Starting phenix.real_space_refine on Fri Jul 3 12:50:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8thg_41261/07_2026/8thg_41261.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thg_41261/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8thg_41261/07_2026/8thg_41261.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thg_41261/07_2026/8thg_41261.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8thg_41261/07_2026/8thg_41261.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thg_41261/07_2026/8thg_41261.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8thg_41261/07_2026/8thg_41261.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8thg_41261/07_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-dev-6108/lib/python3.11/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: 2.43, per 1000 atoms: 0.18 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: 0.94 Conformation dependent library (CDL) restraints added in 512.3 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: 0.33 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: 1.86 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: 18132 3.86 - 7.72: 78 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 - 26.35: 7644 26.35 - 52.71: 610 52.71 - 79.06: 79 79.06 - 105.42: 7 105.42 - 131.77: 8 Dihedral angle restraints: 8348 sinusoidal: 3757 harmonic: 4591 Sorted by residual: dihedral pdb=" O16 P5S A2009 " pdb=" C2 P5S A2009 " pdb=" C3 P5S A2009 " pdb=" O37 P5S A2009 " ideal model delta sinusoidal sigma weight residual -57.33 74.44 -131.77 1 3.00e+01 1.11e-03 1.78e+01 dihedral pdb=" C27 P5S A2009 " pdb=" C28 P5S A2009 " pdb=" C29 P5S A2009 " pdb=" C30 P5S A2009 " ideal model delta sinusoidal sigma weight residual 180.62 51.15 129.47 1 3.00e+01 1.11e-03 1.74e+01 dihedral pdb=" C21 P5S A2009 " pdb=" C17 P5S A2009 " pdb=" C20 P5S A2009 " pdb=" O18 P5S A2009 " ideal model delta sinusoidal sigma weight residual 9.80 -119.64 129.44 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 8345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1833 0.063 - 0.126: 228 0.126 - 0.190: 26 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.320 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6849 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= 0.377 Angle : 0.759 19.296 18269 Z= 0.402 Chirality : 0.044 0.316 2092 Planarity : 0.004 0.125 2187 Dihedral : 18.077 131.773 5347 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/Z covalent geometry : bond 0.00708 / 0.38 (13463) covalent geometry : angle 0.75098 / 0.40 (18214) SS BOND : bond 0.00203 / 0.14 ( 11) SS BOND : angle 0.68815 / 0.51 ( 22) hydrogen bonds : bond 0.13230 / 8.58 ( 794) hydrogen bonds : angle 5.15191 / 3.62 ( 2241) link_BETA1-4 : bond 0.00865 / 0.52 ( 3) link_BETA1-4 : angle 4.02888 / 2.30 ( 9) link_NAG-ASN : bond 0.00422 / 0.27 ( 8) link_NAG-ASN : angle 2.02183 / 1.58 ( 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 : 0.303 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: 0.4540 time to fit residues: 87.0710 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 : 0.433 ------------------------------------------------------------------------------- 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... 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 = 0.187114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.123466 restraints weight = 15344.919| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.42 r_work: 0.3294 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13485 Z= 0.119 Angle : 0.525 8.389 18269 Z= 0.271 Chirality : 0.041 0.319 2092 Planarity : 0.004 0.042 2187 Dihedral : 12.369 115.576 2357 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.56 % Allowed : 20.23 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.22), residues: 1549 helix: 2.26 (0.18), residues: 889 sheet: -0.90 (0.41), residues: 143 loop : -0.02 (0.29), residues: 517 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 