Starting phenix.real_space_refine on Fri Jul 3 13:01:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thh_41262/07_2026/8thh_41262.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 97 5.16 5 Cl 4 4.86 5 C 8789 2.51 5 N 2048 2.21 5 O 2371 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 13319 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 534 Unusual residues: {'IYJ': 2, 'LPE': 6, 'NAG': 2, 'PCW': 3, 'Y01': 4} Classifications: {'peptide': 1, 'undetermined': 17} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-1': 1, 'PCW:plan-4': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.19, per 1000 atoms: 0.24 Number of scatterers: 13319 At special positions: 0 Unit cell: (128.464, 138.824, 128.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 4 17.00 S 97 16.00 P 10 15.00 O 2371 8.00 N 2048 7.00 C 8789 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.04 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2002 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 1.29 Conformation dependent library (CDL) restraints added in 662.4 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2968 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 65.9% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.670A pdb=" N PHE A 12 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 33 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.996A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.290A pdb=" N ASP A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.520A 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 143 removed outlier: 3.931A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.081A 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 205 Processing helix chain 'A' and resid 210 through 218 removed outlier: 3.507A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) 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: 4.009A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.569A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 267 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.916A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.931A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 418 Processing helix chain 'A' and resid 729 through 742 removed outlier: 3.977A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.891A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 832 through 838 removed outlier: 4.155A pdb=" N ARG A 838 " --> pdb=" O LEU A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 removed outlier: 3.838A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.607A pdb=" N MET A 854 " --> pdb=" O PRO A 850 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 855 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.657A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.697A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 973 Processing helix chain 'A' and resid 986 through 1014 Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 4.101A 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: 3.661A 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 1215 through 1218 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 1278 Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 3.602A pdb=" N ARG A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1301 removed outlier: 3.508A pdb=" N ALA A1294 " --> pdb=" O THR A1291 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 3.871A pdb=" N LEU A1301 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix removed outlier: 3.916A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.944A 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 1404 removed outlier: 3.535A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 4.015A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1444 removed outlier: 3.761A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1467 Processing helix chain 'A' and resid 1475 through 1487 removed outlier: 3.780A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS A1487 " --> pdb=" O ASN A1483 " (cutoff:3.500A) Processing helix chain 'A' and resid 1488 through 1490 No H-bonds generated for 'chain 'A' and resid 1488 through 1490' Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1535 removed outlier: 4.070A pdb=" N GLU A1535 " --> pdb=" O THR A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 3.825A 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: 3.975A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1625 Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.854A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix removed outlier: 3.503A pdb=" N ASN