Starting phenix.real_space_refine on Fri Jul 3 14:00:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.cif Found real_map, /net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.cif" model { file = "/net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8s9c_40239/07_2026/8s9c_40239.cif" } resolution = 3.2 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= -0.002 sd= 0.130 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 16 5.49 5 S 97 5.16 5 C 8944 2.51 5 N 2046 2.21 5 O 2431 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13534 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 10262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 10262 Classifications: {'peptide': 1273} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 739 Unusual residues: {'LPE': 9, 'N6W': 1, 'NAG': 2, 'PCW': 4, 'Y01': 5} Classifications: {'peptide': 3, 'undetermined': 21} Link IDs: {None: 23} Unresolved non-hydrogen bonds: 168 Unresolved non-hydrogen angles: 176 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-2': 1, 'P5S:plan-1': 1, 'PCW:plan-4': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.29, per 1000 atoms: 0.17 Number of scatterers: 13534 At special positions: 0 Unit cell: (129.224, 138.136, 126.996, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 16 15.00 O 2431 8.00 N 2046 7.00 C 8944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.03 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.04 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2002 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 510.2 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: 2972 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 9 sheets defined 65.7% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 8 through 12 removed outlier: 3.758A 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: 4.005A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 85 removed outlier: 4.279A pdb=" N ASP A 84 " --> pdb=" O TYR A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 removed outlier: 3.522A 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: 3.976A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 142 " --> pdb=" O THR A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.194A 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 removed outlier: 3.564A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'A' and resid 218 through 221 Processing helix chain 'A' and resid 222 through 228 removed outlier: 3.937A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 243 removed outlier: 3.619A 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 337 through 341 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 4.007A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.969A 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: 3.953A pdb=" N PHE A 733 " --> pdb=" O TYR A 729 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N MET A 742 " --> pdb=" O TYR A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 762 removed outlier: 3.925A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 797 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 832 through 837 Processing helix chain 'A' and resid 838 through 847 removed outlier: 4.065A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 4.290A pdb=" N LEU A 855 " --> pdb=" O THR A 851 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 856 " --> pdb=" O LEU A 852 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.596A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 929 through 940 removed outlier: 3.794A 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: 4.044A 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: 3.586A pdb=" N GLU A1212 " --> pdb=" O LEU A1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1209 through 1212' Processing helix chain 'A' and resid 1214 through 1218 removed outlier: 4.266A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1278 Processing helix chain 'A' and resid 1284 through 1290 removed outlier: 3.533A pdb=" N ARG A1290 " --> pdb=" O ILE A1286 " (cutoff:3.500A) Processing helix chain 'A' and resid 1291 through 1300 removed outlier: 3.589A pdb=" N ALA A1294 " --> pdb=" O THR A1291 " (cutoff:3.500A) Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 removed outlier: 3.583A pdb=" N ALA A1313 " --> pdb=" O VAL A1309 " (cutoff:3.500A) Proline residue: A1319 - end of helix removed outlier: 3.800A pdb=" N ILE A1334 " --> pdb=" O ILE A1330 " (cutoff:3.500A) removed outlier: 3.941A 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: 3.566A pdb=" N LEU A1397 " --> pdb=" O GLY A1393 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1418 removed outlier: 4.131A 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 1467 removed outlier: 3.891A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1447 " --> pdb=" O PHE A1443 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU A1449 " --> pdb=" O SER A1445 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1487 removed outlier: 3.854A pdb=" N LYS A1480 " --> pdb=" O GLU A1476 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N TYR A1481 " --> pdb=" O GLU A1477 " (cutoff:3.500A) removed outlier: 3.743A 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 1534 Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 3.791A 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: 4.013A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1626 removed outlier: 3.510A pdb=" N GLY A1626 " --> pdb=" O LEU A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1627 through 1666 removed outlier: 3.541A pdb=" N THR A1632 " --> pdb=" O LYS A1628 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix removed outlier: 3.606A pdb=" N ASN A1646 " --> pdb=" O PRO A1642 " (cutoff:3.500A) Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.119A 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 1708 No H-bonds generated for 'chain 'A' and resid 1706 through 1708' Processing helix chain 'A' and resid 1732 through 1751 Processing helix chain 'A' and resid 1752 through 1768 removed outlier: 3.684A pdb=" N ALA A1757 " --> pdb=" O ASN A1753 " (cutoff:3.500A) 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 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: 6.155A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.155A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.338A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 129 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE C 83 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 101 removed outlier: 3.726A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) 783 hydrogen bonds defined for protein. 2226 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: 2.42 Time building geometry restraints manager: 1.27 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: 2041 1.32 - 1.44: 3693 1.44 - 1.57: 7889 1.57 - 1.69: 32 1.69 - 1.82: 157 Bond restraints: 13812 Sorted by residual: bond pdb=" C TYR A1228 " pdb=" O TYR A1228 " ideal model delta sigma weight residual 1.236 1.286 -0.050 1.26e-02 6.30e+03 1.56e+01 bond pdb=" N VAL A1752 " pdb=" CA VAL A1752 " ideal model delta sigma weight residual 1.455 1.496 -0.041 1.06e-02 8.90e+03 1.48e+01 bond pdb=" CA ALA A1229 " pdb=" CB ALA A1229 " ideal model delta sigma weight residual 1.528 1.474 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" O33 LPE A2024 " pdb=" P LPE A2024 " ideal model delta sigma weight residual 1.673 1.603 0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C19 PCW A2010 " pdb=" C20 PCW A2010 " ideal model delta sigma weight residual 1.333 1.266 0.067 2.00e-02 2.50e+03 1.14e+01 ... (remaining 13807 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 17975 2.22 - 4.45: 571 4.45 - 6.67: 82 6.67 - 8.89: 22 8.89 - 11.11: 6 Bond angle restraints: 18656 Sorted by residual: angle pdb=" N ILE A1745 " pdb=" CA ILE A1745 " pdb=" C ILE A1745 " ideal model delta sigma weight residual 111.00 106.65 4.35 1.09e+00 8.42e-01 1.59e+01 angle pdb=" N VAL A 218 " pdb=" CA VAL A 218 " pdb=" C VAL A 218 " ideal model delta sigma weight residual 113.07 107.71 5.36 1.36e+00 5.41e-01 1.55e+01 angle pdb=" N PHE A1447 " pdb=" CA PHE A1447 " pdb=" C PHE A1447 " ideal model delta sigma weight residual 112.23 107.33 4.90 1.26e+00 6.30e-01 1.51e+01 angle pdb=" N ASN A1450 " pdb=" CA ASN A1450 " pdb=" C ASN A1450 " ideal model delta sigma weight residual 111.36 107.20 4.16 1.09e+00 8.42e-01 1.46e+01 angle pdb=" CA TRP A1245 " pdb=" C TRP A1245 " pdb=" O TRP A1245 " ideal model delta sigma weight residual 120.70 116.78 3.92 1.03e+00 9.43e-01 1.45e+01 ... (remaining 18651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.37: 7820 34.37 - 68.73: 288 68.73 - 103.10: 24 103.10 - 137.47: 9 137.47 - 171.84: 1 Dihedral angle restraints: 8142 sinusoidal: 3547 harmonic: 4595 Sorted by residual: dihedral pdb=" CD ARG A 214 " pdb=" NE ARG A 214 " pdb=" CZ ARG A 214 " pdb=" NH1 ARG A 214 " ideal model delta sinusoidal sigma weight residual 0.00 -81.14 81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" C33 PCW A2012 " pdb=" C31 PCW A2012 " pdb=" C32 PCW A2012 " pdb=" O2 PCW A2012 " ideal model delta sinusoidal sigma weight residual -168.17 3.67 -171.84 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C21 P5S A2022 " pdb=" C22 P5S A2022 " pdb=" C23 P5S A2022 " pdb=" C24 P5S A2022 " ideal model delta sinusoidal sigma weight residual -177.17 -48.06 -129.11 1 3.00e+01 1.11e-03 1.74e+01 ... (remaining 8139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1577 0.050 - 0.100: 418 0.100 - 0.150: 98 0.150 - 0.200: 19 0.200 - 0.250: 6 Chirality restraints: 2118 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.43 0.03 2.00e-02 2.50e+03 1.81e+00 chirality pdb=" CA VAL A 833 " pdb=" N VAL A 833 " pdb=" C VAL A 833 " pdb=" CB VAL A 833 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+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 -2.29 -0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 2115 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.316 2.00e-02 2.50e+03 2.72e-01 9.23e+02 pdb=" C7 NAG D 2 " 0.070 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.012 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.469 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 PCW A2014 " 0.044 2.00e-02 2.50e+03 2.58e-01 6.63e+02 pdb=" C19 PCW A2014 " -0.285 2.00e-02 2.50e+03 pdb=" C20 PCW A2014 " 0.397 2.00e-02 2.50e+03 pdb=" C21 PCW A2014 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 303 " 0.264 2.00e-02 2.50e+03 2.22e-01 6.16e+02 pdb=" C7 NAG B 303 " -0.070 2.00e-02 2.50e+03 pdb=" C8 NAG B 303 " 0.176 2.00e-02 2.50e+03 pdb=" N2 NAG B 303 " -0.375 2.00e-02 2.50e+03 pdb=" O7 NAG B 303 " 0.004 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 3232 2.79 - 3.32: 12841 3.32 - 3.85: 21641 3.85 - 4.37: 25479 4.37 - 4.90: 44631 Nonbonded interactions: 107824 Sorted by model distance: nonbonded pdb=" O2H LPE A2017 " pdb=" O31 LPE A2017 " model vdw 2.267 3.040 nonbonded pdb=" OG SER B 42 " pdb=" NH2 ARG B 125 " model vdw 2.298 3.120 nonbonded pdb=" NE ARG B 46 " pdb=" OE2 GLU B 48 " model vdw 2.323 3.120 nonbonded pdb=" OG1 THR C 68 " pdb=" OE1 GLU C 77 " model vdw 2.329 3.040 nonbonded pdb=" OE1 GLU A1305 " pdb=" NH1 ARG A1308 " model vdw 2.378 3.120 ... (remaining 107819 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.070 13834 Z= 0.404 Angle : 0.911 11.113 18711 Z= 0.493 Chirality : 0.050 0.250 2118 Planarity : 0.018 0.485 2208 Dihedral : 17.490 171.836 5137 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.71 % Allowed : 15.67 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.22), residues: 1549 helix: 1.46 (0.18), residues: 899 sheet: -1.16 (0.44), residues: 135 loop : -0.78 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 115 TYR 0.019 0.002 TYR A1235 PHE 0.033 0.002 PHE A 739 TRP 0.015 0.001 TRP A1382 HIS 0.008 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00769 / 0.40 (13812) covalent geometry : angle 0.90522 / 0.49 (18656) SS BOND : bond 0.00272 / 0.19 ( 11) SS BOND : angle 0.96377 / 0.73 ( 22) hydrogen bonds : bond 0.13331 / 8.75 ( 775) hydrogen bonds : angle 5.76071 / 4.06 ( 2226) link_BETA1-4 : bond 0.00677 / 0.40 ( 3) link_BETA1-4 : angle 3.10494 / 1.53 ( 9) link_NAG-ASN : bond 0.00281 / 0.20 ( 8) link_NAG-ASN : angle 2.36291 / 1.29 ( 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 249 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.545 Fit side-chains REVERT: A 59 LEU cc_start: 0.7498 (mp) cc_final: 0.7140 (mt) REVERT: A 70 MET cc_start: 0.5975 (mmt) cc_final: 0.5408 (mtt) REVERT: A 76 GLU cc_start: 0.8183 (tp30) cc_final: 0.7924 (tp30) REVERT: A 185 ARG cc_start: 0.8261 (tpp80) cc_final: 0.7259 (mmt-90) REVERT: A 190 TRP cc_start: 0.7620 (m-10) cc_final: 0.6894 (m100) REVERT: A 790 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 810 ILE cc_start: 0.7792 (mm) cc_final: 0.7518 (mm) REVERT: A 902 ASP cc_start: 0.8782 (t0) cc_final: 0.8377 (t0) REVERT: A 1322 MET cc_start: 0.8209 (mmm) cc_final: 0.7996 (mmt) REVERT: A 1462 GLN cc_start: 0.7832 (mm-40) cc_final: 0.7296 (mm110) REVERT: B 96 ARG cc_start: 0.8257 (ttm110) cc_final: 0.7397 (mmt180) REVERT: B 183 LYS cc_start: 0.6943 (ptpt) cc_final: 0.6353 (tppt) outliers start: 10 outliers final: 2 residues processed: 243 average time/residue: 0.1073 time to fit residues: 38.4697 Evaluate side-chains 191 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 189 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 VAL Chi-restraints excluded: chain A residue 1240 GLU 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: 0.5980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 360 GLN A 900 ASN C 143 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.170225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130146 restraints weight = 17017.659| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.86 r_work: 0.3085 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2941 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13834 Z= 0.132 Angle : 0.551 8.706 18711 Z= 0.283 Chirality : 0.040 0.239 2118 Planarity : 0.004 0.057 2208 Dihedral : 14.620 171.374 2144 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.85 % Allowed : 14.96 % Favored : 83.19 % 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: 1.30 (0.22), residues: 1549 helix: 1.91 (0.17), residues: 897 sheet: -0.90 (0.44), residues: 135 loop : -0.46 (0.29), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1610 TYR 0.017 0.001 TYR A1739 PHE 0.032 0.001 PHE A 739 TRP 0.011 0.001 TRP A1245 HIS 0.005 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (13812) covalent geometry : angle 0.53874 / 0.28 (18656) SS BOND : bond 0.00681 / 0.44 ( 11) SS BOND : angle 1.41316 / 1.14 ( 22) hydrogen bonds : bond 0.04699 / 3.02 ( 775) hydrogen bonds : angle 4.31777 / 3.04 ( 2226) link_BETA1-4 : bond 0.00787 / 0.47 ( 3) link_BETA1-4 : angle 3.27567 / 1.56 ( 9) link_NAG-ASN : bond 0.00378 / 0.25 ( 8) link_NAG-ASN : angle 2.20623 / 1.46 ( 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 232 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 206 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7476 (mp) cc_final: 0.7182 (mt) REVERT: A 116 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6972 (ttt90) REVERT: A 190 TRP cc_start: 0.7712 (m-10) cc_final: 0.7252 (m100) REVERT: A 403 MET cc_start: 0.8395 (tpp) cc_final: 0.7800 (tpp) REVERT: A 407 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7555 (mm-30) REVERT: A 730 TRP cc_start: 0.3339 (t60) cc_final: 0.2776 (m-90) REVERT: A 790 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 803 TYR cc_start: 0.7798 (t80) cc_final: 0.7568 (t80) REVERT: A 810 ILE cc_start: 0.8248 (mm) cc_final: 0.8040 (mm) REVERT: A 902 ASP cc_start: 0.8728 (t0) cc_final: 0.8528 (t0) REVERT: A 1193 TRP cc_start: 0.7998 (m-10) cc_final: 0.7622 (m-10) REVERT: A 1305 GLU cc_start: 0.8070 (tp30) cc_final: 0.7417 (tt0) REVERT: A 1462 GLN cc_start: 0.8057 (mm-40) cc_final: 0.7809 (mm110) REVERT: A 1543 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.7445 (tpp) REVERT: A 1762 ASN cc_start: 0.8783 (m-40) cc_final: 0.8554 (m-40) REVERT: B 96 ARG cc_start: 0.8426 (ttm110) cc_final: 0.7862 (mmt180) REVERT: B 183 LYS cc_start: 0.7220 (ptpt) cc_final: 0.6595 (tppt) outliers start: 26 outliers final: 15 residues processed: 220 average time/residue: 0.0933 time to fit residues: 30.8331 Evaluate side-chains 215 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 198 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 116 ARG Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 0.8980 chunk 78 optimal weight: 9.9990 chunk 48 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 46 optimal weight: 0.1980 chunk 67 optimal weight: 8.