0.026 0.001 PHE A 204 TRP 0.014 0.001 TRP A1408 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (13463) covalent geometry : angle 0.51277 / 0.27 (18214) SS BOND : bond 0.00320 / 0.23 ( 11) SS BOND : angle 0.99222 / 0.78 ( 22) hydrogen bonds : bond 0.04247 / 2.71 ( 794) hydrogen bonds : angle 4.11557 / 2.90 ( 2241) link_BETA1-4 : bond 0.00808 / 0.49 ( 3) link_BETA1-4 : angle 3.31847 / 1.71 ( 9) link_NAG-ASN : bond 0.00610 / 0.39 ( 8) link_NAG-ASN : angle 2.26094 / 1.90 ( 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 223 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 173 time to evaluate : 0.356 Fit side-chains REVERT: A 406 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7356 (tm-30) REVERT: A 794 LYS cc_start: 0.7108 (mtpp) cc_final: 0.6875 (ttpt) REVERT: A 796 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5828 (tp) REVERT: A 1456 ILE cc_start: 0.7766 (tt) cc_final: 0.7526 (tt) REVERT: A 1591 VAL cc_start: 0.8651 (t) cc_final: 0.8410 (m) REVERT: A 1600 GLU cc_start: 0.7458 (tt0) cc_final: 0.7207 (pp20) outliers start: 50 outliers final: 17 residues processed: 205 average time/residue: 0.4092 time to fit residues: 93.5391 Evaluate side-chains 176 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 157 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 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 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: 5.9990 chunk 153 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 36 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN A 360 GLN A 408 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 = 0.4152 r_free = 0.4152 target = 0.179275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116223 restraints weight = 15340.423| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.35 r_work: 0.3271 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 moved from start: 0.1163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 13485 Z= 0.210 Angle : 0.581 8.064 18269 Z= 0.298 Chirality : 0.043 0.299 2092 Planarity : 0.004 0.043 2187 Dihedral : 11.600 107.209 2354 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.70 % Allowed : 21.15 % Favored : 75.14 % 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: 1.57 (0.22), residues: 1549 helix: 2.08 (0.17), residues: 894 sheet: -0.86 (0.40), residues: 143 loop : -0.20 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1616 TYR 0.029 0.002 TYR A 367 PHE 0.021 0.002 PHE A1509 TRP 0.011 0.002 TRP A1700 HIS 0.005 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.21 (13463) covalent geometry : angle 0.56882 / 0.29 (18214) SS BOND : bond 0.00327 / 0.22 ( 11) SS BOND : angle 1.03805 / 0.76 ( 22) hydrogen bonds : bond 0.04806 / 3.07 ( 794) hydrogen bonds : angle 4.07597 / 2.87 ( 2241) link_BETA1-4 : bond 0.00657 / 0.40 ( 3) link_BETA1-4 : angle 3.37421 / 1.75 ( 9) link_NAG-ASN : bond 0.00527 / 0.33 ( 8) link_NAG-ASN : angle 2.43677 / 1.96 ( 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 215 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 163 time to evaluate : 0.463 Fit side-chains REVERT: A 296 GLU cc_start: 0.7169 (OUTLIER) cc_final: 0.6661 (tm-30) REVERT: A 406 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7115 (tm-30) REVERT: A 796 ILE cc_start: 0.6216 (OUTLIER) cc_final: 0.5920 (tp) REVERT: A 943 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7454 (mmm) REVERT: A 1283 LEU cc_start: 0.6150 (OUTLIER) cc_final: 0.5873 (tp) REVERT: A 1456 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7272 (tt) REVERT: A 1595 LEU cc_start: 0.8418 (tp) cc_final: 0.8203 (tt) REVERT: A 1600 GLU cc_start: 0.7458 (tt0) cc_final: 0.7172 (pp20) REVERT: A 1673 ASP cc_start: 0.8999 (OUTLIER) cc_final: 0.8781 (m-30) REVERT: A 1760 LEU cc_start: 0.6785 (mp) cc_final: 0.6566 (tt) REVERT: C 54 SER cc_start: 0.8802 (t) cc_final: 0.8508 (t) outliers start: 52 outliers final: 17 residues processed: 200 average time/residue: 