A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.165A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1706 through 1709 removed outlier: 3.824A pdb=" N ASN A1709 " --> pdb=" O PRO A1706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1706 through 1709' Processing helix chain 'A' and resid 1732 through 1752 removed outlier: 3.701A pdb=" N VAL A1752 " --> pdb=" O PHE A1748 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1768 Processing helix chain 'B' and resid 112 through 115 removed outlier: 3.704A pdb=" N HIS B 115 " --> pdb=" O THR B 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 112 through 115' Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 74 through 76 removed outlier: 3.770A pdb=" N THR A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.319A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.465A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA6, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.463A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE C 129 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU C 65 " --> pdb=" O GLN C 82 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN C 82 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N TRP C 67 " --> pdb=" O PHE C 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.540A pdb=" N VAL C 112 " --> pdb=" O LEU C 48 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 2244 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2032 1.32 - 1.45: 3689 1.45 - 1.57: 7708 1.57 - 1.70: 20 1.70 - 1.82: 161 Bond restraints: 13610 Sorted by residual: bond pdb=" C12 IYJ A2003 " pdb=" N05 IYJ A2003 " ideal model delta sigma weight residual 1.339 1.451 -0.112 2.00e-02 2.50e+03 3.13e+01 bond pdb=" C12 IYJ A2004 " pdb=" N05 IYJ A2004 " ideal model delta sigma weight residual 1.339 1.449 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C16 IYJ A2003 " pdb=" N07 IYJ A2003 " ideal model delta sigma weight residual 1.350 1.449 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C16 IYJ A2004 " pdb=" N07 IYJ A2004 " ideal model delta sigma weight residual 1.350 1.449 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" O33 LPE A2008 " pdb=" P LPE A2008 " ideal model delta sigma weight residual 1.673 1.605 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 13605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 18133 2.68 - 5.35: 228 5.35 - 8.03: 34 8.03 - 10.70: 5 10.70 - 13.38: 2 Bond angle restraints: 18402 Sorted by residual: angle pdb=" N06 IYJ A2003 " pdb=" C16 IYJ A2003 " pdb=" N07 IYJ A2003 " ideal model delta sigma weight residual 116.72 103.34 13.38 3.00e+00 1.11e-01 1.99e+01 angle pdb=" N06 IYJ A2004 " pdb=" C16 IYJ A2004 " pdb=" N07 IYJ A2004 " ideal model delta sigma weight residual 116.72 103.53 13.19 3.00e+00 1.11e-01 1.93e+01 angle pdb=" N MET A1307 " pdb=" CA MET A1307 " pdb=" C MET A1307 " ideal model delta sigma weight residual 111.69 107.08 4.61 1.23e+00 6.61e-01 1.41e+01 angle pdb=" N GLN C 62 " pdb=" CA GLN C 62 " pdb=" CB GLN C 62 " ideal model delta sigma weight residual 110.98 106.10 4.88 1.32e+00 5.74e-01 1.37e+01 angle pdb=" N ARG A 220 " pdb=" CA ARG A 220 " pdb=" C ARG A 220 " ideal model delta sigma weight residual 113.01 108.73 4.28 1.20e+00 6.94e-01 1.27e+01 ... (remaining 18397 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.27: 8114 34.27 - 68.55: 357 68.55 - 102.82: 21 102.82 - 137.10: 6 137.10 - 171.37: 3 Dihedral angle restraints: 8501 sinusoidal: 3910 harmonic: 4591 Sorted by residual: dihedral pdb=" C33 PCW A2011 " pdb=" C31 PCW A2011 " pdb=" C32 PCW A2011 " pdb=" O2 PCW A2011 " ideal model delta sinusoidal sigma weight residual -168.17 3.20 -171.37 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" N PCW A2009 " pdb=" C4 PCW A2009 " pdb=" C5 PCW A2009 " pdb=" O4P PCW A2009 " ideal model delta sinusoidal sigma weight residual 293.34 150.83 142.51 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" O16 P5S A2012 " pdb=" C2 P5S A2012 " pdb=" C3 P5S A2012 " pdb=" O37 P5S A2012 " ideal model delta sinusoidal sigma weight residual -57.33 82.49 -139.82 1 3.00e+01 1.11e-03 1.88e+01 ... (remaining 8498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1594 0.046 - 0.092: 418 0.092 - 0.138: 74 0.138 - 0.184: 13 0.184 - 0.230: 3 Chirality restraints: 2102 Sorted by residual: 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 -2.43 0.03 2.00e-02 2.50e+03 1.66e+00 chirality pdb=" C4 NAG E 1 " pdb=" C3 NAG E 1 " pdb=" C5 NAG E 1 " pdb=" O4 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.30 -0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C2 PCW A2011 " pdb=" C1 PCW A2011 " pdb=" C3 PCW A2011 " pdb=" O2 PCW A2011 