Starting phenix.real_space_refine on Fri Jul 3 13:14:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.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/8s9b_40238/07_2026/8s9b_40238.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8s9b_40238/07_2026/8s9b_40238.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= 0.127 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 13 5.49 5 S 97 5.16 5 C 8842 2.51 5 N 2044 2.21 5 O 2413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 13409 Number of models: 1 Model: "" Number of chains: 10 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 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 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 chiralities: 2 Chain: "A" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 604 Unusual residues: {'LPE': 8, 'LQO': 2, 'NAG': 1, 'PCW': 3, 'Y01': 4} Classifications: {'peptide': 2, 'undetermined': 18} Link IDs: {None: 19} Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'P5S:plan-2': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 10 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 chiralities: 3 Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 2.37, per 1000 atoms: 0.18 Number of scatterers: 13409 At special positions: 0 Unit cell: (129.224, 138.136, 126.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 13 15.00 O 2413 8.00 N 2044 7.00 C 8842 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=2.04 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.04 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " 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: 0.83 Conformation dependent library (CDL) restraints added in 394.1 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: 2970 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 10 sheets defined 66.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 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 79 through 85 removed outlier: 4.262A pdb=" N ASP A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.500A pdb=" N TYR A 107 " --> pdb=" O PRO A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.835A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.302A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.571A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLU A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 222 through 228 removed outlier: 4.080A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.643A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.914A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.904A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 418 removed outlier: 3.613A pdb=" N ILE A 394 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.724A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N MET A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.903A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 removed outlier: 3.962A pdb=" N MET A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.593A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.557A pdb=" N MET A 854 " --> pdb=" O PRO A 850 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N LEU A 855 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.544A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.334A 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: 3.835A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 972 Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 3.583A pdb=" N ASN A1180 " --> pdb=" O LYS A1176 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1209 through 1212 removed outlier: 3.717A 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 1214 through 1218 removed outlier: 4.399A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1284 through 1290 Processing helix chain 'A' and resid 1291 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.795A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A1335 " --> pdb=" O PHE A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1375 Processing helix chain 'A' and resid 1391 through 1405 Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 3.888A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1468 removed outlier: 3.789A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N THR A1448 " --> pdb=" O GLY A1444 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU A1449 " --> pdb=" O SER A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1486 removed outlier: 3.716A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) Processing helix chain 'A' and resid 1487 through 1490 Processing helix chain 'A' and resid 1502 through 1513 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: 3.847A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1576 through 1600 Processing helix chain 'A' and resid 1605 through 1613 Processing helix chain 'A' and resid 1616 through 1621 removed outlier: 3.942A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.589A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 4.075A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1667 through 1669 No H-bonds generated