0.4347 time to fit residues: 96.7219 Evaluate side-chains 180 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 361 ASP Chi-restraints excluded: chain A residue 406 GLU 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 1267 ASP 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 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 A residue 1673 ASP 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: 0.8980 chunk 109 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 128 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 115 optimal weight: 0.7980 chunk 95 optimal weight: 0.6980 chunk 144 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A1341 ASN A1462 GLN A1579 ASN A1676 ASN B 79 GLN C 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.182688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.119712 restraints weight = 15334.929| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.37 r_work: 0.3355 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13485 Z= 0.108 Angle : 0.494 8.810 18269 Z= 0.254 Chirality : 0.039 0.309 2092 Planarity : 0.004 0.049 2187 Dihedral : 10.748 98.152 2352 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.92 % Allowed : 21.65 % Favored : 75.43 % 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: 1.83 (0.22), residues: 1549 helix: 2.37 (0.17), residues: 888 sheet: -1.02 (0.39), residues: 148 loop : -0.10 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.017 0.001 TYR A 367 PHE 0.022 0.001 PHE A1509 TRP 0.013 0.001 TRP A 151 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13463) covalent geometry : angle 0.48136 / 0.25 (18214) SS BOND : bond 0.00307 / 0.22 ( 11) SS BOND : angle 0.91658 / 0.71 ( 22) hydrogen bonds : bond 0.03821 / 2.43 ( 794) hydrogen bonds : angle 3.83701 / 2.71 ( 2241) link_BETA1-4 : bond 0.00572 / 0.35 ( 3) link_BETA1-4 : angle 3.00657 / 1.51 ( 9) link_NAG-ASN : bond 0.00568 / 0.37 ( 8) link_NAG-ASN : angle 2.36587 / 1.95 ( 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 197 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 0.482 Fit side-chains REVERT: A 130 MET cc_start: 0.6810 (tpt) cc_final: 0.5461 (mtt) REVERT: A 189 ASN cc_start: 0.7705 (m-40) cc_final: 0.7488 (m-40) REVERT: A 296 GLU cc_start: 0.7129 (OUTLIER) cc_final: 0.6657 (tm-30) REVERT: A 406 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: A 791 MET cc_start: 0.6187 (tpp) cc_final: 0.5710 (tpp) REVERT: A 796 ILE cc_start: 0.6262 (OUTLIER) cc_final: 0.5961 (tp) REVERT: A 803 TYR cc_start: 0.6079 (t80) cc_final: 0.5827 (t80) REVERT: A 844 LYS cc_start: 0.8715 (mttp) cc_final: 0.8357 (mtpt) REVERT: A 943 MET cc_start: 0.7896 (OUTLIER) cc_final: 0.7419 (mmm) REVERT: A 1325 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7608 (tp) REVERT: A 1456 ILE cc_start: 0.7472 (tt) cc_final: 0.7247 (tt) REVERT: A 1591 VAL cc_start: 0.8499 (t) cc_final: 0.8278 (m) REVERT: A 1595 LEU cc_start: 0.8379 (tp) cc_final: 0.8164 (tt) REVERT: A 1600 GLU cc_start: 0.7492 (tt0) cc_final: 0.7146 (pp20) outliers start: 41 outliers final: 14 residues processed: 189 average time/residue: 0.4025 time to fit residues: 84.7516 Evaluate side-chains 169 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 1325 LEU 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 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: 0.6980 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 152 optimal weight: 50.0000 chunk 2 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN 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 = 0.4174 r_free = 0.4174 target = 0.181812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.118985 restraints weight = 15435.574| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.36 r_work: 0.3303 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.1528 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= 0.125 Angle : 0.507 10.271 18269 Z= 0.258 Chirality : 0.040 0.303 2092 Planarity : 0.003 0.044 