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 209 ASN A 265 GLN C 145 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.168906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128509 restraints weight = 17168.604| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.95 r_work: 0.3004 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13834 Z= 0.154 Angle : 0.526 7.547 18711 Z= 0.271 Chirality : 0.040 0.249 2118 Planarity : 0.004 0.051 2208 Dihedral : 13.599 166.236 2143 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.85 % Allowed : 15.38 % Favored : 81.77 % 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: 1.43 (0.22), residues: 1549 helix: 2.00 (0.17), residues: 901 sheet: -0.76 (0.44), residues: 135 loop : -0.42 (0.28), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.015 0.001 TYR A1739 PHE 0.019 0.001 PHE A 739 TRP 0.013 0.001 TRP A1245 HIS 0.004 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 (13812) covalent geometry : angle 0.51654 / 0.27 (18656) SS BOND : bond 0.00262 / 0.17 ( 11) SS BOND : angle 1.23567 / 0.96 ( 22) hydrogen bonds : bond 0.04562 / 2.94 ( 775) hydrogen bonds : angle 4.13186 / 2.91 ( 2226) link_BETA1-4 : bond 0.00580 / 0.35 ( 3) link_BETA1-4 : angle 3.05276 / 1.47 ( 9) link_NAG-ASN : bond 0.00254 / 0.18 ( 8) link_NAG-ASN : angle 1.93336 / 1.26 ( 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 234 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 194 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 PHE cc_start: 0.7438 (m-80) cc_final: 0.6903 (m-80) REVERT: A 59 LEU cc_start: 0.7507 (mp) cc_final: 0.7247 (mt) REVERT: A 70 MET cc_start: 0.7042 (mmt) cc_final: 0.6383 (mtt) REVERT: A 76 GLU cc_start: 0.8385 (tp30) cc_final: 0.7941 (mm-30) REVERT: A 125 HIS cc_start: 0.7982 (OUTLIER) cc_final: 0.7310 (t-90) REVERT: A 190 TRP cc_start: 0.7906 (m-10) cc_final: 0.7378 (m100) REVERT: A 403 MET cc_start: 0.8400 (tpp) cc_final: 0.7602 (tpp) REVERT: A 407 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7434 (mm-30) REVERT: A 902 ASP cc_start: 0.8801 (t0) cc_final: 0.8545 (t0) REVERT: A 979 ILE cc_start: 0.2878 (OUTLIER) cc_final: 0.2432 (pt) REVERT: A 1193 TRP cc_start: 0.7972 (m-10) cc_final: 0.7719 (m-10) REVERT: A 1241 MET cc_start: 0.8657 (ttt) cc_final: 0.8428 (ttt) REVERT: A 1305 GLU cc_start: 0.8078 (tp30) cc_final: 0.7571 (tt0) REVERT: A 1462 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7935 (mm110) REVERT: B 96 ARG cc_start: 0.8484 (ttm110) cc_final: 0.8016 (mmt180) REVERT: B 183 LYS cc_start: 0.7261 (ptpt) cc_final: 0.6604 (tppt) REVERT: C 134 ASP cc_start: 0.8147 (t0) cc_final: 0.7792 (t0) outliers start: 40 outliers final: 28 residues processed: 216 average time/residue: 0.0848 time to fit residues: 27.6699 Evaluate side-chains 214 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 184 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 171 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 134 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.168369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128093 restraints weight = 16935.751| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 1.98 r_work: 0.3047 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13834 Z= 0.150 Angle : 0.517 7.461 18711 Z= 0.266 Chirality : 0.040 0.243 2118 Planarity : 0.004 0.044 2208 Dihedral : 12.937 158.715 2143 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.49 % Allowed : 15.60 % Favored : 80.91 % 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: 1.52 (0.22), residues: 1549 helix: 2.02 (0.17), residues: 909 sheet: -0.61 (0.43), residues: 134 loop : -0.36 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 137 TYR 0.017 0.001 TYR B 32 PHE 0.017 0.001 PHE A1263 TRP 0.015 0.001 TRP A1245 HIS 0.003 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (13812) covalent geometry : angle 0.50710 / 0.26 (18656) SS BOND : bond 0.00259 / 0.17 ( 11) SS BOND : angle 1.14398 / 0.88 ( 22) hydrogen bonds : bond 0.04452 / 2.87 ( 775) hydrogen bonds : angle 4.05139 / 2.85 ( 2226) link_BETA1-4 : bond 0.00588 / 0.35 ( 3) link_BETA1-4 : angle 3.04555 / 1.48 ( 9) link_NAG-ASN : bond 0.00226 / 0.18 ( 8) link_NAG-ASN : angle 1.88940 / 1.22 ( 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 241 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 192 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7490 (mp) cc_final: 0.7149 (mt) REVERT: A 70 MET cc_start: 0.7062 (mmt) cc_final: 0.6394 (mtt) REVERT: A 76 GLU cc_start: 0.8486 (tp30) cc_final: 0.8267 (mm-30) REVERT: A 125 HIS cc_start: 0.7979 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: A 185 ARG cc_start: 0.8226 (tpp80) cc_final: 0.7230 (mmt-90) REVERT: A 190 TRP cc_start: 0.7928 (m-10) cc_final: 0.7379 (m100) REVERT: A 403 MET cc_start: 0.8363 (tpp) cc_final: 0.7526 (tpp) REVERT: A 407 GLU cc_start: 0.7825 (mm-30) cc_final: 0.7480 (mm-30) REVERT: A 902 ASP cc_start: 0.8802 (t0) cc_final: 0.8524 (t0) REVERT: A 1193 TRP cc_start: 0.7968 (m-10) cc_final: 0.7577 (m-10) REVERT: A 1241 MET cc_start: 0.8720 (ttt) cc_final: 0.8505 (ttt) REVERT: A 1305 GLU cc_start: 0.8099 (tp30) cc_final: 0.7625 (tt0) REVERT: A 1483 ASN cc_start: 0.8473 (t0) cc_final: 0.8051 (m-40) REVERT: A 1543 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7709 (ttp) REVERT: B 96 ARG cc_start: 0.8431 (ttm110) cc_final: 0.7937 (mmt180) REVERT: B 152 ARG cc_start: 0.8464 (ttt-90) cc_final: 0.8146 (ttt180) REVERT: B 183 LYS cc_start: 0.7280 (ptpt) cc_final: 0.6609 (tppt) REVERT: C 134 ASP cc_start: 0.8205 (t0) cc_final: 0.7819 (t0) REVERT: C 137 ARG cc_start: 0.7753 (ttt-90) cc_final: 0.7060 (ttp80) outliers start: 49 outliers final: 32 residues processed: 219 average time/residue: 0.0864 time to fit residues: 28.9898 Evaluate side-chains 219 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1504 ILE Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 49 optimal weight: 0.0370 chunk 38 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 138 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 118 optimal weight: 0.0010 chunk 146 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 0.