for 'chain 'A' and resid 1667 through 1669' Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.181A 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 Processing helix chain 'A' and resid 1732 through 1749 Processing helix chain 'A' and resid 1752 through 1767 removed outlier: 3.627A pdb=" N SER A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL A1765 " --> pdb=" O GLU A1761 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.710A 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 sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.828A 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 removed outlier: 3.508A pdb=" N SER A1357 " --> pdb=" O ASN A1352 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.147A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.147A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.350A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE C 80 " --> pdb=" O TRP C 67 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 41 Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 48 824 hydrogen bonds defined for protein. 2325 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: 1.82 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2022 1.29 - 1.42: 3514 1.42 - 1.56: 7953 1.56 - 1.69: 29 1.69 - 1.83: 157 Bond restraints: 13675 Sorted by residual: bond pdb=" C4 LQO A2003 " pdb=" C6 LQO A2003 " ideal model delta sigma weight residual 1.391 1.520 -0.129 2.00e-02 2.50e+03 4.16e+01 bond pdb=" C10 LQO A2003 " pdb=" C7 LQO A2003 " ideal model delta sigma weight residual 1.394 1.520 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C3 LQO A2003 " pdb=" C5 LQO A2003 " ideal model delta sigma weight residual 1.390 1.515 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C3 LQO A2002 " pdb=" C5 LQO A2002 " ideal model delta sigma weight residual 1.390 1.513 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C4 LQO A2002 " pdb=" C6 LQO A2002 " ideal model delta sigma weight residual 1.391 1.503 -0.112 2.00e-02 2.50e+03 3.14e+01 ... (remaining 13670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 17702 2.12 - 4.23: 665 4.23 - 6.35: 78 6.35 - 8.47: 27 8.47 - 10.59: 2 Bond angle restraints: 18474 Sorted by residual: angle pdb=" CA VAL A1758 " pdb=" C VAL A1758 " pdb=" O VAL A1758 " ideal model delta sigma weight residual 121.05 116.61 4.44 1.11e+00 8.12e-01 1.60e+01 angle pdb=" CA SER A1747 " pdb=" C SER A1747 " pdb=" O SER A1747 " ideal model delta sigma weight residual 120.82 116.65 4.17 1.05e+00 9.07e-01 1.58e+01 angle pdb=" CA PRO A 767 " pdb=" C PRO A 767 " pdb=" O PRO A 767 " ideal model delta sigma weight residual 121.38 118.38 3.00 7.70e-01 1.69e+00 1.52e+01 angle pdb=" CA THR A1767 " pdb=" C THR A1767 " pdb=" O THR A1767 " ideal model delta sigma weight residual 122.63 117.62 5.01 1.29e+00 6.01e-01 1.51e+01 angle pdb=" CA VAL A1455 " pdb=" C VAL A1455 " pdb=" O VAL A1455 " ideal model delta sigma weight residual 120.71 116.56 4.15 1.07e+00 8.73e-01 1.51e+01 ... (remaining 18469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.85: 7656 33.85 - 67.69: 386 67.69 - 101.54: 31 101.54 - 135.38: 9 135.38 - 169.23: 2 Dihedral angle restraints: 8084 sinusoidal: 3491 harmonic: 4593 Sorted by residual: dihedral pdb=" CD ARG A 217 " pdb=" NE ARG A 217 " pdb=" CZ ARG A 217 " pdb=" NH1 ARG A 217 " ideal model delta sinusoidal sigma weight residual 0.00 -58.54 58.54 1 1.00e+01 1.00e-02 4.59e+01 dihedral pdb=" CD ARG A 835 " pdb=" NE ARG A 835 " pdb=" CZ ARG A 835 " pdb=" NH1 ARG A 835 " ideal model delta sinusoidal sigma weight residual 0.00 -50.20 50.20 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS A 897 " pdb=" SG CYS A 897 " pdb=" SG CYS A 903 " pdb=" CB CYS A 903 " ideal model delta sinusoidal sigma weight residual 93.00 131.78 -38.78 1 1.00e+01 1.00e-02 2.12e+01 ... (remaining 8081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1764 0.060 - 0.121: 269 0.121 - 0.181: 55 0.181 - 0.241: 14 0.241 - 0.302: 1 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA TYR A1743 " pdb=" N TYR A1743 " pdb=" C TYR A1743 " pdb=" CB TYR A1743 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" C1 NAG D 2 " pdb=" O4 NAG D 1 " pdb=" C2 NAG D 2 " pdb=" O5 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.19e+00 chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.42 0.02 2.00e-02 2.50e+03 1.48e+00 ... (remaining 2100 not shown) Planarity restraints: 2208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2012 " -0.161 2.00e-02 2.50e+03 1.56e-01 2.44e+02 pdb=" C19 PCW A2012 " 0.179 2.00e-02 2.50e+03 pdb=" C20 PCW A2012 " 0.131 2.00e-02 2.50e+03 pdb=" C21 PCW A2012 " -0.149 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 217 " -0.940 9.50e-02 1.11e+02 4.21e-01 1.08e+02 pdb=" NE ARG A 217 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 217 " 0.014 2.00e-02 2.50e+03 pdb=" NH1 ARG A 217 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 217 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 835 " -0.842 9.50e-02 1.11e+02 3.77e-01 8.64e+01 pdb=" NE ARG A 835 " 0.050 2.00e-02 2.50e+03 pdb=" CZ ARG A 835 