2187 Dihedral : 10.148 91.191 2352 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.77 % Allowed : 21.44 % Favored : 74.79 % 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: 1.89 (0.22), residues: 1549 helix: 2.40 (0.17), residues: 889 sheet: -0.93 (0.39), residues: 147 loop : -0.09 (0.29), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.019 0.001 TYR A 367 PHE 0.018 0.001 PHE A1509 TRP 0.012 0.001 TRP A 151 HIS 0.003 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 (13463) covalent geometry : angle 0.49491 / 0.26 (18214) SS BOND : bond 0.00292 / 0.20 ( 11) SS BOND : angle 0.89704 / 0.68 ( 22) hydrogen bonds : bond 0.03879 / 2.47 ( 794) hydrogen bonds : angle 3.78160 / 2.67 ( 2241) link_BETA1-4 : bond 0.00610 / 0.38 ( 3) link_BETA1-4 : angle 2.92299 / 1.52 ( 9) link_NAG-ASN : bond 0.00511 / 0.32 ( 8) link_NAG-ASN : angle 2.36462 / 1.93 ( 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 216 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 163 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6869 (tpt) cc_final: 0.5487 (mtt) REVERT: A 189 ASN cc_start: 0.7651 (m-40) cc_final: 0.7442 (m-40) REVERT: A 296 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6636 (tm-30) REVERT: A 406 GLU cc_start: 0.7440 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: A 796 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5958 (tp) REVERT: A 844 LYS cc_start: 0.8669 (mttp) cc_final: 0.8309 (mtpt) REVERT: A 943 MET cc_start: 0.7936 (OUTLIER) cc_final: 0.7466 (mmm) REVERT: A 982 ASP cc_start: 0.1007 (OUTLIER) cc_final: 0.0368 (t0) REVERT: A 1325 LEU cc_start: 0.7829 (OUTLIER) cc_final: 0.7623 (tp) REVERT: A 1367 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7423 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7566 (OUTLIER) cc_final: 0.7330 (tt) REVERT: A 1533 MET cc_start: 0.8716 (mtp) cc_final: 0.8381 (mtp) REVERT: A 1595 LEU cc_start: 0.8414 (tp) cc_final: 0.8172 (tt) REVERT: A 1600 GLU cc_start: 0.7481 (tt0) cc_final: 0.7095 (pp20) REVERT: A 1760 LEU cc_start: 0.7495 (tt) cc_final: 0.7072 (mp) REVERT: A 1761 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.7134 (tp30) REVERT: C 79 MET cc_start: 0.5470 (ttm) cc_final: 0.4961 (tmm) outliers start: 53 outliers final: 22 residues processed: 205 average time/residue: 0.4161 time to fit residues: 94.8182 Evaluate side-chains 185 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 154 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 A residue 1608 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1761 GLU 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: 0.3980 chunk 145 optimal weight: 20.0000 chunk 127 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 22 optimal weight: 0.0370 chunk 14 optimal weight: 3.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A1341 ASN 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 = 0.4146 r_free = 0.4146 target = 0.180244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117440 restraints weight = 15318.543| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.39 r_work: 0.3308 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1668 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= 0.123 Angle : 0.504 10.777 18269 Z= 0.255 Chirality : 0.039 0.303 2092 Planarity : 0.003 0.045 2187 Dihedral : 9.640 81.826 2350 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.35 % Allowed : 22.29 % Favored : 74.36 % 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: 1.94 (0.22), residues: 1549 helix: 2.43 (0.17), residues: 888 sheet: -0.92 (0.39), residues: 147 loop : -0.04 (0.28), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.019 0.001 TYR A 367 PHE 0.016 0.001 PHE A1509 TRP 0.013 0.001 TRP A 151 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (13463) covalent geometry : angle 0.49256 / 0.25 (18214) SS BOND : bond 0.00285 / 0.20 ( 11) SS BOND : angle 0.88578 / 0.66 ( 22) hydrogen bonds : bond 0.03810 / 2.42 ( 