Starting phenix.real_space_refine on Sun May 3 15:45:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thh_41262/05_2026/8thh_41262.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thh_41262/05_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_41262/05_2026/8thh_41262.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thh_41262/05_2026/8thh_41262.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8thh_41262/05_2026/8thh_41262.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thh_41262/05_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-2.1rc2-6044/lib/python3.9/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: 3.20, 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: 1.22 Conformation dependent library (CDL) restraints added in 586.1 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 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: 0.52 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: 2.30 Time building geometry restraints manager: 1.55 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 - 35.73: 8161 35.73 - 71.46: 320 71.46 - 107.19: 23 107.19 - 142.92: 6 142.92 - 178.65: 2 Dihedral angle restraints: 8512 sinusoidal: 3921 harmonic: 4591 Sorted by residual: dihedral pdb=" C41 P5S A2012 " pdb=" C42 P5S A2012 " pdb=" C43 P5S A2012 " pdb=" C44 P5S A2012 " ideal model delta sinusoidal sigma weight residual 92.81 -85.84 178.65 1 3.00e+01 1.11e-03 2.13e+01 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 ... (remaining 8509 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1594 0.046 - 0.092: 417 0.092 - 0.138: 74 0.138 - 0.184: 14 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.120 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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= 0.296 Angle : 0.741 13.381 18457 Z= 0.364 Chirality : 0.043 0.230 2102 Planarity : 0.010 0.296 2199 Dihedral : 17.985 178.649 5511 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 covalent geometry : bond 0.00569 (13610) covalent geometry : angle 0.73466 (18402) SS BOND : bond 0.00207 ( 11) SS BOND : angle 0.79504 ( 22) hydrogen bonds : bond 0.12303 ( 786) hydrogen bonds : angle 4.85792 ( 2244) link_BETA1-4 : bond 0.00786 ( 3) link_BETA1-4 : angle 3.12870 ( 9) link_NAG-ASN : bond 0.00320 ( 8) link_NAG-ASN : angle 2.05401 ( 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 : 0.340 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: 0.5108 time to fit residues: 95.7891 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 : 0.468 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 987 ASN C 59 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.178953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.115309 restraints weight = 14221.188| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.19 r_work: 0.3312 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3173 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.0623 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= 0.110 Angle : 0.495 7.864 18457 Z= 0.255 Chirality : 0.039 0.235 2102 Planarity : 0.004 0.044 2199 Dihedral : 13.969 177.999 2531 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.71 % Allowed : 17.31 % Favored : 79.99 % 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: 2.09 (0.17), residues: 924 sheet: -0.70 (0.44), residues: 135 loop : -0.45 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1499 TYR 0.016 0.001 TYR A1739 PHE 0.016 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 covalent geometry : bond 0.00232 (13610) covalent geometry : angle 0.48277 (18402) SS BOND : bond 0.00234 ( 11) SS BOND : angle 0.89101 ( 22) hydrogen bonds : bond 0.04076 ( 786) hydrogen bonds : angle 4.04505 ( 2244) link_BETA1-4 : bond 0.00288 ( 3) link_BETA1-4 : angle 3.38922 ( 9) link_NAG-ASN : bond 0.00584 ( 8) link_NAG-ASN : angle 2.08953 ( 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 208 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 170 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 798 MET cc_start: 0.4711 (OUTLIER) cc_final: 0.4397 (pmm) REVERT: A 1251 LYS cc_start: 0.6736 (pttp) cc_final: 0.5182 (pmtt) REVERT: A 1628 LYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6289 (tmmt) REVERT: A 1638 MET cc_start: 0.8311 (ttt) cc_final: 0.8015 (ttt) REVERT: C 130 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6509 (tpp) outliers start: 38 outliers final: 10 residues processed: 189 average time/residue: 0.4814 time to fit residues: 101.1095 Evaluate side-chains 175 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 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: 0.7980 chunk 95 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 99 optimal weight: 0.0050 chunk 65 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN A 154 ASN A 240 GLN A 809 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.177077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112976 restraints weight = 14777.000| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.16 r_work: 0.3174 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 13632 Z= 0.104 Angle : 0.472 8.635 18457 Z= 0.243 Chirality : 0.039 0.214 2102 Planarity : 0.003 0.046 2199 Dihedral : 12.995 177.571 2517 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.21 % Allowed : 17.88 % Favored : 79.91 % 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: 1.77 (0.22), residues: 1549 helix: 2.23 (0.17), residues: 925 sheet: -0.67 (0.43), residues: 134 loop : -0.30 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1619 TYR 0.022 0.001 TYR A1186 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 covalent geometry : bond 0.00226 (13610) covalent geometry : angle 0.46137 (18402) SS BOND : bond 0.00231 ( 11) SS BOND : angle 0.81868 ( 22) hydrogen bonds : bond 0.03848 ( 786) hydrogen bonds : angle 3.90965 ( 2244) link_BETA1-4 : bond 0.00342 ( 3) link_BETA1-4 : angle 3.13198 ( 9) link_NAG-ASN : bond 0.00331 ( 8) link_NAG-ASN : angle 2.02063 ( 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: 31 poor density : 172 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 HIS cc_start: 0.5869 (OUTLIER) cc_final: 0.5631 (t70) REVERT: A 139 ASN cc_start: 0.8289 (t0) cc_final: 0.8073 (t0) REVERT: A 798 MET cc_start: 0.4936 (OUTLIER) cc_final: 0.4612 (pmm) REVERT: A 886 GLN cc_start: 0.8209 (mm-40) cc_final: 0.8004 (mm110) REVERT: A 1251 LYS cc_start: 0.6912 (pttp) cc_final: 0.5311 (pmtt) REVERT: A 1638 MET cc_start: 0.8546 (ttt) cc_final: 0.8194 (ttt) REVERT: B 113 TYR cc_start: 0.8143 (m-80) cc_final: 0.7916 (m-10) REVERT: C 79 MET cc_start: 0.5037 (tmt) cc_final: 0.4060 (mmm) REVERT: C 130 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6714 (tpp) outliers start: 31 outliers final: 11 residues processed: 183 average time/residue: 0.4903 time to fit residues: 99.6304 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 : 0.460 ------------------------------------------------------------------------------- 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 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 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: 9.9990 chunk 26 optimal weight: 2.9990 chunk 122 optimal weight: 0.0010 chunk 142 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 136 optimal weight: 0.8980 chunk 17 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 ASN A 809 ASN A 911 ASN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 145 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.178185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113199 restraints weight = 14545.332| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 2.26 r_work: 0.3292 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.1039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13632 Z= 0.115 Angle : 0.476 7.938 18457 Z= 0.243 Chirality : 0.039 0.216 2102 Planarity : 0.003 0.047 2199 Dihedral : 12.671 176.380 2516 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.85 % Allowed : 17.81 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.22), residues: 1549 helix: 2.26 (0.17), residues: 928 sheet: -0.55 (0.43), residues: 134 loop : -0.27 (0.30), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.016 0.001 TYR A1739 PHE 0.014 0.001 PHE A1440 TRP 0.011 0.001 TRP A 188 HIS 0.002 0.001 HIS A 765 Details of