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 835 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 835 " -0.024 2.00e-02 2.50e+03 ... (remaining 2205 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 116 2.61 - 3.18: 11898 3.18 - 3.75: 19838 3.75 - 4.33: 28289 4.33 - 4.90: 47532 Nonbonded interactions: 107673 Sorted by model distance: nonbonded pdb=" O3 NAG E 2 " pdb=" O7 NAG E 2 " model vdw 2.037 3.040 nonbonded pdb=" N GLU B 65 " pdb=" OE1 GLU B 65 " model vdw 2.065 3.120 nonbonded pdb=" N GLU A 281 " pdb=" OE1 GLU A 281 " model vdw 2.196 3.120 nonbonded pdb=" N GLU A 802 " pdb=" OE1 GLU A 802 " model vdw 2.212 3.120 nonbonded pdb=" NE ARG B 46 " pdb=" OE2 GLU B 48 " model vdw 2.215 3.120 ... (remaining 107668 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.210 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.008 0.129 13696 Z= 0.442 Angle : 0.903 10.587 18526 Z= 0.500 Chirality : 0.049 0.302 2103 Planarity : 0.013 0.421 2201 Dihedral : 19.049 169.229 5081 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.00 % Allowed : 23.15 % Favored : 75.85 % 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: 0.83 (0.22), residues: 1549 helix: 1.57 (0.17), residues: 911 sheet: -1.02 (0.43), residues: 147 loop : -0.83 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1499 TYR 0.024 0.002 TYR C 108 PHE 0.018 0.002 PHE A1763 TRP 0.010 0.001 TRP A 808 HIS 0.003 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00826 / 0.44 (13675) covalent geometry : angle 0.89794 / 0.50 (18474) SS BOND : bond 0.00350 / 0.22 ( 11) SS BOND : angle 0.93471 / 0.65 ( 22) hydrogen bonds : bond 0.13418 / 8.97 ( 797) hydrogen bonds : angle 5.81259 / 4.21 ( 2325) link_BETA1-4 : bond 0.00698 / 0.43 ( 3) link_BETA1-4 : angle 3.84304 / 2.41 ( 9) link_NAG-ASN : bond 0.00425 / 0.26 ( 7) link_NAG-ASN : angle 1.78415 / 1.22 ( 21) *********************** 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 236 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.420 Fit side-chains revert: symmetry clash REVERT: A 249 MET cc_start: 0.8039 (mmm) cc_final: 0.7804 (mmm) REVERT: A 403 MET cc_start: 0.7922 (mmm) cc_final: 0.7531 (mtp) REVERT: A 773 LYS cc_start: 0.8565 (ttmt) cc_final: 0.8262 (mtmm) REVERT: A 1280 TYR cc_start: 0.7646 (m-10) cc_final: 0.7390 (m-10) REVERT: A 1459 ASN cc_start: 0.8053 (t160) cc_final: 0.7805 (t0) REVERT: A 1628 LYS cc_start: 0.8609 (tptm) cc_final: 0.7990 (tppt) REVERT: B 163 MET cc_start: 0.8399 (ttp) cc_final: 0.8140 (ttp) REVERT: C 104 ASN cc_start: 0.7599 (p0) cc_final: 0.7367 (p0) outliers start: 14 outliers final: 2 residues processed: 227 average time/residue: 0.4996 time to fit residues: 125.9127 Evaluate side-chains 192 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 190 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.1980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 886 GLN A1461 ASN A1753 ASN C 60 HIS C 62 GLN C 139 HIS C 145 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.149714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105048 restraints weight = 18695.761| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.00 r_work: 0.3151 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13696 Z= 0.124 Angle : 0.552 7.344 18526 Z= 0.285 Chirality : 0.040 0.219 2103 Planarity : 0.004 0.059 2201 Dihedral : 14.554 167.003 2088 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.13 % Allowed : 21.44 % 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: 1.50 (0.22), residues: 1549 helix: 2.11 (0.17), residues: 918 sheet: -0.95 (0.43), residues: 144 loop : -0.52 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 214 TYR 0.016 0.001 TYR A1743 PHE 0.015 0.001 PHE A1440 TRP 0.014 0.001 TRP A 188 HIS 0.005 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13675) covalent geometry : angle 0.54552 / 0.28 (18474) SS BOND : bond 0.00280 / 0.18 ( 11) SS BOND : angle 0.93758 / 0.74 ( 22) hydrogen bonds : bond 0.04322 / 2.72 ( 797) hydrogen bonds : angle 4.20061 / 3.01 ( 2325) link_BETA1-4 : bond 0.00510 / 0.31 ( 3) link_BETA1-4 : angle 2.92847 / 1.39 ( 9) link_NAG-ASN : bond 0.00339 / 0.19 ( 7) link_NAG-ASN : angle 1.66244 / 0.95 ( 21) *********************** 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 253 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.8299 (mtt) cc_final: 0.8063 (mtp) REVERT: A 217 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7593 (ttt180) REVERT: A 249 MET cc_start: 0.8274 (mmm) cc_final: 0.8009 (mmm) REVERT: A 406 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7692 (tm-30) REVERT: A 742 MET cc_start: 0.7518 (mmm) cc_final: 0.7076 (mmm) REVERT: A 804 PHE cc_start: 0.7924 (m-10) cc_final: 0.7701 (m-80) REVERT: A 854 MET cc_start: 0.7662 (mmp) cc_final: 0.7346 (tpp) REVERT: A 960 LEU cc_start: 0.8959 (tt) cc_final: 0.8736 (tp) REVERT: A 1283 LEU cc_start: 0.7644 (tt) cc_final: 0.7407 (tm) REVERT: A 1603 PHE cc_start: 0.6220 (OUTLIER) cc_final: 0.5362 (m-80) REVERT: A 1753 ASN cc_start: 0.8900 (m110) cc_final: 0.8579 (m-40) REVERT: A 1756 ILE cc_start: 0.8777 (mt) cc_final: 0.8548 (mp) REVERT: C 104 ASN