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1462 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.171054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.130337 restraints weight = 17012.603| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.85 r_work: 0.3047 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13834 Z= 0.101 Angle : 0.463 7.502 18711 Z= 0.239 Chirality : 0.038 0.210 2118 Planarity : 0.003 0.041 2208 Dihedral : 12.096 150.771 2143 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.35 % Allowed : 15.81 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.22), residues: 1549 helix: 2.31 (0.17), residues: 898 sheet: -0.65 (0.42), residues: 140 loop : -0.10 (0.29), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.017 0.001 TYR B 32 PHE 0.015 0.001 PHE A1263 TRP 0.008 0.001 TRP A1382 HIS 0.003 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 (13812) covalent geometry : angle 0.45400 / 0.24 (18656) SS BOND : bond 0.00291 / 0.20 ( 11) SS BOND : angle 0.98305 / 0.78 ( 22) hydrogen bonds : bond 0.03762 / 2.41 ( 775) hydrogen bonds : angle 3.86822 / 2.74 ( 2226) link_BETA1-4 : bond 0.00556 / 0.33 ( 3) link_BETA1-4 : angle 2.78313 / 1.31 ( 9) link_NAG-ASN : bond 0.00228 / 0.19 ( 8) link_NAG-ASN : angle 1.72005 / 1.08 ( 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 247 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7500 (mp) cc_final: 0.7173 (mt) REVERT: A 70 MET cc_start: 0.7147 (mmt) cc_final: 0.6510 (mtt) REVERT: A 125 HIS cc_start: 0.7889 (OUTLIER) cc_final: 0.7264 (t-90) REVERT: A 185 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7790 (mmt-90) REVERT: A 190 TRP cc_start: 0.7908 (m-10) cc_final: 0.7348 (m100) REVERT: A 403 MET cc_start: 0.8282 (tpp) cc_final: 0.7360 (tpp) REVERT: A 407 GLU cc_start: 0.7814 (mm-30) cc_final: 0.7470 (mm-30) REVERT: A 902 ASP cc_start: 0.8742 (t0) cc_final: 0.8442 (t0) REVERT: A 979 ILE cc_start: 0.2921 (OUTLIER) cc_final: 0.2557 (pt) REVERT: A 1193 TRP cc_start: 0.7940 (m-10) cc_final: 0.7536 (m-10) REVERT: A 1241 MET cc_start: 0.8678 (ttt) cc_final: 0.8476 (ttm) REVERT: A 1483 ASN cc_start: 0.8391 (t0) cc_final: 0.8057 (m-40) REVERT: A 1534 VAL cc_start: 0.9407 (OUTLIER) cc_final: 0.9107 (p) REVERT: A 1543 MET cc_start: 0.7805 (OUTLIER) cc_final: 0.7582 (ttt) REVERT: A 1631 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.8070 (ttm170) REVERT: B 96 ARG cc_start: 0.8360 (ttm110) cc_final: 0.8016 (mtt180) REVERT: B 152 ARG cc_start: 0.8427 (ttt-90) cc_final: 0.8142 (ttt180) REVERT: B 183 LYS cc_start: 0.7271 (ptpt) cc_final: 0.6621 (tppt) REVERT: C 134 ASP cc_start: 0.8296 (t0) cc_final: 0.7949 (t0) REVERT: C 137 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7460 (ttp80) outliers start: 47 outliers final: 30 residues processed: 226 average time/residue: 0.0884 time to fit residues: 30.8130 Evaluate side-chains 226 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1661 PHE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 9 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.0470 chunk 101 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN A1551 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.169660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128877 restraints weight = 16877.603| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.91 r_work: 0.3019 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13834 Z= 0.123 Angle : 0.487 10.984 18711 Z= 0.249 Chirality : 0.039 0.219 2118 Planarity : 0.003 0.043 2208 Dihedral : 11.822 145.396 2143 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.28 % Allowed : 15.95 % Favored : 80.77 % 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: 1.88 (0.22), residues: 1549 helix: 2.28 (0.17), residues: 904 sheet: -0.55 (0.42), residues: 140 loop : -0.08 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 137 TYR 0.017 0.001 TYR A1739 PHE 0.016 0.001 PHE A1263 TRP 0.009 0.001 TRP A1382 HIS 0.003 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (13812) covalent geometry : angle 0.47800 / 0.25 (18656) SS BOND : bond 0.00246 / 0.17 ( 11) SS BOND : angle 0.97126 / 0.74 ( 22) hydrogen bonds : bond 0.04018 / 2.58 ( 775) hydrogen bonds : angle 3.89171 / 2.74 ( 2226) link_BETA1-4 : bond 0.00544 / 0.33 ( 3) link_BETA1-4 : angle 2.80529 / 1.35 ( 9) link_NAG-ASN : bond 0.00196 / 0.17 ( 8) link_NAG-ASN : angle 1.76514 / 1.11 ( 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 243 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 197 time to evaluate : 0.