794) hydrogen bonds : angle 3.74168 / 2.64 ( 2241) link_BETA1-4 : bond 0.00558 / 0.34 ( 3) link_BETA1-4 : angle 2.85445 / 1.46 ( 9) link_NAG-ASN : bond 0.00538 / 0.34 ( 8) link_NAG-ASN : angle 2.33247 / 1.92 ( 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 202 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 155 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6868 (tpt) cc_final: 0.5442 (mtt) REVERT: A 296 GLU cc_start: 0.7048 (OUTLIER) cc_final: 0.6635 (tm-30) REVERT: A 406 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: A 790 GLU cc_start: 0.6462 (tm-30) cc_final: 0.6082 (pp20) REVERT: A 796 ILE cc_start: 0.6267 (OUTLIER) cc_final: 0.5955 (tp) REVERT: A 803 TYR cc_start: 0.6095 (t80) cc_final: 0.5673 (t80) REVERT: A 844 LYS cc_start: 0.8707 (mttp) cc_final: 0.8298 (mtpt) REVERT: A 943 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7593 (mmm) REVERT: A 982 ASP cc_start: 0.1030 (OUTLIER) cc_final: 0.0375 (t0) REVERT: A 1367 ARG cc_start: 0.7899 (OUTLIER) cc_final: 0.7427 (ttt-90) REVERT: A 1412 MET cc_start: 0.8725 (mtp) cc_final: 0.8482 (mtm) REVERT: A 1456 ILE cc_start: 0.7639 (OUTLIER) cc_final: 0.7406 (tt) REVERT: A 1533 MET cc_start: 0.8715 (mtp) cc_final: 0.8363 (mtp) REVERT: A 1595 LEU cc_start: 0.8422 (tp) cc_final: 0.8208 (tt) REVERT: A 1600 GLU cc_start: 0.7415 (tt0) cc_final: 0.7045 (pp20) REVERT: C 79 MET cc_start: 0.5361 (OUTLIER) cc_final: 0.4904 (tmm) outliers start: 47 outliers final: 17 residues processed: 190 average time/residue: 0.4250 time to fit residues: 89.7380 Evaluate side-chains 176 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1585 VAL Chi-restraints excluded: chain A residue 1587 ILE Chi-restraints excluded: chain A residue 1588 ILE Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 79 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 89 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN A 408 GLN ** A1312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1462 GLN A1676 ASN B 79 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.180467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.117460 restraints weight = 15375.193| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 2.36 r_work: 0.3290 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3158 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13485 Z= 0.156 Angle : 0.529 11.431 18269 Z= 0.271 Chirality : 0.041 0.299 2092 Planarity : 0.004 0.043 2187 Dihedral : 9.568 77.075 2350 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.21 % Allowed : 22.58 % Favored : 74.22 % 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: 1.78 (0.22), residues: 1549 helix: 2.31 (0.17), residues: 895 sheet: -0.95 (0.39), residues: 152 loop : -0.15 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 907 TYR 0.022 0.001 TYR A 367 PHE 0.016 0.001 PHE B 54 TRP 0.014 0.001 TRP A 151 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (13463) covalent geometry : angle 0.51745 / 0.27 (18214) SS BOND : bond 0.00294 / 0.20 ( 11) SS BOND : angle 0.92144 / 0.68 ( 22) hydrogen bonds : bond 0.04099 / 2.61 ( 794) hydrogen bonds : angle 3.80133 / 2.68 ( 2241) link_BETA1-4 : bond 0.00553 / 0.34 ( 3) link_BETA1-4 : angle 2.96792 / 1.54 ( 9) link_NAG-ASN : bond 0.00515 / 0.33 ( 8) link_NAG-ASN : angle 2.37203 / 1.92 ( 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 204 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 159 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6907 (tpt) cc_final: 0.5462 (mtt) REVERT: A 296 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6649 (tm-30) REVERT: A 406 GLU cc_start: 0.7268 (OUTLIER) cc_final: 0.7011 (tm-30) REVERT: A 791 MET cc_start: 0.6076 (tpp) cc_final: 0.5641 (tpp) REVERT: A 803 TYR cc_start: 0.6049 (t80) cc_final: 0.5702 (t80) REVERT: A 844 LYS cc_start: 0.8715 (mttp) cc_final: 0.8305 (mtpt) REVERT: A 943 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7477 (mmm) REVERT: A 982 ASP cc_start: 0.0842 (OUTLIER) cc_final: 0.0094 (t0) REVERT: A 1212 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7640 (mm-30) REVERT: A 1325 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7555 (tp) REVERT: A 1367 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7421 (ttt-90) REVERT: A 1412 MET cc_start: 0.8698 (mtp) cc_final: 0.8486 (mtm) REVERT: A 1456 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7441 (tt) REVERT: A 1566 LEU cc_start: 0.6316 (mm) cc_final: 0.5991 (mm) REVERT: A 1595 LEU cc_start: 0.8392 (tp) cc_final: 0.8183 (tt) REVERT: A 1600 GLU cc_start: 0.7400 (tt0) cc_final: 0.7024 (pp20) REVERT: B 130 GLU cc_start: 0.8074 (tt0) cc_final: 0.7796 (tm-30) outliers start: 45 outliers final: 23 residues processed: 189 average time/residue: 0.4198 time to fit residues: 87.9906 Evaluate side-chains 188 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1212 GLU Chi-restraints excluded: chain A residue 1224 ILE 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 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 1543 MET 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 62 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 116 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 395 ASN A 408 GLN A1462 GLN A1676 ASN B 79 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.180800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118072 restraints weight = 15367.509| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.39 r_work: 0.3313 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1891 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= 0.110 Angle : 0.506 11.837 18269 Z= 0.257 Chirality : 0.039 0.304 2092 Planarity : 0.003 0.041 2187 Dihedral : 9.216 73.263 2350 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.21 % Allowed : 23.79 % Favored : 74.00 % 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: 1.93 (0.22), residues: 1549 helix: 2.45 (0.17), residues: 894 sheet: -0.94 (0.39), residues: 152 loop : -0.10 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 60 TYR 0.017 0.001 TYR A 367 PHE 0.019 0.001 PHE A1583 TRP 0.018 0.001 TRP A 151 HIS 0.004 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (13463) covalent geometry : angle 0.49523 / 0.25 (18214) SS BOND : bond 0.00271 / 0.19 ( 11) SS BOND : angle 0.87017 / 0.66 ( 22) hydrogen bonds : bond 0.03643 / 2.32 ( 794) hydrogen bonds : angle 3.70415 / 2.62 ( 2241) link_BETA1-4 : bond 0.00583 / 0.36 ( 3) link_BETA1-4 : angle 2.78081 / 1.42 ( 9) link_NAG-ASN : bond 0.00540 / 0.34 ( 8) link_NAG-ASN : angle 2.32178 / 1.93 ( 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 186 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6813 (tpt) cc_final: 0.5408 (mtt) REVERT: A 296 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6627 (tm-30) REVERT: A 406 GLU cc_start: 0.7234 (OUTLIER) cc_final: 0.6980 (tm-30) REVERT: A 844 LYS cc_start: 0.8708 (mttp) cc_final: 0.8333 (mtpt) REVERT: A 902 ASP cc_start: 0.8144 (m-30) cc_final: 0.7883 (m-30) REVERT: A 943 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7476 (mmm) REVERT: A 982 ASP cc_start: 0.1022 (OUTLIER) cc_final: 0.0261 (t0) REVERT: A 1367 ARG cc_start: 0.7874 (OUTLIER) cc_final: 0.7389 (ttt-90) REVERT: A 1412 MET cc_start: 0.8711 (mtp) cc_final: 0.8473 (mtm) REVERT: A 1456 ILE cc_start: 0.7632 (tt) cc_final: 0.7396 (tt) REVERT: A 1485 MET cc_start: 0.5794 (mtt) cc_final: 0.5491 (mtp) REVERT: A 1566 LEU cc_start: 0.6135 (mm) cc_final: 0.5831 (mm) REVERT: A 1595 LEU cc_start: 0.8414 (tp) cc_final: 0.8201 (tt) REVERT: B 96 ARG cc_start: 0.8653 (mtt90) cc_final: 0.8430 (mtt90) REVERT: B 130 GLU cc_start: 0.8091 (tt0) cc_final: 0.7755 (tm-30) outliers start: 31 outliers final: 16 residues processed: 177 average time/residue: 0.4323 time to fit residues: 84.7606 Evaluate side-chains 172 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 319 THR Chi-restraints excluded: chain A residue 361 ASP Chi-restraints excluded: chain A residue 406 GLU 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 982 ASP Chi-restraints excluded: chain A residue 1224 ILE 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 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 1734 SER Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 7 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 408 GLN A1312 ASN A1462 GLN A1676 ASN B 79 GLN ** C 70 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.182224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.119499 restraints weight = 15473.405| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.37 r_work: 0.3312 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3179 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13485 Z= 0.116 Angle : 0.507 12.271 18269 Z= 0.258 Chirality : 0.039 0.289 2092 Planarity : 0.003 0.041 2187 Dihedral : 9.069 68.128 2350 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.32 % Favored : 97.61 % Rotamer: Outliers : 2.14 % Allowed : 24.00 % Favored : 73.86 % 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: 2.45 (0.17), residues: 894 sheet: -0.93 (0.39), residues: 152 loop : -0.10 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.017 0.001 TYR A 367 PHE 0.019 0.001 PHE A1583 TRP 0.021 0.001 TRP A 151 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (13463) covalent geometry : angle 0.49585 / 0.26 (18214) SS BOND : bond 0.00268 / 0.19 ( 11) SS BOND : angle 0.85425 / 0.64 ( 22) hydrogen bonds : bond 0.03661 / 2.33 ( 794) hydrogen bonds : angle 3.68877 / 2.61 ( 2241) link_BETA1-4 : bond 0.00532 / 0.33 ( 3) link_BETA1-4 : angle 2.74232 / 1.41 ( 9) link_NAG-ASN : bond 0.00497 / 0.32 ( 8) link_NAG-ASN : angle 2.28991 / 1.90 ( 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 182 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 MET cc_start: 0.6564 (mpm) cc_final: 0.6331 (mpt) REVERT: A 130 MET cc_start: 0.6841 (tpt) cc_final: 0.5441 (mtt) REVERT: A 296 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6631 (tm-30) REVERT: A 406 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6992 (tm-30) REVERT: A 844 LYS cc_start: 0.8662 (mttp) cc_final: 0.8310 (mtpt) REVERT: A 890 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7797 (mmtp) REVERT: A 902 ASP cc_start: 0.8139 (m-30) cc_final: 0.7881 (m-30) REVERT: A 943 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7533 (mmm) REVERT: A 982 ASP cc_start: 0.1036 (OUTLIER) cc_final: 0.0256 (t0) REVERT: A 1367 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7410 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7659 (OUTLIER) cc_final: 0.7417 (tt) REVERT: A 1485 MET cc_start: 0.5899 (mtt) cc_final: 0.5569 (mtp) REVERT: A 1566 LEU cc_start: 0.6210 (mm) cc_final: 0.5902 (mm) REVERT: A 1595 LEU cc_start: 0.8426 (tp) cc_final: 0.8217 (tt) REVERT: B 96 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8424 (mtt90) REVERT: B 130 GLU cc_start: 0.8096 (tt0) cc_final: 0.7764 (tm-30) outliers start: 30 outliers final: 17 residues processed: 175 average time/residue: 0.4160 time to fit residues: 80.7637 Evaluate side-chains 174 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 319 THR Chi-restraints excluded: chain A residue 361 ASP 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 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 1588 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: 0.9990 chunk 131 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 144 optimal weight: 8.9990 chunk 151 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 106 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 146 optimal weight: 20.0000 chunk 130 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4182 r_free = 0.4182 target = 0.182697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120206 restraints weight = 15378.595| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.37 r_work: 0.3320 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2053 