bonding type rmsd covalent geometry : bond 0.00262 (13610) covalent geometry : angle 0.46424 (18402) SS BOND : bond 0.00221 ( 11) SS BOND : angle 0.81184 ( 22) hydrogen bonds : bond 0.03857 ( 786) hydrogen bonds : angle 3.84074 ( 2244) link_BETA1-4 : bond 0.00369 ( 3) link_BETA1-4 : angle 3.16680 ( 9) link_NAG-ASN : bond 0.00448 ( 8) link_NAG-ASN : angle 2.12493 ( 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: 40 poor density : 169 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5349 (mm-30) cc_final: 0.5098 (mm-30) REVERT: A 125 HIS cc_start: 0.5840 (OUTLIER) cc_final: 0.5617 (t70) REVERT: A 217 ARG cc_start: 0.7892 (mtt180) cc_final: 0.7006 (ttp-110) REVERT: A 798 MET cc_start: 0.4785 (OUTLIER) cc_final: 0.4467 (pmm) REVERT: A 1251 LYS cc_start: 0.6865 (pttp) cc_final: 0.5355 (pmtt) REVERT: A 1628 LYS cc_start: 0.6794 (OUTLIER) cc_final: 0.6370 (tmmt) REVERT: A 1638 MET cc_start: 0.8327 (ttt) cc_final: 0.7961 (ttt) REVERT: A 1768 GLU cc_start: 0.5143 (OUTLIER) cc_final: 0.4446 (mp0) REVERT: B 113 TYR cc_start: 0.8211 (m-80) cc_final: 0.7999 (m-10) REVERT: C 79 MET cc_start: 0.5143 (tmt) cc_final: 0.4259 (mmm) REVERT: C 130 MET cc_start: 0.6905 (OUTLIER) cc_final: 0.6608 (tpp) outliers start: 40 outliers final: 13 residues processed: 185 average time/residue: 0.4861 time to fit residues: 99.9233 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 : 0.346 ------------------------------------------------------------------------------- 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 798 MET 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 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: 8.9990 chunk 26 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 15 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 154 ASN A 886 GLN C 59 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.178804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.113734 restraints weight = 14546.084| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.28 r_work: 0.3304 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3166 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 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 : 0.002 0.028 13632 Z= 0.101 Angle : 0.458 8.253 18457 Z= 0.234 Chirality : 0.038 0.202 2102 Planarity : 0.003 0.045 2199 Dihedral : 12.329 178.623 2516 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.49 % Allowed : 18.09 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.22), residues: 1549 helix: 2.47 (0.17), residues: 913 sheet: -0.47 (0.43), residues: 134 loop : -0.21 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.016 0.001 TYR A1739 PHE 0.013 0.001 PHE B 54 TRP 0.010 0.001 TRP A 188 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00224 (13610) covalent geometry : angle 0.44858 (18402) SS BOND : bond 0.00222 ( 11) SS BOND : angle 0.79998 ( 22) hydrogen bonds : bond 0.03626 ( 786) hydrogen bonds : angle 3.75219 ( 2244) link_BETA1-4 : bond 0.00618 ( 3) link_BETA1-4 : angle 2.97622 ( 9) link_NAG-ASN : bond 0.00253 ( 8) link_NAG-ASN : angle 1.79552 ( 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 206 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLU cc_start: 0.5334 (OUTLIER) cc_final: 0.4989 (mm-30) REVERT: A 125 HIS cc_start: 0.5843 (OUTLIER) cc_final: 0.5615 (t70) REVERT: A 217 ARG cc_start: 0.7936 (mtt180) cc_final: 0.6880 (ttp-170) REVERT: A 1251 LYS cc_start: 0.6807 (pttp) cc_final: 0.5322 (pmtt) REVERT: A 1628 LYS cc_start: 0.6758 (OUTLIER) cc_final: 0.6297 (tmmt) REVERT: A 1638 MET cc_start: 0.8323 (ttt) cc_final: 0.7896 (ttt) REVERT: A 1768 GLU cc_start: 0.5263 (OUTLIER) cc_final: 0.4510 (mp0) REVERT: B 79 GLN cc_start: 0.7769 (mt0) cc_final: 0.6992 (tp40) REVERT: B 113 TYR cc_start: 0.8233 (m-80) cc_final: 0.8024 (m-10) REVERT: B 152 ARG cc_start: 0.7673 (ttt90) cc_final: 0.7267 (ttt180) REVERT: B 162 MET cc_start: 0.6948 (OUTLIER) cc_final: 0.5316 (ptt) REVERT: C 79 MET cc_start: 0.5230 (tmt) cc_final: 0.4400 (mmm) REVERT: C 130 MET cc_start: 0.6937 (OUTLIER) cc_final: 0.6606 (tpp) outliers start: 35 outliers final: 12 residues processed: 186 average time/residue: 0.5307 time to fit residues: 