Starting phenix.real_space_refine on Wed Mar 4 02:19:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uz3_20951/03_2026/6uz3_20951.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uz3_20951/03_2026/6uz3_20951.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uz3_20951/03_2026/6uz3_20951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uz3_20951/03_2026/6uz3_20951.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uz3_20951/03_2026/6uz3_20951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uz3_20951/03_2026/6uz3_20951.map" } resolution = 3.5 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= 0.024 sd= 0.849 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 5 5.49 5 S 67 5.16 5 C 6309 2.51 5 N 1424 2.21 5 O 1641 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9446 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 8887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 8887 Classifications: {'peptide': 1126} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 28, 'TRANS': 1095} Chain breaks: 7 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 201 Unresolved non-hydrogen dihedrals: 148 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'HIS:plan': 1, 'ARG:plan': 3, 'PHE:plan': 3, 'GLU:plan': 6, 'ASP:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 464 Unusual residues: {'6OU': 11, '9Z9': 5, 'NAG': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-3': 1, '6OU:plan-2': 2} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 2.04, per 1000 atoms: 0.22 Number of scatterers: 9446 At special positions: 0 Unit cell: (135.168, 125.664, 110.88, 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 67 16.00 P 5 15.00 O 1641 8.00 N 1424 7.00 C 6309 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.02 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.02 Simple disulfide: pdb=" SG CYS A1730 " - pdb=" SG CYS A1744 " 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=3, symmetry=0 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A3003 " - " ASN A 319 " " NAG A3009 " - " ASN A 284 " " NAG B 1 " - " ASN A1382 " " NAG C 1 " - " ASN A 329 " " NAG D 1 " - " ASN A1390 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 356.0 milliseconds 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 78.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'A' and resid 131 through 151 removed outlier: 4.035A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 181 removed outlier: 3.671A pdb=" N LYS A 159 " --> pdb=" O PRO A 155 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 160 " --> pdb=" O PRO A 156 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 161 " --> pdb=" O TRP A 157 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N THR A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 191 Processing helix chain 'A' and resid 192 through 211 removed outlier: 3.538A pdb=" N TRP A 196 " --> pdb=" O ASP A 192 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU A 197 " --> pdb=" O PRO A 193 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 227 removed outlier: 3.527A pdb=" N ARG A 226 " --> pdb=" O ARG A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.674A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE A 234 " --> pdb=" O THR A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 251 removed outlier: 4.007A pdb=" N GLN A 246 " --> pdb=" O GLY A 242 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.693A pdb=" N HIS A 279 " --> pdb=" O ASN A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 311 Processing helix chain 'A' and resid 312 through 315 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.822A pdb=" N ALA A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.766A pdb=" N LEU A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 390 through 401 Processing helix chain 'A' and resid 401 through 424 Processing helix chain 'A' and resid 700 through 716 Processing helix chain 'A' and resid 720 through 737 Processing helix chain 'A' and resid 743 through 772 removed outlier: 3.660A pdb=" N ILE A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 780 Processing helix chain 'A' and resid 780 through 798 Processing helix chain 'A' and resid 806 through 810 removed outlier: 4.267A pdb=" N ARG A 809 " --> pdb=" O SER A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 823 removed outlier: 4.113A