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7481 (mp) cc_final: 0.7165 (mt) REVERT: A 70 MET cc_start: 0.7092 (mmt) cc_final: 0.6434 (mtt) REVERT: A 125 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7305 (t-90) REVERT: A 185 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7203 (mmt-90) REVERT: A 190 TRP cc_start: 0.7929 (m-10) cc_final: 0.7376 (m100) REVERT: A 403 MET cc_start: 0.8337 (tpp) cc_final: 0.7392 (tpp) REVERT: A 407 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7443 (mm-30) REVERT: A 902 ASP cc_start: 0.8812 (t0) cc_final: 0.8601 (t0) REVERT: A 982 ASP cc_start: -0.2832 (OUTLIER) cc_final: -0.3102 (t70) REVERT: A 1241 MET cc_start: 0.8668 (ttt) cc_final: 0.8442 (ttm) REVERT: A 1462 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7746 (mm110) REVERT: A 1483 ASN cc_start: 0.8433 (t0) cc_final: 0.8092 (m-40) REVERT: A 1534 VAL cc_start: 0.9438 (OUTLIER) cc_final: 0.9135 (p) REVERT: A 1600 GLU cc_start: 0.6892 (tp30) cc_final: 0.6297 (tt0) REVERT: A 1631 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.8098 (ttm170) REVERT: B 96 ARG cc_start: 0.8340 (ttm110) cc_final: 0.8042 (mtt180) REVERT: B 183 LYS cc_start: 0.7291 (ptpt) cc_final: 0.6641 (tppt) REVERT: C 134 ASP cc_start: 0.8328 (t0) cc_final: 0.7992 (t0) outliers start: 46 outliers final: 34 residues processed: 223 average time/residue: 0.0870 time to fit residues: 29.8811 Evaluate side-chains 226 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 818 LEU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 121 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 69 optimal weight: 0.0980 chunk 85 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 0.3980 chunk 33 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.129805 restraints weight = 17009.872| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.97 r_work: 0.3034 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13834 Z= 0.105 Angle : 0.472 9.695 18711 Z= 0.242 Chirality : 0.038 0.205 2118 Planarity : 0.003 0.043 2208 Dihedral : 11.587 141.528 2143 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.56 % Allowed : 17.02 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.22), residues: 1549 helix: 2.36 (0.17), residues: 904 sheet: -0.51 (0.42), residues: 140 loop : -0.05 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 137 TYR 0.018 0.001 TYR B 32 PHE 0.015 0.001 PHE A1263 TRP 0.008 0.001 TRP A1382 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (13812) covalent geometry : angle 0.46383 / 0.24 (18656) SS BOND : bond 0.00229 / 0.16 ( 11) SS BOND : angle 0.91953 / 0.71 ( 22) hydrogen bonds : bond 0.03802 / 2.44 ( 775) hydrogen bonds : angle 3.85012 / 2.71 ( 2226) link_BETA1-4 : bond 0.00532 / 0.32 ( 3) link_BETA1-4 : angle 2.73684 / 1.31 ( 9) link_NAG-ASN : bond 0.00199 / 0.17 ( 8) link_NAG-ASN : angle 1.71861 / 1.08 ( 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 232 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 196 time to evaluate : 0.507 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7465 (mp) cc_final: 0.7155 (mt) REVERT: A 70 MET cc_start: 0.7182 (mmt) cc_final: 0.6749 (mtt) REVERT: A 76 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8110 (mm-30) REVERT: A 185 ARG cc_start: 0.8325 (tpp80) cc_final: 0.7193 (mmt-90) REVERT: A 190 TRP cc_start: 0.7942 (m-10) cc_final: 0.7383 (m100) REVERT: A 403 MET cc_start: 0.8348 (tpp) cc_final: 0.7411 (tpp) REVERT: A 407 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7477 (mm-30) REVERT: A 902 ASP cc_start: 0.8804 (t0) cc_final: 0.8473 (t0) REVERT: A 982 ASP cc_start: -0.2322 (OUTLIER) cc_final: -0.2577 (t70) REVERT: A 1241 MET cc_start: 0.8609 (ttt) cc_final: 0.8370 (ttm) REVERT: A 1462 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7759 (mm110) REVERT: A 1483 ASN cc_start: 0.8492 (t0) cc_final: 0.8111 (m-40) REVERT: A 1543 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7591 (ttt) REVERT: A 1600 GLU cc_start: 0.6848 (tp30) cc_final: 0.6314 (tt0) REVERT: A 1631 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8079 (ttm170) REVERT: A 1638 MET cc_start: 0.9235 (ttt) cc_final: 0.9014 (ttp) REVERT: B 96 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8026 (mtt180) REVERT: B 183 LYS cc_start: 0.7265 (ptpt) cc_final: 0.6640 (tppt) REVERT: C 81 LEU cc_start: 0.5316 (OUTLIER) cc_final: 0.4872 (mp) REVERT: C 104 ASN cc_start: 0.6976 (p0) cc_final: 0.6759 (t0) REVERT: C 134 ASP cc_start: 0.8311 (t0) cc_final: 0.7964 (t0) outliers start: 36 outliers final: 29 residues processed: 218 average time/residue: 0.0883 time to fit residues: 30.1351 Evaluate side-chains 226 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1661 PHE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 81 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 39 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 chunk 145 optimal weight: 30.0000 chunk 93 optimal weight: 0.0670 chunk 120 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 150 optimal weight: 20.0000 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.169936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.129109 restraints weight = 16919.405| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.96 r_work: 0.3022 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13834 Z= 0.121 Angle : 0.482 8.863 18711 Z= 0.248 Chirality : 0.039 0.211 2118 Planarity : 0.003 0.045 2208 Dihedral : 11.437 138.000 2143 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.92 % Allowed : 17.02 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.97 (0.22), residues: 1549 helix: 2.34 (0.17), residues: 904 sheet: -0.50 (0.42), residues: 140 loop : -0.02 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 137 TYR 0.018 0.001 TYR B 32 PHE 0.014 0.001 PHE A1263 TRP 0.009 0.001 TRP A1382 HIS 0.002 0.001 HIS B 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (13812) covalent geometry : angle 0.47349 / 0.25 (18656) SS BOND : bond 0.00232 / 0.16 ( 11) SS BOND : angle 0.96112 / 0.73 ( 22) hydrogen bonds : bond 0.03949 / 2.54 ( 775) hydrogen bonds : angle 3.86744 / 2.72 ( 2226) link_BETA1-4 : bond 0.00587 / 0.36 ( 3) link_BETA1-4 : angle 2.72383 / 1.32 ( 9) link_NAG-ASN : bond 0.00196 / 0.17 ( 8) link_NAG-ASN : angle 1.72401 / 1.09 ( 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 