108.8942 Evaluate side-chains 181 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 163 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 125 HIS 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 793 LEU Chi-restraints excluded: chain A residue 869 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 1768 GLU Chi-restraints excluded: chain B residue 64 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 162 MET 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: 0.7980 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 139 optimal weight: 7.9990 chunk 104 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 154 ASN A 886 GLN ** A 941 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.176247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.110865 restraints weight = 14510.713| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.27 r_work: 0.3273 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 13632 Z= 0.156 Angle : 0.512 8.807 18457 Z= 0.260 Chirality : 0.040 0.236 2102 Planarity : 0.004 0.047 2199 Dihedral : 12.366 170.975 2516 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.78 % Allowed : 18.52 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.80 (0.22), residues: 1549 helix: 2.24 (0.17), residues: 926 sheet: -0.48 (0.42), residues: 134 loop : -0.33 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1570 TYR 0.019 0.001 TYR A1739 PHE 0.020 0.001 PHE A1440 TRP 0.010 0.001 TRP A 188 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd covalent geometry : bond 0.00374 (13610) covalent geometry : angle 0.49996 (18402) SS BOND : bond 0.00260 ( 11) SS BOND : angle 0.87801 ( 22) hydrogen bonds : bond 0.04256 ( 786) hydrogen bonds : angle 3.85487 ( 2244) link_BETA1-4 : bond 0.00498 ( 3) link_BETA1-4 : angle 3.29496 ( 9) link_NAG-ASN : bond 0.00222 ( 8) link_NAG-ASN : angle 2.31813 ( 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 210 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 171 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5383 (mpp) cc_final: 0.5070 (mpp) REVERT: A 217 ARG cc_start: 0.7898 (mtt180) cc_final: 0.7062 (ttp-170) REVERT: A 220 ARG cc_start: 0.8215 (OUTLIER) cc_final: 0.6909 (mtt90) REVERT: A 1251 LYS cc_start: 0.6822 (pttp) cc_final: 0.5329 (pmtt) REVERT: A 1485 MET cc_start: 0.5832 (mtm) cc_final: 0.5630 (ttp) REVERT: A 1603 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6486 (m-80) REVERT: A 1628 LYS cc_start: 0.6908 (OUTLIER) cc_final: 0.6385 (tmmt) REVERT: A 1638 MET cc_start: 0.8361 (ttt) cc_final: 0.7935 (ttt) REVERT: A 1768 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4583 (mp0) REVERT: B 31 VAL cc_start: 0.8514 (m) cc_final: 0.8088 (t) REVERT: B 79 GLN cc_start: 0.7789 (mt0) cc_final: 0.7000 (tp40) REVERT: B 152 ARG cc_start: 0.7745 (ttt90) cc_final: 0.7438 (ttt180) REVERT: B 161 ILE cc_start: 0.7323 (mm) cc_final: 0.7078 (mt) REVERT: B 162 MET cc_start: 0.7059 (mmm) cc_final: 0.6721 (mmm) REVERT: C 79 MET cc_start: 0.5291 (tmt) cc_final: 0.4530 (mmm) outliers start: 39 outliers final: 13 residues processed: 196 average time/residue: 0.4939 time to fit residues: 106.8100 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 : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 753 CYS Chi-restraints excluded: chain A residue 793 LEU 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 1603 PHE Chi-restraints excluded: chain A residue 1628 LYS 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: 0.9990 chunk 92 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 99 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 151 optimal weight: 0.0010 chunk 16 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4147 r_free = 0.4147 target = 0.178706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.113834 restraints weight = 14496.288| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.26 r_work: 0.3304 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13632 Z= 0.095 Angle : 0.453 8.761 18457 Z= 0.232 Chirality : 0.038 0.198 2102 Planarity : 0.003 0.047 2199 Dihedral : 11.940 169.390 2516 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.99 % Allowed : 