cc_start: 0.7509 (p0) cc_final: 0.7213 (p0) outliers start: 44 outliers final: 12 residues processed: 230 average time/residue: 0.4688 time to fit residues: 120.6587 Evaluate side-chains 206 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 88 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 133 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 941 GLN B 131 ASN C 60 HIS C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.149499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.110724 restraints weight = 18881.260| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.14 r_work: 0.3138 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13696 Z= 0.125 Angle : 0.507 6.904 18526 Z= 0.262 Chirality : 0.039 0.218 2103 Planarity : 0.004 0.050 2201 Dihedral : 13.729 161.797 2086 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.06 % Allowed : 22.08 % Favored : 74.86 % 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: 1.72 (0.22), residues: 1549 helix: 2.27 (0.17), residues: 919 sheet: -0.69 (0.41), residues: 152 loop : -0.47 (0.30), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1499 TYR 0.018 0.001 TYR B 180 PHE 0.013 0.001 PHE A1440 TRP 0.013 0.001 TRP A 188 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (13675) covalent geometry : angle 0.50018 / 0.26 (18474) SS BOND : bond 0.00284 / 0.19 ( 11) SS BOND : angle 0.88377 / 0.65 ( 22) hydrogen bonds : bond 0.04129 / 2.59 ( 797) hydrogen bonds : angle 4.03157 / 2.90 ( 2325) link_BETA1-4 : bond 0.00478 / 0.29 ( 3) link_BETA1-4 : angle 2.81850 / 1.42 ( 9) link_NAG-ASN : bond 0.00256 / 0.15 ( 7) link_NAG-ASN : angle 1.64713 / 0.95 ( 21) *********************** 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 246 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 0.516 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.8346 (mtt) cc_final: 0.8101 (mtp) REVERT: A 217 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7685 (ttt180) REVERT: A 249 MET cc_start: 0.8363 (mmm) cc_final: 0.8080 (mmm) REVERT: A 406 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7674 (tm-30) REVERT: A 742 MET cc_start: 0.7593 (mmm) cc_final: 0.7139 (mmm) REVERT: A 804 PHE cc_start: 0.7884 (m-10) cc_final: 0.7483 (m-80) REVERT: A 960 LEU cc_start: 0.8984 (tt) cc_final: 0.8782 (tp) REVERT: A 1283 LEU cc_start: 0.7911 (tt) cc_final: 0.7637 (tm) REVERT: A 1603 PHE cc_start: 0.6266 (OUTLIER) cc_final: 0.5437 (m-80) REVERT: C 104 ASN cc_start: 0.7555 (p0) cc_final: 0.7290 (p0) outliers start: 43 outliers final: 16 residues processed: 224 average time/residue: 0.4820 time to fit residues: 120.7092 Evaluate side-chains 211 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 22 optimal weight: 0.8980 chunk 110 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 96 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 780 ASN A 989 GLN B 131 ASN C 60 HIS C 62 GLN ** C 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.149513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.104792 restraints weight = 18768.692| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.01 r_work: 0.3150 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13696 Z= 0.125 Angle : 0.503 6.998 18526 Z= 0.259 Chirality : 0.039 0.220 2103 Planarity : 0.003 0.051 2201 Dihedral : 13.028 156.048 2086 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.21 % Allowed : 21.94 % Favored : 74.86 % 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: 1.90 (0.22), residues: 1549 helix: 2.40 (0.17), residues: 909 sheet: -0.74 (0.42), residues: 144 loop : -0.24 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1499 TYR 0.019 0.001 TYR B 180 PHE 0.014 0.001 PHE A1440 TRP 0.012 0.001 TRP A 188 HIS 0.004 0.001 HIS C 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13675) covalent geometry : angle 0.49584 / 0.26 (18474) SS BOND : bond 0.00263 / 0.18 ( 11) SS BOND : angle 0.84438 / 0.62 ( 22) hydrogen bonds : bond 0.03964 / 2.48 ( 797) hydrogen bonds : angle 3.96430 / 2.86 ( 2325) link_BETA1-4 : bond 0.00536 / 0.32 ( 3) link_BETA1-4 : angle 2.80011 / 1.39 ( 9) link_NAG-ASN : bond 0.00258 / 0.15 ( 7) link_NAG-ASN : angle 1.63410 / 0.93 ( 21) *********************** 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 246 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 201 time to evaluate : 0.361 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.8290 (mtt) cc_final: 0.8033 (mtp) REVERT: A 217 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7753 (ttt180) REVERT: A 249 MET cc_start: 0.8255 (mmm) cc_final: 0.7937 (mmm) REVERT: A 406 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7726 (tm-30) REVERT: A 742 MET cc_start: 0.7531 (mmm) cc_final: 0.7125 (mmm) REVERT: A 804 PHE cc_start: 0.7861 (m-10) cc_final: 0.7504 (m-80) REVERT: A 960 LEU cc_start: 0.8910 (tt) cc_final: 0.8681 (tp) REVERT: A 1283 LEU cc_start: 0.7883 (tt) cc_final: 0.7619 (tm) REVERT: A 1603 PHE cc_start: 0.6227 (OUTLIER) cc_final: 0.5384 (m-80) REVERT: C 82 GLN cc_start: 0.3980 (mm110) cc_final: 0.3620 (mm110) REVERT: C 88 ILE cc_start: 0.5102 (OUTLIER) cc_final: 0.4795 (pp) REVERT: C 104 ASN cc_start: 0.7652 (p0) cc_final: 0.7450 (p0) outliers start: 45 outliers final: 19 residues processed: 221 average time/residue: 0.4173 time to fit residues: 103.5715 Evaluate side-chains 217 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.7980 chunk 78 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 989 GLN B 131 ASN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.149146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.110233 restraints weight = 18829.464| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.16 r_work: 0.3128 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13696 Z= 0.137 Angle : 0.511 7.452 18526 Z= 0.263 Chirality : 0.039 0.225 2103 Planarity : 0.003 0.047 2201 Dihedral : 12.699 151.815 2086 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.63 % Allowed : 22.15 % 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: 1.95 (0.22), residues: 1549 helix: 2.43 (0.17), residues: 908 sheet: -0.52 (0.41), residues: 148 loop : -0.25 (0.29), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1499 TYR 0.019 0.001 TYR B 180 PHE 0.014 0.001 PHE A1440 TRP 0.010 0.001 TRP A 188 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (13675) covalent geometry : angle 0.50392 / 0.26 (18474) SS BOND : bond 0.00279 / 0.18 ( 11) SS BOND : angle 0.90042 / 0.62 ( 22) hydrogen bonds : bond 0.04003 / 2.51 ( 797) hydrogen bonds : angle 3.93945 / 2.84 ( 2325) link_BETA1-4 : bond 0.00478 / 0.29 ( 3) link_BETA1-4 : angle 2.83456 / 1.42 ( 9) link_NAG-ASN : bond 0.00265 / 0.15 ( 7) link_NAG-ASN : angle 1.66719 / 0.96 ( 21) *********************** 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 258 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 78 LEU cc_start: 0.5545 (OUTLIER) cc_final: 0.5258 (mp) REVERT: A 89 ILE cc_start: 0.7645 (mt) cc_final: 0.6967 (pp) REVERT: A 145 MET cc_start: 0.8365 (mtt) cc_final: 0.8097 (mtp) REVERT: A 184 LEU cc_start: 0.8070 (OUTLIER) cc_final: 0.7599 (mm) REVERT: A 217 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7755 (ttt180) REVERT: A 249 MET cc_start: 0.8359 (mmm) cc_final: 0.8042 (mmm) REVERT: A 406 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7805 (tm-30) REVERT: A 742 MET cc_start: 0.7609 (mmm) cc_final: 0.7146 (mmm) REVERT: A 804 PHE cc_start: 0.7818 (m-10) cc_final: 0.7502 (m-80) REVERT: A 960 LEU cc_start: 0.9084 (tt) cc_final: 0.8811 (tp) REVERT: A 1287 LYS cc_start: 0.8652 (ttmt) cc_final: 0.8397 (mtmp) REVERT: A 1561 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.6884 (tt0) REVERT: A 1603 PHE cc_start: 0.6278 (OUTLIER) cc_final: 0.5429 (m-80) REVERT: A 1763 PHE cc_start: 0.9001 (t80) cc_final: 0.8751 (t80) REVERT: B 163 MET cc_start: 0.8639 (ttp) cc_final: 0.8335 (ttp) REVERT: C 88 ILE cc_start: 0.5073 (OUTLIER) cc_final: 0.4697 (pp) outliers start: 51 outliers final: 23 residues processed: 233 average time/residue: 0.4481 time to fit residues: 116.9159 Evaluate side-chains 228 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1355 ASP Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 chunk 24 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 94 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 989 GLN A1180 ASN B 131 ASN C 62 GLN C 104 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.152160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.105498 restraints weight = 19123.196| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.35 r_work: 0.3169 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13696 Z= 0.113 Angle : 0.512 9.713 18526 Z= 0.259 Chirality : 0.039 0.209 2103 Planarity : 0.003 0.045 2201 Dihedral : 12.377 147.027 2086 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.49 % Allowed : 22.79 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.22), residues: 1549 helix: 2.52 (0.17), residues: 906 sheet: -0.46 (0.41), residues: 148 loop : -0.21 (0.30), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1499 TYR 0.019 0.001 TYR B 180 PHE 0.021 0.001 PHE A1583 TRP 0.011 0.001 TRP A 188 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (13675) covalent geometry : angle 0.50555 / 0.26 (18474) SS BOND : bond 0.00281 / 0.19 ( 11) SS BOND : angle 0.82516 / 0.60 ( 22) hydrogen bonds : bond 0.03729 / 2.33 ( 797) hydrogen bonds : angle 3.85791 / 2.79 ( 2325) link_BETA1-4 : bond 0.00526 / 0.32 ( 3) link_BETA1-4 : angle 2.73904 / 1.36 ( 9) link_NAG-ASN : bond 0.00249 / 0.14 ( 7) link_NAG-ASN : angle 1.63860 / 0.94 ( 21) *********************** 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 253 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 204 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7153 (mt) cc_final: 0.6371 (pp) REVERT: A 184 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7192 (mm) REVERT: A 217 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.7539 (ttt180) REVERT: A 249 MET cc_start: 0.8040 (mmm) cc_final: 0.7698 (mmm) REVERT: A 403 MET cc_start: 0.8021 (ttm) cc_final: 0.7243 (mmt) REVERT: A 406 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7394 (tm-30) REVERT: A 413 ILE cc_start: 0.6357 (OUTLIER) cc_final: 