239 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.474 Fit side-chains revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7456 (mp) cc_final: 0.7238 (mt) REVERT: A 70 MET cc_start: 0.7148 (mmt) cc_final: 0.6646 (mtt) REVERT: A 76 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8102 (mm-30) REVERT: A 185 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7188 (mmt-90) REVERT: A 190 TRP cc_start: 0.7953 (m-10) cc_final: 0.7376 (m100) REVERT: A 403 MET cc_start: 0.8354 (tpp) cc_final: 0.7415 (tpp) REVERT: A 407 GLU cc_start: 0.7826 (mm-30) cc_final: 0.7455 (mm-30) REVERT: A 753 CYS cc_start: 0.7769 (m) cc_final: 0.7467 (m) REVERT: A 791 MET cc_start: 0.6934 (tpp) cc_final: 0.6615 (tpp) REVERT: A 902 ASP cc_start: 0.8804 (t0) cc_final: 0.8569 (t0) REVERT: A 982 ASP cc_start: -0.2775 (OUTLIER) cc_final: -0.3079 (t70) REVERT: A 1462 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7800 (mm110) REVERT: A 1470 GLN cc_start: 0.8563 (mm-40) cc_final: 0.8237 (mm110) REVERT: A 1483 ASN cc_start: 0.8531 (t0) cc_final: 0.8234 (m-40) REVERT: A 1534 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9137 (p) REVERT: A 1543 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7606 (ttt) REVERT: A 1600 GLU cc_start: 0.6765 (tp30) cc_final: 0.6218 (tt0) REVERT: A 1631 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8090 (ttm170) REVERT: A 1638 MET cc_start: 0.9312 (ttt) cc_final: 0.9102 (ttp) REVERT: B 96 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8137 (mtt180) REVERT: B 183 LYS cc_start: 0.7288 (ptpt) cc_final: 0.6645 (tppt) REVERT: C 81 LEU cc_start: 0.5284 (OUTLIER) cc_final: 0.4846 (mp) REVERT: C 104 ASN cc_start: 0.7087 (p0) cc_final: 0.6765 (t0) REVERT: C 134 ASP cc_start: 0.8261 (t0) cc_final: 0.7926 (t0) outliers start: 41 outliers final: 35 residues processed: 223 average time/residue: 0.0881 time to fit residues: 30.4251 Evaluate side-chains 230 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1476 GLU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1661 PHE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 81 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 13 optimal weight: 4.9990 chunk 145 optimal weight: 30.0000 chunk 67 optimal weight: 20.0000 chunk 47 optimal weight: 0.2980 chunk 32 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 0.0770 chunk 146 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.169227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128359 restraints weight = 17019.203| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.95 r_work: 0.3060 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13834 Z= 0.142 Angle : 0.502 8.323 18711 Z= 0.259 Chirality : 0.039 0.218 2118 Planarity : 0.003 0.045 2208 Dihedral : 11.482 136.241 2143 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.85 % Allowed : 17.17 % 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: 1.92 (0.22), residues: 1549 helix: 2.29 (0.17), residues: 905 sheet: -0.43 (0.42), residues: 139 loop : -0.04 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 137 TYR 0.019 0.001 TYR B 32 PHE 0.016 0.001 PHE A 739 TRP 0.009 0.001 TRP A1382 HIS 0.003 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 (13812) covalent geometry : angle 0.49346 / 0.26 (18656) SS BOND : bond 0.00240 / 0.17 ( 11) SS BOND : angle 1.00896 / 0.75 ( 22) hydrogen bonds : bond 0.04114 / 2.64 ( 775) hydrogen bonds : angle 3.91519 / 2.74 ( 2226) link_BETA1-4 : bond 0.00547 / 0.33 ( 3) link_BETA1-4 : angle 2.79240 / 1.34 ( 9) link_NAG-ASN : bond 0.00194 / 0.16 ( 8) link_NAG-ASN : angle 1.74438 / 1.11 ( 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 228 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7490 (mp) cc_final: 0.7280 (mt) REVERT: A 70 MET cc_start: 0.7204 (mmt) cc_final: 0.6508 (mtt) REVERT: A 76 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8056 (mm-30) REVERT: A 190 TRP cc_start: 0.7977 (m-10) cc_final: 0.7406 (m100) REVERT: A 403 MET cc_start: 0.8318 (tpp) cc_final: 0.7364 (tpp) REVERT: A 407 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7435 (mm-30) REVERT: A 753 CYS cc_start: 0.7759 (m) cc_final: 0.7452 (m) REVERT: A 791 MET cc_start: 0.6867 (tpp) cc_final: 0.6515 (tpp) REVERT: A 902 ASP cc_start: 0.8814 (t0) cc_final: 0.8495 (t0) REVERT: A 982 ASP cc_start: -0.2723 (OUTLIER) cc_final: -0.3063 (t70) REVERT: A 1462 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7787 (mm110) REVERT: A 1470 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8233 (mm110) REVERT: A 1483 ASN cc_start: 0.8435 (t0) cc_final: 0.8102 (m-40) REVERT: A 1534 VAL cc_start: 0.9443 (OUTLIER) cc_final: 0.9143 (p) REVERT: A 1543 MET cc_start: 0.7902 (OUTLIER) cc_final: 0.7627 (ttt) REVERT: A 1600 GLU cc_start: 0.6595 (tp30) cc_final: 0.6052 (tt0) REVERT: A 1638 MET cc_start: 0.9305 (ttt) cc_final: 0.9082 (ttp) REVERT: B 96 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8102 (mtt180) REVERT: B 183 LYS cc_start: 0.7292 (ptpt) cc_final: 0.6636 (tppt) REVERT: C 30 MET cc_start: 0.6035 (ttp) cc_final: 0.5679 (mtm) REVERT: C 81 LEU cc_start: 0.5225 (OUTLIER) cc_final: 0.4788 (mp) REVERT: C 104 ASN cc_start: 0.7090 (p0) cc_final: 0.6772 (t0) REVERT: C 134 ASP cc_start: 0.8246 (t0) cc_final: 0.7953 (t0) outliers start: 40 outliers final: 33 residues processed: 213 average time/residue: 0.0889 time to fit residues: 29.3835 Evaluate side-chains 223 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 186 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1661 PHE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 103 optimal weight: 0.8980 chunk 