19.44 % Favored : 78.56 % 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: 2.07 (0.22), residues: 1549 helix: 2.47 (0.17), residues: 913 sheet: -0.38 (0.43), residues: 134 loop : -0.16 (0.29), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 841 TYR 0.014 0.001 TYR A1739 PHE 0.013 0.001 PHE B 54 TRP 0.011 0.001 TRP A 188 HIS 0.003 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00202 (13610) covalent geometry : angle 0.44276 (18402) SS BOND : bond 0.00212 ( 11) SS BOND : angle 0.77303 ( 22) hydrogen bonds : bond 0.03556 ( 786) hydrogen bonds : angle 3.72301 ( 2244) link_BETA1-4 : bond 0.00639 ( 3) link_BETA1-4 : angle 2.95057 ( 9) link_NAG-ASN : bond 0.00236 ( 8) link_NAG-ASN : angle 1.84305 ( 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 198 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 170 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5526 (mpp) cc_final: 0.5006 (mpm) REVERT: A 217 ARG cc_start: 0.7890 (mtt180) cc_final: 0.6957 (ttp-170) REVERT: A 894 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 1251 LYS cc_start: 0.6793 (pttp) cc_final: 0.5298 (pmtt) REVERT: A 1318 ILE cc_start: 0.7332 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 1628 LYS cc_start: 0.6755 (OUTLIER) cc_final: 0.6281 (tmmt) REVERT: A 1768 GLU cc_start: 0.5395 (OUTLIER) cc_final: 0.4575 (mp0) REVERT: B 79 GLN cc_start: 0.7756 (mt0) cc_final: 0.6986 (tp40) REVERT: B 113 TYR cc_start: 0.8188 (m-80) cc_final: 0.7970 (m-10) REVERT: B 152 ARG cc_start: 0.7735 (ttt90) cc_final: 0.7429 (ttt180) REVERT: B 161 ILE cc_start: 0.7189 (mm) cc_final: 0.6953 (mt) REVERT: B 162 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6593 (mmm) REVERT: C 79 MET cc_start: 0.5079 (tmt) cc_final: 0.4386 (mmm) outliers start: 28 outliers final: 14 residues processed: 183 average time/residue: 0.4950 time to fit residues: 100.1580 Evaluate side-chains 184 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 319 THR Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 919 ILE 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 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 162 MET Chi-restraints excluded: chain B residue 172 ILE 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: 3.9990 chunk 106 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 114 optimal weight: 0.9980 chunk 47 optimal weight: 0.0270 chunk 60 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 154 ASN A 809 ASN A 886 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.178819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.113819 restraints weight = 14385.492| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.29 r_work: 0.3314 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.1536 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= 0.097 Angle : 0.456 9.665 18457 Z= 0.232 Chirality : 0.038 0.192 2102 Planarity : 0.003 0.047 2199 Dihedral : 11.544 165.585 2516 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.14 % Allowed : 19.73 % Favored : 78.13 % 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: -0.31 (0.43), residues: 134 loop : -0.15 (0.30), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.016 0.001 TYR A1739 PHE 0.012 0.001 PHE B 54 TRP 0.009 0.001 TRP A 188 HIS 0.003 0.000 HIS A 14 Details of bonding type rmsd covalent geometry : bond 0.00211 (13610) covalent geometry : angle 0.44655 (18402) SS BOND : bond 0.00211 ( 11) SS BOND : angle 0.76890 ( 22) hydrogen bonds : bond 0.03486 ( 786) hydrogen bonds : angle 3.67305 ( 2244) link_BETA1-4 : bond 0.00591 ( 3) link_BETA1-4 : angle 2.85773 ( 9) link_NAG-ASN : bond 0.00218 ( 8) link_NAG-ASN : angle 1.80690 ( 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 204 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 174 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5772 (mpp) cc_final: 0.5206 (mpm) REVERT: A 217 ARG cc_start: 0.7964 (mtt180) cc_final: 0.7101 (ttp-170) REVERT: A 307 GLU cc_start: 0.8781 (tp30) cc_final: 0.8444 (tm-30) REVERT: A 791 MET cc_start: 0.6104 (OUTLIER) cc_final: 0.5504 (tpt) REVERT: A 894 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7564 (mm-30) REVERT: A 1251 LYS