pdb=" N SER A 822 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 836 Processing helix chain 'A' and resid 840 through 858 removed outlier: 3.607A pdb=" N VAL A 846 " --> pdb=" O ASN A 842 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL A 856 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 867 removed outlier: 5.426A pdb=" N LYS A 864 " --> pdb=" O GLN A 860 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASN A 865 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 874 removed outlier: 3.912A pdb=" N ILE A 873 " --> pdb=" O LEU A 869 " (cutoff:3.500A) Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 902 through 913 removed outlier: 4.502A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 944 removed outlier: 3.629A pdb=" N LEU A 924 " --> pdb=" O LEU A 920 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1205 Processing helix chain 'A' and resid 1206 through 1226 Processing helix chain 'A' and resid 1230 through 1233 Processing helix chain 'A' and resid 1234 through 1264 removed outlier: 3.705A pdb=" N LYS A1238 " --> pdb=" O ARG A1234 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1271 removed outlier: 3.874A pdb=" N ASN A1271 " --> pdb=" O LYS A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1271 through 1293 Processing helix chain 'A' and resid 1305 through 1313 removed outlier: 3.693A pdb=" N ARG A1308 " --> pdb=" O ARG A1305 " (cutoff:3.500A) Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1314 through 1319 removed outlier: 4.315A pdb=" N ARG A1318 " --> pdb=" O ARG A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1321 through 1331 removed outlier: 3.804A pdb=" N VAL A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1359 removed outlier: 4.666A pdb=" N ASN A1338 " --> pdb=" O PRO A1334 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VAL A1339 " --> pdb=" O SER A1335 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1386 through 1390 Processing helix chain 'A' and resid 1407 through 1419 Processing helix chain 'A' and resid 1423 through 1432 Processing helix chain 'A' and resid 1445 through 1447 No H-bonds generated for 'chain 'A' and resid 1445 through 1447' Processing helix chain 'A' and resid 1448 through 1462 removed outlier: 3.924A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1462 through 1482 removed outlier: 3.517A pdb=" N ASP A1473 " --> pdb=" O GLY A1469 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LYS A1480 " --> pdb=" O ASN A1476 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS A1481 " --> pdb=" O GLN A1477 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A1482 " --> pdb=" O GLN A1478 " (cutoff:3.500A) Processing helix chain 'A' and resid 1490 through 1503 Processing helix chain 'A' and resid 1517 through 1528 Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 4.279A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1582 Processing helix chain 'A' and resid 1586 through 1591 removed outlier: 4.272A pdb=" N ASN A1591 " --> pdb=" O TYR A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1591 through 1617 removed outlier: 3.879A pdb=" N ASP A1597 " --> pdb=" O TRP A1593 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1628 Processing helix chain 'A' and resid 1629 through 1636 Processing helix chain 'A' and resid 1637 through 1642 Processing helix chain 'A' and resid 1643 through 1655 removed outlier: 3.918A pdb=" N PHE A1650 " --> pdb=" O ARG A1646 " (cutoff:3.500A) Processing helix chain 'A' and resid 1655 through 1681 Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.542A pdb=" N SER A1702 " --> pdb=" O THR A1698 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 Proline residue: A1721 - end of helix removed outlier: 3.847A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1780 removed outlier: 3.573A pdb=" N ALA A1780 " --> pdb=" O ASN A1776 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 280 through 282 Processing sheet with id=AA2, first strand: chain 'A' and resid 1366 through 1367 599 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1406 1.27 - 1.40: 2503 1.40 - 1.54: 5535 1.54 - 1.68: 102 1.68 - 1.81: 124 Bond restraints: 9670 Sorted by residual: bond pdb=" C06 9Z9 A3014 " pdb=" C07 9Z9 A3014 " ideal model delta sigma weight residual 1.520 1.131 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C06 9Z9 A3010 " pdb=" C07 9Z9 