0.6132 (mp) REVERT: A 742 MET cc_start: 0.7313 (mmm) cc_final: 0.6824 (mmm) REVERT: A 804 PHE cc_start: 0.7727 (m-10) cc_final: 0.7490 (m-80) REVERT: A 960 LEU cc_start: 0.8666 (tt) cc_final: 0.8408 (tp) REVERT: A 1518 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: A 1561 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6771 (tt0) REVERT: A 1603 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.5250 (m-80) REVERT: A 1761 GLU cc_start: 0.7980 (tt0) cc_final: 0.7685 (tt0) REVERT: C 88 ILE cc_start: 0.5000 (OUTLIER) cc_final: 0.4602 (pp) outliers start: 49 outliers final: 19 residues processed: 228 average time/residue: 0.3924 time to fit residues: 100.2764 Evaluate side-chains 219 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 193 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 34 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 2 optimal weight: 0.9990 chunk 130 optimal weight: 0.5980 chunk 8 optimal weight: 0.0670 chunk 133 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 144 optimal weight: 7.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.5720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 989 GLN B 131 ASN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.150487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105879 restraints weight = 18728.936| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.01 r_work: 0.3170 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 13696 Z= 0.110 Angle : 0.509 10.788 18526 Z= 0.257 Chirality : 0.039 0.197 2103 Planarity : 0.003 0.042 2201 Dihedral : 12.096 142.400 2086 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.78 % Allowed : 23.36 % 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: 2.05 (0.22), residues: 1549 helix: 2.48 (0.17), residues: 918 sheet: -0.47 (0.42), residues: 140 loop : -0.25 (0.30), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1499 TYR 0.021 0.001 TYR B 182 PHE 0.016 0.001 PHE A1583 TRP 0.011 0.001 TRP A1179 HIS 0.002 0.000 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (13675) covalent geometry : angle 0.50290 / 0.26 (18474) SS BOND : bond 0.00266 / 0.18 ( 11) SS BOND : angle 0.77840 / 0.57 ( 22) hydrogen bonds : bond 0.03617 / 2.26 ( 797) hydrogen bonds : angle 3.80699 / 2.75 ( 2325) link_BETA1-4 : bond 0.00506 / 0.30 ( 3) link_BETA1-4 : angle 2.70618 / 1.34 ( 9) link_NAG-ASN : bond 0.00246 / 0.14 ( 7) link_NAG-ASN : angle 1.62841 / 0.93 ( 21) *********************** 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 240 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 201 time to evaluate : 0.541 Fit side-chains revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7444 (mt) cc_final: 0.6645 (pp) REVERT: A 145 MET cc_start: 0.8161 (mtt) cc_final: 0.7928 (mtp) REVERT: A 184 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7421 (mm) REVERT: A 217 ARG cc_start: 0.8499 (OUTLIER) cc_final: 0.7682 (ttt180) REVERT: A 249 MET cc_start: 0.8281 (mmm) cc_final: 0.7938 (mmm) REVERT: A 403 MET cc_start: 0.8149 (ttm) cc_final: 0.7525 (mmt) REVERT: A 406 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 413 ILE cc_start: 0.6712 (OUTLIER) cc_final: 0.6465 (mp) REVERT: A 742 MET cc_start: 0.7517 (mmm) cc_final: 0.7048 (mmm) REVERT: A 804 PHE cc_start: 0.7749 (m-10) cc_final: 0.7524 (m-80) REVERT: A 960 LEU cc_start: 0.8993 (tt) cc_final: 0.8734 (tp) REVERT: A 1518 ASP cc_start: 0.7721 (OUTLIER) cc_final: 0.7448 (m-30) REVERT: A 1561 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: A 1603 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: A 1761 GLU cc_start: 0.8114 (tt0) cc_final: 0.7819 (tt0) REVERT: C 59 ASN cc_start: 0.8695 (t0) cc_final: 0.8480 (t0) outliers start: 39 outliers final: 20 residues processed: 219 average time/residue: 0.4362 time to fit residues: 106.9392 Evaluate side-chains 220 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 194 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 102 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 148 optimal weight: 9.9990 chunk 73 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 989 GLN B 131 ASN C 62 GLN ** C 82 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 = 0.3864 r_free = 0.3864 target = 0.147508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101430 restraints weight = 19143.223| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.31 r_work: 0.3134 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13696 Z= 0.291 Angle : 0.665 11.276 18526 Z= 0.335 Chirality : 0.045 0.289 2103 Planarity : 0.004 0.060 2201 Dihedral : 12.764 134.807 2086 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.70 % Allowed : 23.15 % Favored : 73.15 % 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: 1.62 (0.22), residues: 1549 helix: 2.18 (0.17), residues: 904 sheet: -0.38 (0.42), residues: 147 loop : -0.51 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C 135 TYR 0.019 0.002 TYR A1739 PHE 0.020 0.002 PHE A1440 TRP 0.014 0.002 TRP A 808 HIS 0.006 0.002 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.29 (13675) covalent geometry : angle 0.65738 / 0.33 (18474) SS BOND : bond 0.00424 / 0.28 ( 11) SS BOND : angle 1.22255 / 0.75 ( 22) hydrogen bonds : bond 0.05209 / 3.27 ( 797) hydrogen bonds : angle 4.15047 / 2.99 ( 2325) link_BETA1-4 : bond 0.00335 / 0.21 ( 3) link_BETA1-4 : angle 3.31519 / 1.78 ( 9) link_NAG-ASN : bond 0.00449 / 0.27 ( 7) link_NAG-ASN : angle 2.00527 / 1.22 ( 21) *********************** 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 258 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 206 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 145 MET cc_start: 0.8247 (mtt) cc_final: 0.8039 (mtp) REVERT: A 217 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.7560 (ttt180) REVERT: A 249 MET cc_start: 0.8266 (mmm) cc_final: 0.7861 (mmm) REVERT: A 403 MET cc_start: 0.8199 (ttm) cc_final: 0.7421 (mmt) REVERT: A 406 GLU cc_start: 0.8053 (tm-30) cc_final: 0.7596 (tm-30) REVERT: A 407 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7864 (tp30) REVERT: A 413 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6293 (mp) REVERT: A 838 ARG cc_start: 0.8274 (ttm170) cc_final: 0.7779 (ptp-170) REVERT: A 854 MET cc_start: 0.7501 (mmp) cc_final: 0.7200 (tpp) REVERT: A 1193 TRP cc_start: 0.7239 (OUTLIER) cc_final: 0.6161 (m-90) REVERT: A 1287 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8309 (mtmp) REVERT: A 1518 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7390 (m-30) REVERT: A 1561 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.6847 (tt0) REVERT: A 1603 PHE cc_start: 0.6306 (OUTLIER) cc_final: 0.5491 (m-80) REVERT: B 84 GLU cc_start: 0.8323 (pm20) cc_final: 0.7665 (pp20) REVERT: B 180 TYR cc_start: 0.7884 (t80) cc_final: 0.7577 (t80) REVERT: C 59 ASN cc_start: 0.8741 (t0) cc_final: 0.8526 (t0) REVERT: C 88 ILE cc_start: 0.5022 (OUTLIER) cc_final: 0.4637 (pp) outliers start: 52 outliers final: 27 residues processed: 229 average time/residue: 0.4274 time to fit residues: 109.2917 Evaluate side-chains 232 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 197 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 774 ASN Chi-restraints excluded: chain A residue 814 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 952 MET Chi-restraints excluded: chain A residue 1193 TRP Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1590 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 92 optimal weight: 0.0970 chunk 122 optimal weight: 0.3980 chunk 19 optimal weight: 3.9990 chunk 42 optimal weight: 0.0870 chunk 6 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 107 optimal weight: 0.5980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 989 GLN A1753 ASN B 131 ASN ** C 82 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 = 0.3995 r_free = 0.3995 target = 0.155412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.110675 restraints weight = 19281.225| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 2.27 r_work: 0.3258 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 13696 Z= 0.109 Angle : 0.544 11.207 18526 Z= 0.274 Chirality : 0.039 0.200 2103 Planarity : 0.003 0.043 2201 Dihedral : 12.057 131.218 2086 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.35 % Allowed : 25.50 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.99 (0.22), residues: 1549 helix: 2.46 (0.17), residues: 906 sheet: -0.57 (0.42), residues: 140 loop : -0.22 (0.29), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1499 TYR 0.015 0.001 TYR B 182 PHE 0.012 0.001 PHE A1583 TRP 0.018 0.001 TRP A1179 HIS 0.002 0.001 HIS A1542 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13675) covalent geometry : angle 0.53735 / 0.27 (18474) SS BOND : bond 0.00242 / 0.16 ( 11) SS BOND : angle 0.83042 / 0.58 ( 22) hydrogen bonds : bond 0.03709 / 2.31 ( 797) hydrogen bonds : angle 3.86021 / 2.79 ( 2325) link_BETA1-4 : bond 0.00511 / 0.31 ( 3) link_BETA1-4 : angle 2.80911 / 1.37 ( 9) link_NAG-ASN : bond 0.00269 / 0.15 ( 7) link_NAG-ASN : angle 1.70587 / 0.97 ( 21) *********************** 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 236 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 203 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7474 (mt) cc_final: 0.6773 (pp) REVERT: A 145 MET cc_start: 0.8242 (mtt) cc_final: 0.8006 (mtp) REVERT: A 184 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7464 (tm) REVERT: A 217 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7802 (ttt180) REVERT: A 249 MET cc_start: 0.8404 (mmm) cc_final: 0.8076 (mmm) REVERT: A 403 MET cc_start: 0.8291 (ttm) cc_final: 0.7586 (mmt) REVERT: A 406 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7746 (tm-30) REVERT: A 760 PHE cc_start: 0.8345 (t80) cc_final: 0.8101 (t80) REVERT: A 1518 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7468 (m-30) REVERT: A 1561 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: A 1603 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.5570 (m-80) REVERT: A 1761 GLU cc_start: 0.8215 (tt0) cc_final: 0.7958 (tt0) REVERT: B 84 GLU cc_start: 0.8218 (pm20) cc_final: 0.7547 (pp20) REVERT: B 113 TYR cc_start: 0.8722 (m-80) cc_final: 0.8476 (m-80) REVERT: B 180 TYR cc_start: 