cc_start: 0.6800 (pttp) cc_final: 0.5302 (pmtt) REVERT: A 1318 ILE cc_start: 0.7359 (OUTLIER) cc_final: 0.7091 (mt) REVERT: A 1628 LYS cc_start: 0.6746 (OUTLIER) cc_final: 0.6290 (tmmt) REVERT: B 79 GLN cc_start: 0.7743 (mt0) cc_final: 0.7013 (tp40) REVERT: B 113 TYR cc_start: 0.8143 (m-80) cc_final: 0.7942 (m-10) REVERT: B 152 ARG cc_start: 0.7829 (ttt90) cc_final: 0.7367 (ttt180) REVERT: B 162 MET cc_start: 0.7026 (OUTLIER) cc_final: 0.6619 (mmm) REVERT: C 79 MET cc_start: 0.5101 (tmt) cc_final: 0.4383 (mmm) REVERT: C 130 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6648 (tpp) outliers start: 30 outliers final: 14 residues processed: 189 average time/residue: 0.5247 time to fit residues: 109.1924 Evaluate side-chains 187 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 791 MET Chi-restraints excluded: chain A residue 869 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 1628 LYS 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 B residue 162 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.0270 chunk 138 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4148 r_free = 0.4148 target = 0.178905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113812 restraints weight = 14548.869| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.29 r_work: 0.3313 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13632 Z= 0.099 Angle : 0.459 9.640 18457 Z= 0.233 Chirality : 0.038 0.190 2102 Planarity : 0.003 0.048 2199 Dihedral : 11.359 162.899 2516 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.99 % Allowed : 20.16 % 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: 2.09 (0.22), residues: 1549 helix: 2.43 (0.17), residues: 925 sheet: -0.32 (0.43), residues: 134 loop : -0.12 (0.30), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 841 TYR 0.015 0.001 TYR A1739 PHE 0.012 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 covalent geometry : bond 0.00219 (13610) covalent geometry : angle 0.45003 (18402) SS BOND : bond 0.00214 ( 11) SS BOND : angle 0.77629 ( 22) hydrogen bonds : bond 0.03463 ( 786) hydrogen bonds : angle 3.65884 ( 2244) link_BETA1-4 : bond 0.00626 ( 3) link_BETA1-4 : angle 2.86386 ( 9) link_NAG-ASN : bond 0.00260 ( 8) link_NAG-ASN : angle 1.83933 ( 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 199 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.5934 (mpp) cc_final: 0.5446 (mpm) REVERT: A 217 ARG cc_start: 0.7954 (mtt180) cc_final: 0.7120 (ttp-170) REVERT: A 307 GLU cc_start: 0.8778 (tp30) cc_final: 0.8449 (tm-30) REVERT: A 791 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5453 (tpt) REVERT: A 894 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7567 (mm-30) REVERT: A 1251 LYS cc_start: 0.6797 (pttp) cc_final: 0.5321 (pmtt) REVERT: A 1293 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7960 (mtp85) REVERT: A 1318 ILE cc_start: 0.7394 (OUTLIER) cc_final: 0.7123 (mt) REVERT: A 1371 PHE cc_start: 0.7754 (m-10) cc_final: 0.7531 (m-10) REVERT: B 79 GLN cc_start: 0.7752 (mt0) cc_final: 0.6999 (tp40) REVERT: B 152 ARG cc_start: 0.7846 (ttt90) cc_final: 0.7550 (ttt180) REVERT: B 161 ILE cc_start: 0.7218 (mm) cc_final: 0.6988 (mt) REVERT: B 162 MET cc_start: 0.7037 (OUTLIER) cc_final: 0.6635 (mmm) REVERT: C 79 MET cc_start: 0.5102 (tmt) cc_final: 0.4416 (mmm) REVERT: C 130 MET cc_start: 0.6941 (OUTLIER) cc_final: 0.6598 (tpp) outliers start: 28 outliers final: 15 residues processed: 184 average time/residue: 0.5342 time to fit residues: 108.4800 Evaluate side-chains 190 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 791 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1293 ARG 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 B residue 162 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 139 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 100 optimal weight: 7.9990 chunk 107 optimal weight: 0.9980 chunk 47 optimal weight: 0.0050 chunk 41 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4152 r_free = 0.4152 target = 0.179174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.114135 restraints weight = 14481.179| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.28 r_work: 