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 2099 not shown) Planarity restraints: 2207 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.342 2.00e-02 2.50e+03 2.96e-01 1.10e+03 pdb=" C7 NAG D 2 " 0.078 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.063 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.522 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.195 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " 0.236 2.00e-02 2.50e+03 1.97e-01 4.87e+02 pdb=" C7 NAG B 303 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " 0.165 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " -0.328 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2001 " 0.208 2.00e-02 2.50e+03 1.73e-01 3.75e+02 pdb=" C7 NAG A2001 " -0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A2001 " 0.148 2.00e-02 2.50e+03 pdb=" N2 NAG A2001 " -0.285 2.00e-02 2.50e+03 pdb=" O7 NAG A2001 " -0.014 2.00e-02 2.50e+03 ... (remaining 2204 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2267 2.76 - 3.30: 12442 3.30 - 3.83: 21790 3.83 - 4.37: 25483 4.37 - 4.90: 44686 Nonbonded interactions: 106668 Sorted by model distance: nonbonded pdb=" OD1 ASN A 395 " pdb=" O HOH A2101 " model vdw 2.231 3.040 nonbonded pdb=" N GLU A 294 " pdb=" OE1 GLU A 294 " model vdw 2.272 3.120 nonbonded pdb=" O2H LPE A2015 " pdb=" O31 LPE A2015 " model vdw 2.295 3.040 nonbonded pdb=" OH TYR A1235 " pdb=" OG1 THR B 171 " model vdw 2.296 3.040 nonbonded pdb=" O LEU A 115 " pdb=" OG SER A 119 " model vdw 2.308 3.040 ... (remaining 106663 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.260 Find NCS groups from input model: 0.060 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:8.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 13632 Z= 0.295 Angle : 0.741 13.381 18457 Z= 0.364 Chirality : 0.042 0.230 2102 Planarity : 0.010 0.296 2199 Dihedral : 17.662 171.369 5500 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.78 % Allowed : 19.73 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.22), residues: 1549 helix: 1.76 (0.17), residues: 926 sheet: -0.66 (0.45), residues: 129 loop : -0.50 (0.29), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1619 TYR 0.014 0.001 TYR A1739 PHE 0.018 0.001 PHE A1440 TRP 0.010 0.001 TRP A1700 HIS 0.004 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.30 (13610) covalent geometry : angle 0.73494 / 0.36 (18402) SS BOND : bond 0.00207 / 0.15 ( 11) SS BOND : angle 0.79504 / 0.67 ( 22) hydrogen bonds : bond 0.12303 / 8.37 ( 786) hydrogen bonds : angle 4.85792 / 3.57 ( 2244) link_BETA1-4 : bond 0.00786 / 0.48 ( 3) link_BETA1-4 : angle 3.12870 / 2.32 ( 9) link_NAG-ASN : bond 0.00320 / 0.22 ( 8) link_NAG-ASN : angle 2.05401 / 1.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7650 (mtt90) REVERT: A 1251 LYS cc_start: 0.6367 (pttp) cc_final: 0.4850 (pmtt) REVERT: A 1638 MET cc_start: 0.8168 (ttt) cc_final: 0.7820 (ttt) outliers start: 11 outliers final: 10 residues processed: 170 average time/residue: 0.5544 time to fit residues: 104.0373 Evaluate side-chains 169 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 321 SER Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1189 VAL Chi-restraints excluded: chain A residue 1309 VAL Chi-restraints excluded: chain A residue 1534 VAL 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: 0.6980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 30.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.178314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113702 restraints weight = 14445.492| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.22 r_work: 0.3304 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13632 Z= 0.110 Angle : 0.497 7.954 18457 Z= 0.257 Chirality : 0.039 0.243 2102 Planarity : 0.004 0.045 2199 Dihedral : 13.269 177.311 2520 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.64 % Allowed : 17.09 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.22), residues: 1549 helix: 2.08 (0.17), residues: 924 sheet: -0.68 (0.44), residues: 135 loop : -0.44 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1619 TYR 0.016 0.001 TYR A1739 PHE 0.014 0.001 PHE B 54 TRP 0.012 0.001 TRP A 188 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 (13610) covalent geometry : angle 0.48415 / 0.25 (18402) SS BOND : bond 0.00241 / 0.16 ( 11) SS BOND : angle 0.89854 / 0.76 ( 22) hydrogen bonds : bond 0.04160 / 2.72 ( 786) hydrogen bonds : angle 4.07460 / 2.94 ( 2244) link_BETA1-4 : bond 0.00288 / 0.17 ( 3) link_BETA1-4 : angle 3.57540 / 2.70 ( 9) link_NAG-ASN : bond 0.00506 / 0.30 ( 8) link_NAG-ASN : angle 2.08456 / 1.08 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 798 MET cc_start: 0.4635 (OUTLIER) cc_final: 0.4329 (pmm) REVERT: A 1251 LYS cc_start: 0.6754 (pttp) cc_final: 0.5200 (pmtt) REVERT: A 1628 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6366 (tmmt) REVERT: A 1638 MET cc_start: 0.8321 (ttt) cc_final: 0.7960 (ttt) REVERT: C 130 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6578 (tpp) outliers start: 37 outliers final: 11 residues processed: 186 average time/residue: 0.4792 time to fit residues: 99.3481 Evaluate side-chains 176 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 84 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 128 optimal weight: 0.6980 chunk 95 optimal weight: 0.7980 chunk 127 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 65 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 144 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 147 ASN A 154 ASN A 240 GLN A 809 ASN A 987 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113013 restraints weight = 14797.414| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.14 r_work: 0.3172 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.0880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13632 Z= 0.107 Angle : 0.477 8.275 18457 Z= 0.246 Chirality : 0.039 0.216 2102 Planarity : 0.003 0.046 2199 Dihedral : 12.433 177.282 2506 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.07 % Allowed : 18.09 % Favored : 79.84 % 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: 1.76 (0.22), residues: 1549 helix: 2.23 (0.17), residues: 925 sheet: -0.67 (0.43), residues: 134 loop : -0.31 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1619 TYR 0.015 0.001 TYR A1739 PHE 0.014 0.001 PHE B 54 TRP 0.011 0.001 TRP A 188 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (13610) covalent geometry : angle 0.46670 / 0.24 (18402) SS BOND : bond 0.00233 / 0.16 ( 11) SS BOND : angle 0.83308 / 0.70 ( 22) hydrogen bonds : bond 0.03851 / 2.50 ( 786) hydrogen bonds : angle 3.92137 / 2.82 ( 2244) link_BETA1-4 : bond 0.00604 / 0.36 ( 3) link_BETA1-4 : angle 3.21458 / 2.40 ( 9) link_NAG-ASN : bond 0.00271 / 0.18 ( 8) link_NAG-ASN : angle 1.94026 / 1.09 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 174 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.5905 (OUTLIER) cc_final: 0.5664 (t70) REVERT: A 139 ASN cc_start: 0.8301 (t0) cc_final: 0.8084 (t0) REVERT: A 798 MET cc_start: 0.4952 (OUTLIER) cc_final: 0.4618 (pmm) REVERT: A 886 GLN cc_start: 0.8208 (mm-40) cc_final: 0.8007 (mm110) REVERT: A 1251 LYS cc_start: 0.6848 (pttp) cc_final: 0.5216 (pmtt) REVERT: A 1602 TYR cc_start: 0.7520 (m-80) cc_final: 0.7319 (m-10) REVERT: A 1628 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6542 (tmmt) REVERT: A 1638 MET cc_start: 0.8545 (ttt) cc_final: 0.8178 (ttt) REVERT: C 79 MET cc_start: 0.5051 (tmt) cc_final: 0.4073 (mmm) REVERT: C 130 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6726 (tpp) outliers start: 29 outliers final: 10 residues processed: 185 average time/residue: 0.5325 time to fit residues: 109.4442 Evaluate side-chains 177 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 798 MET Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 78 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 122 optimal weight: 0.0770 chunk 142 optimal weight: 0.8980 chunk 138 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 136 optimal weight: 0.9980 chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 0.1980 chunk 72 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 911 ASN C 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.179950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116201 restraints weight = 14322.248| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.22 r_work: 0.3324 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13632 Z= 0.096 Angle : 0.464 8.086 18457 Z= 0.236 Chirality : 0.038 0.201 2102 Planarity : 0.003 0.048 2199 Dihedral : 11.925 177.584 2505 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.78 % Allowed : 17.74 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.22), residues: 1549 helix: 2.35 (0.17), residues: 927 sheet: -0.51 (0.43), residues: 134 loop : -0.24 (0.30), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.022 0.001 TYR A1186 PHE 0.012 0.001 PHE B 54 TRP 0.011 0.001 TRP A 188 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.10 (13610) covalent geometry : angle 0.45320 / 0.23 (18402) SS BOND : bond 0.00217 / 0.15 ( 11) SS BOND : angle 0.77505 / 0.66 ( 22) hydrogen bonds : bond 0.03582 / 2.33 ( 786) hydrogen bonds : angle 3.78950 / 2.71 ( 2244) link_BETA1-4 : bond 0.00254 / 0.14 ( 3) link_BETA1-4 : angle 3.07022 / 2.27 ( 9) link_NAG-ASN : bond 0.00338 / 0.22 ( 8) link_NAG-ASN : angle 2.00697 / 1.12 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5232 (mm-30) cc_final: 0.4964 (mm-30) REVERT: A 125 HIS cc_start: 0.5835 (OUTLIER) cc_final: 0.5613 (t70) REVERT: A 139 ASN cc_start: 0.8077 (t0) cc_final: 0.7875 (t0) REVERT: A 217 ARG cc_start: 0.7894 (mtt180) cc_final: 0.7001 (ttp-110) REVERT: A 1251 LYS cc_start: 0.6918 (pttp) cc_final: 0.5358 (pmtt) REVERT: A 1628 LYS cc_start: 0.6727 (OUTLIER) cc_final: 0.6323 (tmmt) REVERT: A 1638 MET cc_start: 0.8270 (ttt) cc_final: 0.7902 (ttt) REVERT: A 1768 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.4497 (mp0) REVERT: B 79 GLN cc_start: 0.7801 (mt0) cc_final: 0.6980 (tp40) REVERT: C 79 MET cc_start: 0.5148 (tmt) cc_final: 0.4259 (mmm) REVERT: C 130 MET cc_start: 0.6943 (OUTLIER) cc_final: 0.6611 (tpp) outliers start: 39 outliers final: 14 residues processed: 184 average time/residue: 0.4908 time to fit residues: 100.5309 Evaluate side-chains 183 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 165 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 149 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 chunk 109 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 35 optimal weight: 0.9980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 886 GLN C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.180129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.116376 restraints weight = 14321.956| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.21 r_work: 0.3326 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3187 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13632 Z= 0.096 Angle : 0.452 8.416 18457 Z= 0.231 Chirality : 0.038 0.196 2102 Planarity : 0.003 0.045 2199 Dihedral : 11.640 175.197 2505 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.42 % Allowed : 18.02 % Favored : 79.56 % 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: 2.12 (0.22), residues: 1549 helix: 2.51 (0.17), residues: 915 sheet: -0.41 (0.43), residues: 134 loop : -0.15 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1570 TYR 0.016 0.001 TYR A1739 PHE 0.012 0.001 PHE B 54 TRP 0.010 0.001 TRP A 188 HIS 0.004 0.000 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (13610) covalent geometry : angle 0.44279 / 0.23 (18402) SS BOND : bond 0.00212 / 0.15 ( 11) SS BOND : angle 0.76534 / 0.63 ( 22) hydrogen bonds : bond 0.03500 / 2.27 ( 786) hydrogen bonds : angle 3.73224 / 2.67 ( 2244) link_BETA1-4 : bond 0.00747 / 0.46 ( 3) link_BETA1-4 : angle 2.93795 / 2.15 ( 9) link_NAG-ASN : bond 0.00230 / 0.17 ( 8) link_NAG-ASN : angle 1.80806 / 1.03 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.470 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5290 (mm-30) cc_final: 0.5001 (mm-30) REVERT: A 125 HIS cc_start: 0.5826 (OUTLIER) cc_final: 0.5603 (t70) REVERT: A 217 ARG cc_start: 0.7921 (mtt180) cc_final: 0.6871 (ttp-170) REVERT: A 307 GLU cc_start: 0.8771 (tp30) cc_final: 0.8434 (tm-30) REVERT: A 1251 LYS cc_start: 0.6777 (pttp) cc_final: 0.5283 (pmtt) REVERT: A 1638 MET cc_start: 0.8333 (ttt) cc_final: 0.7926 (ttt) REVERT: A 1768 GLU cc_start: 0.5175 (OUTLIER) cc_final: 0.4482 (mp0) REVERT: B 79 GLN cc_start: 0.7815 (mt0) cc_final: 0.6987 (tp40) REVERT: B 113 TYR cc_start: 0.8231 (m-80) cc_final: 0.8010 (m-10) REVERT: B 152 ARG cc_start: 0.7663 (ttt90) cc_final: 0.7312 (ttt180) REVERT: C 79 MET cc_start: 0.5363 (tmt) cc_final: 0.4582 (mmm) REVERT: C 130 MET cc_start: 0.6902 (OUTLIER) cc_final: 0.6575 (tpp) outliers start: 34 outliers final: 15 residues processed: 183 average time/residue: 0.4718 time to fit residues: 95.6342 Evaluate side-chains 182 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 753 CYS Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 69 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 154 ASN A 809 ASN A 886 GLN ** A 941 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 = 0.4115 r_free = 0.4115 target = 0.175457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.110198 restraints weight = 14529.263| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.23 r_work: 0.3258 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3121 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13632 Z= 0.187 Angle : 0.546 8.911 18457 Z= 0.277 Chirality : 0.042 0.257 2102 Planarity : 0.004 0.048 2199 Dihedral : 11.830 168.473 2505 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.99 % Allowed : 18.52 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.22), residues: 1549 helix: 2.16 (0.17), residues: 925 sheet: -0.48 (0.42), residues: 134 loop : -0.38 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 841 TYR 0.021 0.002 TYR A1739 PHE 0.023 