A3010 " ideal model delta sigma weight residual 1.520 1.137 0.383 2.00e-02 2.50e+03 3.67e+02 bond pdb=" C06 9Z9 A3011 " pdb=" C07 9Z9 A3011 " ideal model delta sigma weight residual 1.520 1.138 0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" C06 9Z9 A3012 " pdb=" C07 9Z9 A3012 " ideal model delta sigma weight residual 1.520 1.157 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C06 9Z9 A3013 " pdb=" C07 9Z9 A3013 " ideal model delta sigma weight residual 1.520 1.160 0.360 2.00e-02 2.50e+03 3.23e+02 ... (remaining 9665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 12819 4.09 - 8.18: 240 8.18 - 12.27: 42 12.27 - 16.36: 5 16.36 - 20.45: 2 Bond angle restraints: 13108 Sorted by residual: angle pdb=" N LYS A1616 " pdb=" CA LYS A1616 " pdb=" C LYS A1616 " ideal model delta sigma weight residual 111.36 122.77 -11.41 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N LYS A1302 " pdb=" CA LYS A1302 " pdb=" C LYS A1302 " ideal model delta sigma weight residual 113.18 102.85 10.33 1.21e+00 6.83e-01 7.28e+01 angle pdb=" N PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta sigma weight residual 103.25 111.59 -8.34 1.05e+00 9.07e-01 6.30e+01 angle pdb=" N THR A1622 " pdb=" CA THR A1622 " pdb=" CB THR A1622 " ideal model delta sigma weight residual 110.81 100.46 10.35 1.48e+00 4.57e-01 4.89e+01 angle pdb=" N THR A1622 " pdb=" CA THR A1622 " pdb=" C THR A1622 " ideal model delta sigma weight residual 114.04 105.84 8.20 1.24e+00 6.50e-01 4.37e+01 ... (remaining 13103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 5829 35.96 - 71.92: 254 71.92 - 107.88: 26 107.88 - 143.83: 12 143.83 - 179.79: 7 Dihedral angle restraints: 6128 sinusoidal: 2849 harmonic: 3279 Sorted by residual: dihedral pdb=" CA ARG A1364 " pdb=" C ARG A1364 " pdb=" N CYS A1365 " pdb=" CA CYS A1365 " ideal model delta harmonic sigma weight residual -180.00 -126.13 -53.87 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" N PRO A1621 " pdb=" C PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta harmonic sigma weight residual 115.10 141.39 -26.29 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" C PRO A1621 " pdb=" N PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta harmonic sigma weight residual -120.70 -141.82 21.12 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.649: 1532 0.649 - 1.298: 9 1.298 - 1.947: 5 1.947 - 2.596: 0 2.596 - 3.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.78 -1.62 2.00e-02 2.50e+03 6.56e+03 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 3.98e+02 chirality pdb=" C1 NAG A3009 " pdb=" ND2 ASN A 284 " pdb=" C2 NAG A3009 " pdb=" O5 NAG A3009 " both_signs ideal model delta sigma weight residual False -2.40 0.84 -3.24 2.00e-01 2.50e+01 2.63e+02 ... (remaining 1544 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.361 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG D 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.550 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG D 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3009 " -0.260 2.00e-02 2.50e+03 2.23e-01 6.19e+02 pdb=" C7 NAG A3009 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A3009 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG A3009 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG A3009 " -0.195 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 6 1.99 - 2.72: 770 2.72 - 3.44: 14930 3.44 - 4.17: 21633 4.17 - 4.90: 38462 Nonbonded interactions: 75801 Sorted by model distance: nonbonded pdb=" O LEU A 129 " pdb=" CE2 PHE A 134 " model vdw 1.260 3.340 nonbonded pdb=" CD1 ILE A 138 " pdb=" OE2 GLU A 172 " model vdw 1.659 3.460 nonbonded pdb=" O LEU A 129 " pdb=" CZ PHE A 134 " model vdw 1.838 3.340 nonbonded pdb=" O CYS A 342 " pdb=" O7 NAG C 1 " model vdw 1.942 3.040 nonbonded pdb=" O CYS A 342 " pdb=" C7 NAG C 1 " model vdw 1.953 3.270 ... (remaining 75796 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 'B' selection = chain 'D' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 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: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 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 : 0.023 0.485 9685 Z= 1.197 Angle : 1.481 38.517 13141 Z= 0.659 Chirality : 0.154 3.245 1547 Planarity : 0.015 0.310 1541 Dihedral : 20.904 179.792 3999 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 