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= 0.109 Angle : 0.502 11.305 18269 Z= 0.254 Chirality : 0.039 0.300 2092 Planarity : 0.003 0.041 2187 Dihedral : 8.909 64.910 2350 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.26 % Favored : 97.68 % Rotamer: Outliers : 2.14 % Allowed : 24.00 % Favored : 73.86 % 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: 2.01 (0.22), residues: 1549 helix: 2.51 (0.17), residues: 894 sheet: -0.83 (0.40), residues: 147 loop : -0.10 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 96 TYR 0.019 0.001 TYR A 803 PHE 0.021 0.001 PHE A1583 TRP 0.027 0.001 TRP A 151 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13463) covalent geometry : angle 0.49184 / 0.25 (18214) SS BOND : bond 0.00261 / 0.19 ( 11) SS BOND : angle 0.84599 / 0.64 ( 22) hydrogen bonds : bond 0.03590 / 2.26 ( 794) hydrogen bonds : angle 3.67165 / 2.60 ( 2241) link_BETA1-4 : bond 0.00562 / 0.34 ( 3) link_BETA1-4 : angle 2.67481 / 1.37 ( 9) link_NAG-ASN : bond 0.00544 / 0.35 ( 8) link_NAG-ASN : angle 2.27710 / 1.90 ( 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 188 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 158 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6856 (tpt) cc_final: 0.5433 (mtt) REVERT: A 406 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7022 (tm-30) REVERT: A 844 LYS cc_start: 0.8661 (mttp) cc_final: 0.8307 (mtpt) REVERT: A 890 LYS cc_start: 0.8007 (OUTLIER) cc_final: 0.7786 (mmtp) REVERT: A 902 ASP cc_start: 0.8130 (m-30) cc_final: 0.7876 (m-30) REVERT: A 943 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7475 (mmm) REVERT: A 982 ASP cc_start: 0.1055 (OUTLIER) cc_final: 0.0266 (t0) REVERT: A 1367 ARG cc_start: 0.7813 (OUTLIER) cc_final: 0.7335 (ttt-90) REVERT: A 1456 ILE cc_start: 0.7635 (OUTLIER) cc_final: 0.7393 (tt) REVERT: A 1485 MET cc_start: 0.5892 (mtt) cc_final: 0.5569 (mtp) REVERT: A 1566 LEU cc_start: 0.6226 (mm) cc_final: 0.5924 (mm) REVERT: A 1595 LEU cc_start: 0.8437 (tp) cc_final: 0.8229 (tt) REVERT: B 96 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8257 (mtt90) REVERT: B 130 GLU cc_start: 0.8094 (tt0) cc_final: 0.7763 (tm-30) outliers start: 30 outliers final: 19 residues processed: 181 average time/residue: 0.4372 time to fit residues: 87.5292 Evaluate side-chains 176 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 1588 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: 0.8980 chunk 114 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 93 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 152 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4179 r_free = 0.4179 target = 0.182535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.119952 restraints weight = 15337.939| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.36 r_work: 0.3326 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13485 Z= 0.117 Angle : 0.512 10.502 18269 Z= 0.262 Chirality : 0.039 0.301 2092 Planarity : 0.003 0.042 2187 Dihedral : 8.879 63.833 2350 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 2.21 % Allowed : 24.50 % 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: 1.98 (0.22), residues: 1549 helix: 2.48 (0.17), residues: 894 sheet: -0.80 (0.40), residues: 147 loop : -0.11 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 841 TYR 0.017 0.001 TYR A 367 PHE 0.019 0.001 PHE A1583 TRP 0.029 0.001 TRP A 151 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13463) covalent geometry : angle 0.50143 / 0.26 (18214) SS BOND : bond 0.00266 / 0.19 ( 11) SS BOND : angle 1.25759 / 0.78 ( 22) hydrogen bonds : bond 0.03627 / 2.29 ( 794) hydrogen bonds : angle 3.67905 / 2.60 ( 2241) link_BETA1-4 : bond 0.00542 / 0.33 ( 3) link_BETA1-4 : angle 2.69912 / 1.40 ( 9) link_NAG-ASN : bond 0.00544 / 0.34 ( 8) link_NAG-ASN : angle 2.22266 / 1.89 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4539.13 seconds wall clock time: 77 minutes 45.39 seconds (4665.39 seconds total)