0.002 PHE A1440 TRP 0.010 0.001 TRP A 188 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (13610) covalent geometry : angle 0.53393 / 0.27 (18402) SS BOND : bond 0.00321 / 0.23 ( 11) SS BOND : angle 0.93707 / 0.65 ( 22) hydrogen bonds : bond 0.04628 / 2.99 ( 786) hydrogen bonds : angle 3.92546 / 2.80 ( 2244) link_BETA1-4 : bond 0.00324 / 0.17 ( 3) link_BETA1-4 : angle 3.43178 / 2.53 ( 9) link_NAG-ASN : bond 0.00229 / 0.18 ( 8) link_NAG-ASN : angle 2.31429 / 1.29 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5341 (OUTLIER) cc_final: 0.5078 (mm-30) REVERT: A 217 ARG cc_start: 0.7924 (mtt180) cc_final: 0.7084 (ttp-170) REVERT: A 220 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.7055 (mtt90) REVERT: A 1251 LYS cc_start: 0.6870 (pttp) cc_final: 0.5367 (pmtt) REVERT: A 1603 PHE cc_start: 0.6768 (OUTLIER) cc_final: 0.6556 (m-80) REVERT: A 1638 MET cc_start: 0.8427 (ttt) cc_final: 0.8078 (ttt) REVERT: A 1754 MET cc_start: 0.8450 (mtt) cc_final: 0.8121 (mtt) REVERT: A 1768 GLU cc_start: 0.5415 (OUTLIER) cc_final: 0.4605 (mp0) REVERT: B 152 ARG cc_start: 0.7723 (ttt90) cc_final: 0.7402 (ttt180) REVERT: B 161 ILE cc_start: 0.7444 (mm) cc_final: 0.7220 (mt) REVERT: C 79 MET cc_start: 0.5281 (tmt) cc_final: 0.4530 (mmm) outliers start: 42 outliers final: 13 residues processed: 194 average time/residue: 0.5144 time to fit residues: 110.6859 Evaluate side-chains 183 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 166 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 50 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 7.9990 chunk 99 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 122 optimal weight: 0.8980 chunk 151 optimal weight: 0.0970 chunk 16 optimal weight: 0.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 154 ASN A 886 GLN A 961 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.113117 restraints weight = 14509.270| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.28 r_work: 0.3296 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13632 Z= 0.101 Angle : 0.464 8.721 18457 Z= 0.237 Chirality : 0.038 0.208 2102 Planarity : 0.003 0.048 2199 Dihedral : 11.311 169.060 2505 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.21 % Allowed : 19.59 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.22), residues: 1549 helix: 2.41 (0.17), residues: 915 sheet: -0.40 (0.42), residues: 134 loop : -0.18 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.015 0.001 TYR A1739 PHE 0.013 0.001 PHE B 54 TRP 0.011 0.001 TRP A 188 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13610) covalent geometry : angle 0.45363 / 0.23 (18402) SS BOND : bond 0.00208 / 0.14 ( 11) SS BOND : angle 0.78526 / 0.65 ( 22) hydrogen bonds : bond 0.03696 / 2.41 ( 786) hydrogen bonds : angle 3.75721 / 2.68 ( 2244) link_BETA1-4 : bond 0.00597 / 0.37 ( 3) link_BETA1-4 : angle 3.03779 / 2.22 ( 9) link_NAG-ASN : bond 0.00238 / 0.18 ( 8) link_NAG-ASN : angle 1.88139 / 1.05 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5273 (OUTLIER) cc_final: 0.4923 (mm-30) REVERT: A 217 ARG cc_start: 0.7885 (mtt180) cc_final: 0.6946 (ttp-170) REVERT: A 894 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7497 (mm-30) REVERT: A 1251 LYS cc_start: 0.6860 (pttp) cc_final: 0.5376 (pmtt) REVERT: A 1318 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.7112 (mt) REVERT: A 1485 MET cc_start: 0.5701 (mtm) cc_final: 0.5465 (ttp) REVERT: A 1603 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6513 (m-80) REVERT: A 1628 LYS cc_start: 0.6756 (OUTLIER) cc_final: 0.6277 (tmmt) REVERT: A 1638 MET cc_start: 0.8356 (ttt) cc_final: 0.7954 (ttt) REVERT: A 1768 GLU cc_start: 0.5412 (OUTLIER) cc_final: 0.4632 (mp0) REVERT: B 79 GLN cc_start: 0.7778 (mt0) cc_final: 0.6999 (tp40) REVERT: B 152 ARG cc_start: 0.7767 (ttt90) cc_final: 0.7478 (ttt180) REVERT: B 161 ILE cc_start: 0.7315 (mm) cc_final: 0.7098 (mt) REVERT: C 79 MET cc_start: 0.5072 (tmt) cc_final: 0.4377 (mmm) REVERT: C 130 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6602 (tpp) outliers start: 31 outliers final: 11 residues processed: 188 average time/residue: 0.4448 time to fit residues: 92.8997 Evaluate side-chains 185 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 168 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 109 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 114 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 154 ASN A 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.178387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.113328 restraints weight = 14379.748| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.25 r_work: 0.3302 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3162 