32.32 Ramachandran Plot: Outliers : 0.36 % Allowed : 11.17 % Favored : 88.47 % Rotamer: Outliers : 1.05 % Allowed : 12.12 % Favored : 86.83 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.89 (0.22), residues: 1110 helix: -2.29 (0.15), residues: 783 sheet: -2.87 (1.28), residues: 10 loop : -2.83 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 384 TYR 0.024 0.003 TYR A1201 PHE 0.030 0.003 PHE A 148 TRP 0.058 0.003 TRP A1423 HIS 0.010 0.002 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.02197 ( 9670) covalent geometry : angle 1.32993 (13108) SS BOND : bond 0.00710 ( 3) SS BOND : angle 2.65709 ( 6) hydrogen bonds : bond 0.17140 ( 599) hydrogen bonds : angle 7.18305 ( 1737) Misc. bond : bond 0.27975 ( 3) link_BETA1-4 : bond 0.03272 ( 4) link_BETA1-4 : angle 7.66862 ( 12) link_NAG-ASN : bond 0.05193 ( 5) link_NAG-ASN : angle 18.05642 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 258 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 163 TYR cc_start: 0.7909 (m-80) cc_final: 0.7653 (m-80) REVERT: A 251 LEU cc_start: 0.8831 (tp) cc_final: 0.8146 (tp) REVERT: A 353 TYR cc_start: 0.7128 (m-80) cc_final: 0.6763 (m-80) REVERT: A 404 TYR cc_start: 0.7439 (t80) cc_final: 0.7154 (t80) REVERT: A 407 ASN cc_start: 0.8948 (t0) cc_final: 0.8602 (t0) REVERT: A 422 GLN cc_start: 0.7161 (mt0) cc_final: 0.6877 (pp30) REVERT: A 819 LEU cc_start: 0.8612 (tp) cc_final: 0.8247 (tp) REVERT: A 907 TRP cc_start: 0.7849 (m-10) cc_final: 0.7501 (m-90) REVERT: A 908 ASP cc_start: 0.8235 (m-30) cc_final: 0.7844 (m-30) REVERT: A 1274 CYS cc_start: 0.8065 (m) cc_final: 0.7743 (m) REVERT: A 1323 ARG cc_start: 0.7497 (ttp80) cc_final: 0.6576 (ttp80) REVERT: A 1496 TYR cc_start: 0.7900 (m-10) cc_final: 0.7538 (m-80) REVERT: A 1497 TYR cc_start: 0.7653 (t80) cc_final: 0.7233 (t80) REVERT: A 1500 MET cc_start: 0.6295 (ttm) cc_final: 0.5751 (ttp) REVERT: A 1560 ASN cc_start: 0.8597 (t0) cc_final: 0.8342 (t0) REVERT: A 1581 MET cc_start: 0.2436 (ttt) cc_final: 0.2229 (tpt) REVERT: A 1588 TYR cc_start: 0.6200 (p90) cc_final: 0.5980 (p90) REVERT: A 1622 THR cc_start: 0.7464 (m) cc_final: 0.7251 (t) REVERT: A 1654 MET cc_start: 0.7012 (mmm) cc_final: 0.6778 (mmm) outliers start: 10 outliers final: 7 residues processed: 264 average time/residue: 0.0868 time to fit residues: 33.0543 Evaluate side-chains 221 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1297 GLU Chi-restraints excluded: chain A residue 1419 THR Chi-restraints excluded: chain A residue 1421 LYS Chi-restraints excluded: chain A residue 1618 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1711 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 195 ASN A 314 ASN A 731 ASN A 739 HIS A 780 GLN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 HIS ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN A1327 ASN ** A1403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 GLN A1767 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.173417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.140381 restraints weight = 17058.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.144264 restraints weight = 8555.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.146767 restraints weight = 5657.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.148305 restraints weight = 4456.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148952 restraints weight = 3881.713| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9685 Z= 0.190 Angle : 0.890 18.572 13141 Z= 0.417 Chirality : 0.047 0.483 1547 Planarity : 0.005 0.049 1541 Dihedral : 19.956 178.187 2055 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 2.95 % Allowed : 19.39 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.20 (0.24), residues: 1110 helix: -1.00 (0.17), residues: 791 sheet: -2.78 (1.36), residues: 10 loop : -2.27 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 384 TYR 0.025 0.002 TYR A 417 PHE 0.034 0.002 PHE A 785 TRP 0.024 0.002 TRP A1423 HIS 0.006 0.002 HIS A 131 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 9670) covalent geometry : angle 0.82758 (13108) SS BOND : bond 0.00330 ( 3) SS BOND : angle 1.84852 ( 6) hydrogen bonds : bond 0.05683 ( 599) hydrogen bonds : angle 5.68199 ( 1737) Misc. bond : bond 0.00292 ( 3) link_BETA1-4 : bond 0.00826 ( 4) link_BETA1-4 : angle 3.26235 ( 12) link_NAG-ASN : bond 