0.3316 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3177 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.1672 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= 0.098 Angle : 0.465 9.733 18457 Z= 0.235 Chirality : 0.038 0.187 2102 Planarity : 0.003 0.047 2199 Dihedral : 11.222 160.127 2516 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.99 % Allowed : 20.44 % Favored : 77.56 % 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: 2.45 (0.17), residues: 925 sheet: -0.07 (0.45), residues: 124 loop : -0.17 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1619 TYR 0.015 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 covalent geometry : bond 0.00216 (13610) covalent geometry : angle 0.45128 (18402) SS BOND : bond 0.00221 ( 11) SS BOND : angle 0.76118 ( 22) hydrogen bonds : bond 0.03447 ( 786) hydrogen bonds : angle 3.65361 ( 2244) link_BETA1-4 : bond 0.00485 ( 3) link_BETA1-4 : angle 2.82827 ( 9) link_NAG-ASN : bond 0.00235 ( 8) link_NAG-ASN : angle 2.53307 ( 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 196 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6027 (mpp) cc_final: 0.5501 (mpm) REVERT: A 217 ARG cc_start: 0.7983 (mtt180) cc_final: 0.7146 (ttp-170) REVERT: A 307 GLU cc_start: 0.8775 (tp30) cc_final: 0.8444 (tm-30) REVERT: A 791 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5486 (tpt) REVERT: A 894 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7558 (mm-30) REVERT: A 1251 LYS cc_start: 0.6910 (pttp) cc_final: 0.5411 (pmtt) REVERT: A 1293 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7965 (mtp85) REVERT: A 1318 ILE cc_start: 0.7388 (OUTLIER) cc_final: 0.7117 (mt) REVERT: B 31 VAL cc_start: 0.8498 (m) cc_final: 0.8129 (t) REVERT: B 79 GLN cc_start: 0.7753 (mt0) cc_final: 0.7004 (tp40) REVERT: B 152 ARG cc_start: 0.7885 (ttt90) cc_final: 0.7590 (ttt180) REVERT: B 161 ILE cc_start: 0.7211 (mm) cc_final: 0.6981 (mt) REVERT: B 162 MET cc_start: 0.7034 (OUTLIER) cc_final: 0.6670 (mmm) REVERT: C 79 MET cc_start: 0.5113 (OUTLIER) cc_final: 0.4426 (mmm) REVERT: C 130 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6558 (tpp) outliers start: 28 outliers final: 15 residues processed: 181 average time/residue: 0.5435 time to fit residues: 108.2900 Evaluate side-chains 190 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 791 MET Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 927 GLU Chi-restraints excluded: chain A residue 1293 ARG 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 B residue 162 MET Chi-restraints excluded: chain B residue 172 ILE Chi-restraints excluded: chain C residue 79 MET Chi-restraints excluded: chain C residue 130 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 14 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 141 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 47 optimal weight: 0.0670 chunk 68 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4150 r_free = 0.4150 target = 0.178995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.113877 restraints weight = 14499.964| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.29 r_work: 0.3314 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13632 Z= 0.101 Angle : 0.464 9.575 18457 Z= 0.235 Chirality : 0.038 0.187 2102 Planarity : 0.003 0.048 2199 Dihedral : 11.119 157.052 2516 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.85 % Allowed : 20.73 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.22), residues: 1549 helix: 2.44 (0.17), residues: 926 sheet: -0.41 (0.42), residues: 138 loop : -0.12 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1619 TYR 0.015 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 covalent geometry : bond 0.00228 (13610) covalent geometry : angle 0.45255 (18402) SS BOND : bond 0.00218 ( 11) SS BOND : angle 0.76775 ( 22) hydrogen bonds : bond 0.03474 ( 786) hydrogen bonds : angle 3.65404 ( 2244) link_BETA1-4 : bond 0.00559 ( 3) link_BETA1-4 : angle 2.78738 ( 9) link_NAG-ASN : bond 0.00235 ( 8) link_NAG-ASN : angle 2.31843 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5476.82 seconds wall clock time: 93 minutes 44.28 seconds (5624.28 seconds total)