148 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 59 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.130134 restraints weight = 16854.324| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.93 r_work: 0.3034 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13834 Z= 0.110 Angle : 0.486 13.041 18711 Z= 0.249 Chirality : 0.038 0.199 2118 Planarity : 0.003 0.044 2208 Dihedral : 11.116 130.800 2143 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 17.31 % 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: 2.03 (0.22), residues: 1549 helix: 2.39 (0.17), residues: 905 sheet: -0.42 (0.42), residues: 140 loop : -0.01 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 137 TYR 0.020 0.001 TYR B 32 PHE 0.015 0.001 PHE A 739 TRP 0.008 0.001 TRP A1382 HIS 0.002 0.001 HIS A1191 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.11 (13812) covalent geometry : angle 0.47815 / 0.25 (18656) SS BOND : bond 0.00230 / 0.17 ( 11) SS BOND : angle 0.91630 / 0.70 ( 22) hydrogen bonds : bond 0.03767 / 2.41 ( 775) hydrogen bonds : angle 3.86079 / 2.70 ( 2226) link_BETA1-4 : bond 0.00560 / 0.34 ( 3) link_BETA1-4 : angle 2.65773 / 1.27 ( 9) link_NAG-ASN : bond 0.00200 / 0.17 ( 8) link_NAG-ASN : angle 1.66108 / 1.05 ( 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 232 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 193 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 LEU cc_start: 0.7442 (mp) cc_final: 0.7227 (mt) REVERT: A 70 MET cc_start: 0.7250 (mmt) cc_final: 0.6593 (mtt) REVERT: A 76 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 125 HIS cc_start: 0.7828 (OUTLIER) cc_final: 0.7290 (t-90) REVERT: A 185 ARG cc_start: 0.8289 (tpp80) cc_final: 0.7126 (mmt-90) REVERT: A 190 TRP cc_start: 0.7955 (m-10) cc_final: 0.7390 (m100) REVERT: A 403 MET cc_start: 0.8295 (tpp) cc_final: 0.7359 (tpp) REVERT: A 407 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7456 (mm-30) REVERT: A 753 CYS cc_start: 0.7760 (m) cc_final: 0.7460 (m) REVERT: A 902 ASP cc_start: 0.8819 (t0) cc_final: 0.8589 (t0) REVERT: A 982 ASP cc_start: -0.2619 (OUTLIER) cc_final: -0.2963 (t70) REVERT: A 1462 GLN cc_start: 0.8078 (mm-40) cc_final: 0.7779 (mm110) REVERT: A 1470 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8208 (mm110) REVERT: A 1483 ASN cc_start: 0.8514 (t0) cc_final: 0.8240 (m-40) REVERT: A 1534 VAL cc_start: 0.9416 (OUTLIER) cc_final: 0.9119 (p) REVERT: A 1543 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7592 (ttt) REVERT: A 1600 GLU cc_start: 0.6564 (tp30) cc_final: 0.6038 (tt0) REVERT: A 1631 ARG cc_start: 0.8349 (OUTLIER) cc_final: 0.8142 (ttm170) REVERT: A 1638 MET cc_start: 0.9298 (ttt) cc_final: 0.9069 (ttp) REVERT: B 96 ARG cc_start: 0.8337 (ttm110) cc_final: 0.8107 (mtt180) REVERT: B 183 LYS cc_start: 0.7282 (ptpt) cc_final: 0.6647 (tppt) REVERT: C 81 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4790 (mp) REVERT: C 104 ASN cc_start: 0.7089 (p0) cc_final: 0.6752 (t0) REVERT: C 134 ASP cc_start: 0.8242 (t0) cc_final: 0.7981 (t0) outliers start: 39 outliers final: 32 residues processed: 219 average time/residue: 0.0937 time to fit residues: 31.7107 Evaluate side-chains 227 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 125 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 737 ILE Chi-restraints excluded: chain A residue 761 MET Chi-restraints excluded: chain A residue 784 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 919 ILE Chi-restraints excluded: chain A residue 979 ILE Chi-restraints excluded: chain A residue 982 ASP Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1410 ILE Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1534 VAL Chi-restraints excluded: chain A residue 1543 MET Chi-restraints excluded: chain A residue 1553 VAL Chi-restraints excluded: chain A residue 1631 ARG Chi-restraints excluded: chain A residue 1661 PHE Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 95 SER Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 81 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 chunk 119 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 4 optimal weight: 0.0060 chunk 70 optimal weight: 0.7980 chunk 143 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.5406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.170531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.130166 restraints weight = 16984.818| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 1.94 r_work: 0.3033 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.107 13834 Z= 0.139 Angle : 0.749 59.198 18711 Z= 0.431 Chirality : 0.056 1.884 2118 Planarity : 0.003 0.065 2208 Dihedral : 11.114 130.774 2143 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.78 % Allowed : 17.24 % Favored : 79.99 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.22), residues: 1549 helix: 2.39 (0.17), residues: 905 sheet: -0.40 (0.42), residues: 140 loop : -0.02 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 137 TYR 0.018 0.001 TYR B 32 PHE 0.013 0.001 PHE A1263 TRP 0.008 0.001 TRP A1382 HIS 0.002 0.001 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (13812) covalent geometry : angle 0.74513 / 0.43 (18656) SS BOND : bond 0.00232 / 0.17 ( 11) SS BOND : angle 0.91132 / 0.70 ( 22) hydrogen bonds : bond 0.03760 / 2.41 ( 775) hydrogen bonds : angle 3.86322 / 2.70 ( 2226) link_BETA1-4 : bond 0.00446 / 0.27 ( 3) link_BETA1-4 : angle 2.66179 / 1.27 ( 9) link_NAG-ASN : bond 0.00199 / 0.17 ( 8) link_NAG-ASN : angle 1.66339 / 1.05 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3242.87 seconds wall clock time: 56 minutes 18.03 seconds (3378.03 seconds total)