0.01116 ( 5) link_NAG-ASN : angle 9.25730 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 234 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8605 (tptt) cc_final: 0.7670 (mtpp) REVERT: A 160 TYR cc_start: 0.6973 (OUTLIER) cc_final: 0.5597 (m-80) REVERT: A 404 TYR cc_start: 0.7518 (t80) cc_final: 0.7071 (t80) REVERT: A 1265 PHE cc_start: 0.7288 (m-80) cc_final: 0.6721 (t80) REVERT: A 1274 CYS cc_start: 0.8317 (m) cc_final: 0.7954 (m) REVERT: A 1323 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6405 (ttp80) REVERT: A 1496 TYR cc_start: 0.7849 (m-10) cc_final: 0.7558 (m-80) REVERT: A 1497 TYR cc_start: 0.7640 (t80) cc_final: 0.7216 (t80) REVERT: A 1500 MET cc_start: 0.6284 (ttm) cc_final: 0.5923 (ttp) REVERT: A 1629 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8407 (tt) REVERT: A 1671 PHE cc_start: 0.7868 (t80) cc_final: 0.7622 (t80) REVERT: A 1703 MET cc_start: 0.7686 (tpt) cc_final: 0.7451 (tpt) REVERT: A 1729 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5568 (p90) outliers start: 28 outliers final: 14 residues processed: 254 average time/residue: 0.0829 time to fit residues: 30.5668 Evaluate side-chains 235 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 218 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 1198 LYS Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1239 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1629 LEU Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 71 optimal weight: 0.5980 chunk 50 optimal weight: 30.0000 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 731 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.174861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.141846 restraints weight = 17197.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.145677 restraints weight = 8499.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.148279 restraints weight = 5590.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.149856 restraints weight = 4388.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.150467 restraints weight = 3835.830| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 9685 Z= 0.165 Angle : 0.794 14.459 13141 Z= 0.377 Chirality : 0.044 0.424 1547 Planarity : 0.004 0.050 1541 Dihedral : 18.344 179.755 2044 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.88 % Rotamer: Outliers : 4.64 % Allowed : 20.34 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -1.29 (0.25), residues: 1110 helix: -0.32 (0.17), residues: 785 sheet: -3.12 (1.26), residues: 10 loop : -1.90 (0.40), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.023 0.002 TYR A 308 PHE 0.017 0.002 PHE A1753 TRP 0.019 0.001 TRP A1423 HIS 0.003 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9670) covalent geometry : angle 0.75048 (13108) SS BOND : bond 0.00421 ( 3) SS BOND : angle 1.66793 ( 6) hydrogen bonds : bond 0.04957 ( 599) hydrogen bonds : angle 5.38620 ( 1737) Misc. bond : bond 0.00102 ( 3) link_BETA1-4 : bond 0.00891 ( 4) link_BETA1-4 : angle 2.67932 ( 12) link_NAG-ASN : bond 0.01134 ( 5) link_NAG-ASN : angle 7.33421 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 235 time to evaluate : 0.267 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8553 (tptt) cc_final: 0.8095 (mttm) REVERT: A 160 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.5673 (m-80) REVERT: A 174 LEU cc_start: 0.8249 (tt) cc_final: 0.7911 (mt) REVERT: A 404 TYR cc_start: 0.7351 (t80) cc_final: 0.7086 (t80) REVERT: A 1265 PHE cc_start: 0.7292 (m-80) cc_final: 0.6639 (t80) REVERT: A 1274 CYS cc_start: 0.8308 (m) cc_final: 0.7929 (m) REVERT: A 1323 ARG cc_start: 0.7213 (ttp80) cc_final: 0.6400 (ttp80) REVERT: A 1496 TYR cc_start: 0.7881 (m-10) cc_final: 0.7571 (m-80) REVERT: A 1497 TYR cc_start: 0.7710 (t80) cc_final: 0.7288 (t80) REVERT: A 1581 MET cc_start: 0.3558 (tpt) cc_final: 0.3287 (tpt) REVERT: A 1588 TYR cc_start: 0.5839 (p90) cc_final: 0.5601 (p90) REVERT: A 1671 PHE cc_start: 0.7696 (t80) cc_final: 0.7454 (t80) REVERT: A 1729 TYR cc_start: 0.5974 (OUTLIER) cc_final: 0.5385 (p90) outliers start: 44 outliers final: 26 residues processed: 260 average time/residue: 0.0827 time to fit residues: 31.3587 Evaluate side-chains 246 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 218 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1543 ASN Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 10 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 chunk 72 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 1 optimal weight: 20.0000 chunk 68 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 ASN A 731 ASN A 860 GLN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.144320 restraints weight = 17196.