 (t0) REVERT: A 1283 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5861 (OUTLIER) REVERT: A 1367 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7355 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7653 (OUTLIER) cc_final: 0.7411 (tt) REVERT: A 1485 MET cc_start: 0.5953 (mtt) cc_final: 0.5601 (mtp) REVERT: A 1533 MET cc_start: 0.8661 (mtp) cc_final: 0.8352 (mtp) REVERT: A 1566 LEU cc_start: 0.6248 (mm) cc_final: 0.6018 (mm) REVERT: B 96 ARG cc_start: 0.8636 (mtt90) cc_final: 0.8250 (mtt90) REVERT: B 130 GLU cc_start: 0.8122 (tt0) cc_final: 0.7833 (tm-30) outliers start: 36 outliers final: 20 residues processed: 186 average time/residue: 0.5100 time to fit residues: 105.0707 Evaluate side-chains 180 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1367 ARG Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 125 optimal weight: 0.6980 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 151 optimal weight: 0.4980 chunk 137 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 408 GLN A1462 GLN A1676 ASN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.183036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120435 restraints weight = 15332.920| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.37 r_work: 0.3333 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13485 Z= 0.105 Angle : 0.504 12.512 18269 Z= 0.253 Chirality : 0.039 0.302 2092 Planarity : 0.003 0.041 2187 Dihedral : 9.600 136.639 2363 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.45 % Favored : 97.48 % Rotamer: Outliers : 2.14 % Allowed : 24.15 % Favored : 73.72 % 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: 2.03 (0.22), residues: 1549 helix: 2.51 (0.17), residues: 896 sheet: -0.82 (0.39), residues: 152 loop : -0.06 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.020 0.001 TYR A1482 PHE 0.020 0.001 PHE A1583 TRP 0.023 0.001 TRP A 151 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00236 (13463) covalent geometry : angle 0.49392 (18214) SS BOND : bond 0.00263 ( 11) SS BOND : angle 1.06711 ( 22) hydrogen bonds : bond 0.03485 ( 794) hydrogen bonds : angle 3.65868 ( 2241) link_BETA1-4 : bond 0.00570 ( 3) link_BETA1-4 : angle 2.54111 ( 9) link_NAG-ASN : bond 0.00561 ( 8) link_NAG-ASN : angle 2.21610 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 157 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6815 (tpt) cc_final: 0.5402 (mtt) REVERT: A 405 TYR cc_start: 0.7069 (t80) cc_final: 0.6748 (t80) REVERT: A 406 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6928 (tm-30) REVERT: A 844 LYS cc_start: 0.8690 (mttp) cc_final: 0.8347 (mtpt) REVERT: A 890 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7805 (mmtp) REVERT: A 902 ASP cc_start: 0.8122 (m-30) cc_final: 0.7865 (m-30) REVERT: A 943 MET cc_start: 0.7974 (OUTLIER) cc_final: 0.7515 (mmm) REVERT: A 982 ASP cc_start: 0.1188 (OUTLIER) cc_final: 0.0408 (t0) REVERT: A 1283 LEU cc_start: 0.6099 (OUTLIER) cc_final: 0.5855 (OUTLIER) REVERT: A 1367 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7329 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7393 (tt) REVERT: A 1485 MET cc_start: 0.5945 (mtt) cc_final: 0.5657 (mtp) REVERT: A 1533 MET cc_start: 0.8661 (mtp) cc_final: 0.8333 (mtp) REVERT: A 1761 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7524 (tp30) REVERT: B 96 ARG cc_start: 0.8661 (mtt90) cc_final: 0.8453 (mtt90) REVERT: B 130 GLU cc_start: 0.8106 (tt0) cc_final: 0.7766 (tm-30) outliers start: 30 outliers final: 19 residues processed: 180 average time/residue: 0.5305 time to fit residues: 105.2359 Evaluate side-chains 178 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ILE Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 811 PHE Chi-restraints excluded: chain A residue 890 LYS Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1224 ILE Chi-restraints excluded: chain A residue 1283 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1367 ARG Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 168 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 133 optimal weight: 0.4980 chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 0.5980 chunk 93 optimal weight: 1.9990 chunk 50 optimal weight: 0.0870 chunk 152 optimal weight: 6.9990 chunk 129 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 323 GLN A 408 GLN A1462 GLN A1676 ASN B 79 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.120836 restraints weight = 15270.754| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.37 r_work: 0.3330 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13485 Z= 0.103 Angle : 0.499 11.445 18269 Z= 0.252 Chirality : 0.039 0.302 2092 Planarity : 0.003 0.041 2187 Dihedral : 9.400 128.599 2363 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.58 % Favored : 97.35 % Rotamer: Outliers : 1.99 % Allowed : 24.72 % Favored : 73.29 % 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: 2.08 (0.22), residues: 1549 helix: 2.52 (0.17), residues: 900 sheet: -0.70 (0.40), residues: 147 loop : -0.05 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1570 TYR 0.019 0.001 TYR A1482 PHE 0.021 0.001 PHE A1583 TRP 0.028 0.001 TRP A 151 HIS 0.002 0.001 HIS A1571 Details of bonding type rmsd covalent geometry : bond 0.00228 (13463) covalent geometry : angle 0.48907 (18214) SS BOND : bond 0.00252 ( 11) SS BOND : angle 0.94787 ( 22) hydrogen bonds : bond 0.03409 ( 794) hydrogen bonds : angle 3.63490 ( 2241) link_BETA1-4 : bond 0.00546 ( 3) link_BETA1-4 : angle 2.47715 ( 9) link_NAG-ASN : bond 0.00543 ( 8) link_NAG-ASN : angle 2.21775 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5283.32 seconds wall clock time: 90 minutes 34.69 seconds (5434.69 seconds total)