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13632 Z= 0.103 Angle : 0.462 9.406 18457 Z= 0.235 Chirality : 0.038 0.201 2102 Planarity : 0.003 0.047 2199 Dihedral : 10.955 164.685 2505 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.85 % Allowed : 19.87 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.22), residues: 1549 helix: 2.40 (0.17), residues: 923 sheet: -0.33 (0.42), residues: 134 loop : -0.17 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.014 0.001 TYR A1739 PHE 0.012 0.001 PHE B 54 TRP 0.009 0.001 TRP A 188 HIS 0.002 0.000 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (13610) covalent geometry : angle 0.45202 / 0.23 (18402) SS BOND : bond 0.00213 / 0.15 ( 11) SS BOND : angle 0.77776 / 0.64 ( 22) hydrogen bonds : bond 0.03626 / 2.36 ( 786) hydrogen bonds : angle 3.71160 / 2.64 ( 2244) link_BETA1-4 : bond 0.00580 / 0.36 ( 3) link_BETA1-4 : angle 2.97155 / 2.17 ( 9) link_NAG-ASN : bond 0.00214 / 0.16 ( 8) link_NAG-ASN : angle 1.86422 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5126 (OUTLIER) cc_final: 0.4746 (mm-30) REVERT: A 217 ARG cc_start: 0.7979 (mtt180) cc_final: 0.7110 (ttp-170) REVERT: A 894 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7569 (mm-30) REVERT: A 1251 LYS cc_start: 0.6866 (pttp) cc_final: 0.5361 (pmtt) REVERT: A 1318 ILE cc_start: 0.7403 (OUTLIER) cc_final: 0.7136 (mt) REVERT: A 1603 PHE cc_start: 0.6709 (OUTLIER) cc_final: 0.6487 (m-80) REVERT: A 1628 LYS cc_start: 0.6786 (OUTLIER) cc_final: 0.6322 (tmmt) REVERT: A 1638 MET cc_start: 0.8374 (ttt) cc_final: 0.7987 (ttt) REVERT: B 79 GLN cc_start: 0.7760 (mt0) cc_final: 0.7032 (tp40) REVERT: B 113 TYR cc_start: 0.8169 (m-80) cc_final: 0.7956 (m-10) REVERT: B 152 ARG cc_start: 0.7825 (ttt90) cc_final: 0.7542 (ttt180) REVERT: B 161 ILE cc_start: 0.7266 (mm) cc_final: 0.7051 (mt) REVERT: C 79 MET cc_start: 0.5069 (tmt) cc_final: 0.4373 (mmm) outliers start: 26 outliers final: 15 residues processed: 182 average time/residue: 0.4853 time to fit residues: 98.0641 Evaluate side-chains 184 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 172 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 127 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 147 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 154 ASN A 886 GLN A 941 GLN C 139 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.110032 restraints weight = 14559.659| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.25 r_work: 0.3252 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13632 Z= 0.186 Angle : 0.541 9.932 18457 Z= 0.274 Chirality : 0.041 0.256 2102 Planarity : 0.004 0.048 2199 Dihedral : 11.293 154.982 2505 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.35 % Allowed : 19.80 % Favored : 77.85 % 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: 1.69 (0.22), residues: 1549 helix: 2.12 (0.17), residues: 928 sheet: -0.47 (0.42), residues: 134 loop : -0.33 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.022 0.002 TYR A1739 PHE 0.021 0.002 PHE A1440 TRP 0.009 0.001 TRP B 173 HIS 0.004 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00456 / 0.19 (13610) covalent geometry : angle 0.53175 / 0.27 (18402) SS BOND : bond 0.00271 / 0.19 ( 11) SS BOND : angle 0.95540 / 0.67 ( 22) hydrogen bonds : bond 0.04541 / 2.93 ( 786) hydrogen bonds : angle 3.88366 / 2.76 ( 2244) link_BETA1-4 : bond 0.00561 / 0.35 ( 3) link_BETA1-4 : angle 3.31767 / 2.44 ( 9) link_NAG-ASN : bond 0.00240 / 0.19 ( 8) link_NAG-ASN : angle 1.87626 / 1.04 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5208 (OUTLIER) cc_final: 0.4908 (mm-30) REVERT: A 217 ARG cc_start: 0.7931 (mtt180) cc_final: 0.7247 (ttp-170) REVERT: A 220 ARG cc_start: 0.8278 (OUTLIER) cc_final: 0.7142 (mtt90) REVERT: A 894 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 1251 LYS cc_start: 0.6895 (pttp) cc_final: 0.5431 (pmtt) REVERT: A 1318 ILE cc_start: 0.7537 (OUTLIER) cc_final: 0.7241 (mt) REVERT: A 1485 MET cc_start: 0.5786 (mtm) cc_final: 0.5566 (ttp) REVERT: A 1603 PHE cc_start: 0.6898 (OUTLIER) cc_final: 0.6635 (m-80) REVERT: A 1638 MET cc_start: 0.8432 (ttt) cc_final: 0.8021 (ttt) REVERT: A 1768 GLU cc_start: 0.5341 (OUTLIER) cc_final: 0.4456 (mp0) REVERT: B 152 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7666 (ttt180) REVERT: C 79 MET cc_start: 0.5081 (OUTLIER) cc_final: 0.4374 (mmm) outliers start: 33 outliers final: 13 residues processed: 189 average time/residue: 0.4278 time to fit residues: 89.9419 Evaluate side-chains 189 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 220 ARG Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 833 