0.7919 (t80) cc_final: 0.7634 (t80) REVERT: C 88 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.4930 (pp) outliers start: 33 outliers final: 15 residues processed: 221 average time/residue: 0.4783 time to fit residues: 118.4662 Evaluate side-chains 219 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 198 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 823 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 135 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 143 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 989 GLN B 131 ASN C 62 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.154331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.109480 restraints weight = 19091.555| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 2.26 r_work: 0.3239 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13696 Z= 0.133 Angle : 0.554 9.598 18526 Z= 0.280 Chirality : 0.040 0.213 2103 Planarity : 0.003 0.044 2201 Dihedral : 11.853 127.230 2086 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.99 % Allowed : 26.28 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (0.22), residues: 1549 helix: 2.47 (0.17), residues: 907 sheet: -0.37 (0.41), residues: 148 loop : -0.24 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1499 TYR 0.015 0.001 TYR A1739 PHE 0.027 0.001 PHE A 176 TRP 0.019 0.001 TRP A1179 HIS 0.002 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (13675) covalent geometry : angle 0.54785 / 0.28 (18474) SS BOND : bond 0.00274 / 0.18 ( 11) SS BOND : angle 0.83970 / 0.58 ( 22) hydrogen bonds : bond 0.03905 / 2.44 ( 797) hydrogen bonds : angle 3.85917 / 2.79 ( 2325) link_BETA1-4 : bond 0.00496 / 0.30 ( 3) link_BETA1-4 : angle 2.79464 / 1.44 ( 9) link_NAG-ASN : bond 0.00267 / 0.15 ( 7) link_NAG-ASN : angle 1.71393 / 1.00 ( 21) ********************** 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 227 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 89 ILE cc_start: 0.7519 (mt) cc_final: 0.6805 (pp) REVERT: A 184 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7473 (tm) REVERT: A 217 ARG cc_start: 0.8535 (OUTLIER) cc_final: 0.7791 (ttt180) REVERT: A 249 MET cc_start: 0.8406 (mmm) cc_final: 0.8067 (mmm) REVERT: A 297 GLU cc_start: 0.7918 (tp30) cc_final: 0.7687 (tp30) REVERT: A 403 MET cc_start: 0.8336 (ttm) cc_final: 0.7613 (mmt) REVERT: A 406 GLU cc_start: 0.8145 (tm-30) cc_final: 0.7779 (tm-30) REVERT: A 1518 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7499 (m-30) REVERT: A 1561 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7008 (tt0) REVERT: A 1603 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5613 (m-80) REVERT: A 1761 GLU cc_start: 0.8219 (tt0) cc_final: 0.7957 (tt0) REVERT: B 84 GLU cc_start: 0.8232 (pm20) cc_final: 0.7544 (pp20) REVERT: B 180 TYR cc_start: 0.7943 (t80) cc_final: 0.7652 (t80) REVERT: C 88 ILE cc_start: 0.5299 (OUTLIER) cc_final: 0.4916 (pp) REVERT: C 130 MET cc_start: 0.7873 (tpt) cc_final: 0.7598 (tpp) outliers start: 28 outliers final: 15 residues processed: 213 average time/residue: 0.4992 time to fit residues: 118.6202 Evaluate side-chains 218 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 197 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 217 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 407 GLU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1328 CYS Chi-restraints excluded: chain A residue 1518 ASP Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 44 SER Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 88 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 27 optimal weight: 0.0870 chunk 20 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 111 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A 989 GLN B 131 ASN C 62 GLN ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.155651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.110907 restraints weight = 19167.012| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.27 r_work: 0.3258 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13696 Z= 0.114 Angle : 0.537 9.906 18526 Z= 0.271 Chirality : 0.039 0.202 2103 Planarity : 0.003 0.041 2201 Dihedral : 11.498 121.534 2086 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.78 % Allowed : 26.21 % Favored : 72.01 % 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: 2.43 (0.17), residues: 918 sheet: -0.46 (0.43), residues: 140 loop : -0.28 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1499 TYR 0.014 0.001 TYR A1739 PHE 0.014 0.001 PHE A1583 TRP 0.019 0.001 TRP A1179 HIS 0.002 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (13675) covalent geometry : angle 0.53116 / 0.27 (18474) SS BOND : bond 0.00250 / 0.17 ( 11) SS BOND : angle 0.77227 / 0.57 ( 22) hydrogen bonds : bond 0.03627 / 2.27 ( 797) hydrogen bonds : angle 3.79990 / 2.75 ( 2325) link_BETA1-4 : bond 0.00530 / 0.32 ( 3) link_BETA1-4 : angle 2.70905 / 1.37 ( 9) link_NAG-ASN : bond 0.00258 / 0.14 ( 7) link_NAG-ASN : angle 1.66486 / 0.97 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5141.36 seconds wall clock time: 88 minutes 15.99 seconds (5295.99 seconds total)