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 79 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 3.9990 chunk 148 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 47 optimal weight: 0.0570 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 0.3980 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN A 154 ASN A 886 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.179176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.115580 restraints weight = 14202.013| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.20 r_work: 0.3305 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13632 Z= 0.096 Angle : 0.465 9.693 18457 Z= 0.237 Chirality : 0.038 0.199 2102 Planarity : 0.003 0.047 2199 Dihedral : 10.881 155.145 2505 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 20.66 % Favored : 77.71 % 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: 2.04 (0.22), residues: 1549 helix: 2.44 (0.17), residues: 916 sheet: -0.38 (0.42), residues: 134 loop : -0.17 (0.29), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.014 0.001 TYR A1739 PHE 0.012 0.001 PHE B 54 TRP 0.012 0.001 TRP A 188 HIS 0.002 0.000 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00203 / 0.10 (13610) covalent geometry : angle 0.45581 / 0.24 (18402) SS BOND : bond 0.00218 / 0.15 ( 11) SS BOND : angle 0.79548 / 0.64 ( 22) hydrogen bonds : bond 0.03609 / 2.36 ( 786) hydrogen bonds : angle 3.72093 / 2.64 ( 2244) link_BETA1-4 : bond 0.00590 / 0.36 ( 3) link_BETA1-4 : angle 2.99356 / 2.19 ( 9) link_NAG-ASN : bond 0.00236 / 0.17 ( 8) link_NAG-ASN : angle 1.78037 / 0.98 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 166 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5238 (OUTLIER) cc_final: 0.4886 (mm-30) REVERT: A 217 ARG cc_start: 0.7997 (mtt180) cc_final: 0.7173 (ttp-170) REVERT: A 894 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 1251 LYS cc_start: 0.6884 (pttp) cc_final: 0.5406 (pmtt) REVERT: A 1318 ILE cc_start: 0.7399 (OUTLIER) cc_final: 0.7126 (mt) REVERT: A 1355 ASP cc_start: 0.7368 (t0) cc_final: 0.7102 (p0) REVERT: A 1485 MET cc_start: 0.5544 (mtm) cc_final: 0.5319 (ttp) REVERT: A 1603 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6572 (m-80) REVERT: A 1638 MET cc_start: 0.8394 (ttt) cc_final: 0.7989 (ttt) REVERT: B 79 GLN cc_start: 0.7758 (mt0) cc_final: 0.7023 (tp40) REVERT: B 113 TYR cc_start: 0.8079 (m-80) cc_final: 0.7870 (m-10) REVERT: B 152 ARG cc_start: 0.7978 (ttt90) cc_final: 0.7699 (ttt180) REVERT: B 161 ILE cc_start: 0.7215 (mm) cc_final: 0.7004 (mt) REVERT: C 79 MET cc_start: 0.5151 (OUTLIER) cc_final: 0.4432 (mmm) outliers start: 23 outliers final: 14 residues processed: 178 average time/residue: 0.5248 time to fit residues: 103.6483 Evaluate side-chains 182 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 164 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLU Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 793 LEU Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1594 PHE Chi-restraints excluded: chain A residue 1603 PHE Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 79 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 141 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 63 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 68 optimal weight: 0.0770 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 ASN A 886 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113730 restraints weight = 14434.154| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.24 r_work: 0.3305 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13632 Z= 0.099 Angle : 0.461 9.528 18457 Z= 0.235 Chirality : 0.038 0.196 2102 Planarity : 0.003 0.046 2199 Dihedral : 10.596 148.014 2505 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.64 % Allowed : 20.44 % Favored : 77.92 % 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: 2.09 (0.22), residues: 1549 helix: 2.45 (0.17), residues: 922 sheet: -0.30 (0.43), residues: 134 loop : -0.15 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.014 0.001 TYR A1739 PHE 0.012 0.001 PHE B 54 TRP 0.010 0.001 TRP A 188 HIS 0.002 0.000 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 (13610) covalent geometry : angle 0.45203 / 0.23 (18402) SS BOND : bond 0.00221 / 0.16 ( 11) SS BOND : angle 0.78584 / 0.64 ( 22) hydrogen bonds : bond 0.03528 / 2.30 ( 786) hydrogen bonds : angle 3.67342 / 2.61 ( 2244) link_BETA1-4 : bond 0.00609 / 0.37 ( 3) link_BETA1-4 : angle 2.87093 / 2.10 ( 9) link_NAG-ASN : bond 0.00219 / 0.17 ( 8) link_NAG-ASN : angle 1.75444 / 0.97 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5348.84 seconds wall clock time: 91 minutes 42.90 seconds (5502.90 seconds total)