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.148268 restraints weight = 8406.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150843 restraints weight = 5494.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.152395 restraints weight = 4309.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.153101 restraints weight = 3760.227| |-----------------------------------------------------------------------------| r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9685 Z= 0.148 Angle : 0.766 13.161 13141 Z= 0.361 Chirality : 0.043 0.383 1547 Planarity : 0.004 0.054 1541 Dihedral : 17.003 176.961 2044 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.24 % Rotamer: Outliers : 5.06 % Allowed : 22.23 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.82 (0.25), residues: 1110 helix: 0.03 (0.18), residues: 788 sheet: -3.12 (1.32), residues: 10 loop : -1.71 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1640 TYR 0.024 0.001 TYR A 308 PHE 0.016 0.001 PHE A1753 TRP 0.011 0.001 TRP A1715 HIS 0.007 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 9670) covalent geometry : angle 0.72793 (13108) SS BOND : bond 0.00335 ( 3) SS BOND : angle 1.43606 ( 6) hydrogen bonds : bond 0.04564 ( 599) hydrogen bonds : angle 5.21768 ( 1737) Misc. bond : bond 0.00113 ( 3) link_BETA1-4 : bond 0.00868 ( 4) link_BETA1-4 : angle 2.61863 ( 12) link_NAG-ASN : bond 0.01214 ( 5) link_NAG-ASN : angle 6.72107 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8569 (tptt) cc_final: 0.8124 (mttm) REVERT: A 160 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5644 (m-80) REVERT: A 174 LEU cc_start: 0.8189 (tt) cc_final: 0.7770 (mt) REVERT: A 404 TYR cc_start: 0.7293 (t80) cc_final: 0.7065 (t80) REVERT: A 422 GLN cc_start: 0.6975 (mt0) cc_final: 0.6750 (pp30) REVERT: A 1215 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6960 (t80) REVERT: A 1265 PHE cc_start: 0.7281 (m-80) cc_final: 0.6707 (t80) REVERT: A 1274 CYS cc_start: 0.8173 (m) cc_final: 0.7816 (m) REVERT: A 1323 ARG cc_start: 0.7001 (ttp80) cc_final: 0.6329 (ttp80) REVERT: A 1364 ARG cc_start: 0.6658 (pmt-80) cc_final: 0.5981 (pmt-80) REVERT: A 1444 ASP cc_start: 0.7889 (t70) cc_final: 0.7413 (t70) REVERT: A 1497 TYR cc_start: 0.7711 (t80) cc_final: 0.7227 (t80) REVERT: A 1581 MET cc_start: 0.3372 (tpt) cc_final: 0.3096 (tpt) REVERT: A 1588 TYR cc_start: 0.5710 (p90) cc_final: 0.5412 (p90) REVERT: A 1729 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5464 (p90) outliers start: 48 outliers final: 25 residues processed: 266 average time/residue: 0.0831 time to fit residues: 32.3648 Evaluate side-chains 250 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 222 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1544 MET Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 25 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.178833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.146855 restraints weight = 17125.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.150819 restraints weight = 8358.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153414 restraints weight = 5464.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154679 restraints weight = 4296.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.155773 restraints weight = 3814.665| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6866 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9685 Z= 0.137 Angle : 0.770 12.464 13141 Z= 0.359 Chirality : 0.044 0.358 1547 Planarity : 0.004 0.045 1541 Dihedral : 16.095 173.745 2044 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 4.53 % Allowed : 23.60 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.52 (0.25), residues: 1110 helix: 0.27 (0.18), residues: 793 sheet: -3.10 (1.34), residues: 10 loop : -1.69 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.018 0.001 TYR A 308 PHE 0.019 0.001 PHE A1762 TRP 0.017 0.001 TRP A 902 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9670) covalent geometry : angle 0.73483 (13108) SS BOND : bond 0.00261 ( 3) SS BOND : angle 1.33221 ( 6) hydrogen bonds : bond 0.04342 ( 599) hydrogen bonds : angle 5.11729 ( 1737) Misc. bond : bond 0.00109 ( 3) link_BETA1-4 : bond 0.00851 ( 4) link_BETA1-4 : angle 2.64619 ( 12) link_NAG-ASN : bond 0.01210 ( 5) link_NAG-ASN : angle 6.44179 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8562 (tptt) cc_final: 0.8027 (mtpp) REVERT: A 160 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5670 (m-80) REVERT: A 174 LEU cc_start: 0.8022 (tt) cc_final: 0.7575 (mt) REVERT: A 369 LEU cc_start: 0.7955 (mp) cc_final: 0.7720 (mt) REVERT: A 404 TYR cc_start: 0.7524 (t80) cc_final: 0.7168 (t80) REVERT: A 422 GLN cc_start: 0.6950 (mt0) cc_final: 0.6730 (pp30) REVERT: A 1215 PHE cc_start: 0.7302 (OUTLIER) cc_final: 0.6762 (t80) REVERT: A 1265 PHE cc_start: 0.7202 (m-80) cc_final: 0.6693 (t80) REVERT: A 1274 CYS cc_start: 0.8123 (m) cc_final: 0.7778 (m) REVERT: A 1364 ARG cc_start: 0.6469 (pmt-80) cc_final: 0.6120 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8595 (mt) REVERT: A 1496 TYR cc_start: 0.7616 (m-80) cc_final: 0.7409 (m-80) REVERT: A 1497 TYR cc_start: 0.7723 (t80) cc_final: 0.7204 (t80) REVERT: A 1588 TYR cc_start: 0.5579 (p90) cc_final: 0.5248 (p90) REVERT: A 1613 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6969 (mp) REVERT: A 1729 TYR cc_start: 0.6048 (OUTLIER) cc_final: 0.5437 (p90) outliers start: 43 outliers final: 26 residues processed: 267 average time/residue: 0.0816 time to fit residues: 32.2354 Evaluate side-chains 253 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 22 optimal weight: 0.0370 chunk 109 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 overall best weight: 2.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.177175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.145560 restraints weight = 16966.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.149536 restraints weight = 8245.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.152090 restraints weight = 5345.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.153676 restraints weight = 4184.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.154378 restraints weight = 3642.892| |-----------------------------------------------------------------------------| r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9685 Z= 0.150 Angle : 0.777 15.351 13141 Z= 0.364 Chirality : 0.044 0.372 1547 Planarity : 0.004 0.046 1541 Dihedral : 15.523 170.268 2043 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.24 % Rotamer: Outliers : 4.74 % Allowed : 25.50 % Favored : 69.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.42 (0.25), residues: 1110 helix: 0.34 (0.18), residues: 797 sheet: -3.15 (1.26), residues: 10 loop : -1.67 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1640 TYR 0.015 0.001 TYR A 308 PHE 0.014 0.001 PHE A1762 TRP 0.019 0.001 TRP A1442 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9670) covalent geometry : angle 0.74311 (13108) SS BOND : bond 0.00320 ( 3) SS BOND : angle 1.37051 ( 6) hydrogen bonds : bond 0.04285 ( 599) hydrogen bonds : angle 5.10678 ( 1737) Misc. bond : bond 0.00142 ( 3) link_BETA1-4 : bond 0.00903 ( 4) link_BETA1-4 : angle 2.76393 ( 12) link_NAG-ASN : bond 0.01186 ( 5) link_NAG-ASN : angle 6.30333 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 227 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8573 (tptt) cc_final: 0.8160 (mttm) REVERT: A 160 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.5648 (m-80) REVERT: A 174 LEU cc_start: 0.7950 (tt) cc_final: 0.7558 (mt) REVERT: A 404 TYR cc_start: 0.7480 (t80) cc_final: 0.7180 (t80) REVERT: A 1215 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6732 (t80) REVERT: A 1265 PHE cc_start: 0.7187 (m-80) cc_final: 0.6713 (t80) REVERT: A 1274 CYS cc_start: 0.8079 (m) cc_final: 0.7751 (m) REVERT: A 1364 ARG cc_start: 0.6455 (pmt-80) cc_final: 0.5954 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8567 (mt) REVERT: A 1496 TYR cc_start: 0.7577 (m-80) cc_final: 0.7150 (m-80) REVERT: A 1497 TYR cc_start: 0.7671 (t80) cc_final: 0.7206 (t80) REVERT: A 1613 ILE cc_start: 0.7343 (OUTLIER) cc_final: 0.7044 (mp) REVERT: A 1656 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7866 (mm) REVERT: A 1685 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7516 (ttmt) REVERT: A 1729 TYR cc_start: 0.6077 (OUTLIER) cc_final: 0.5630 (p90) outliers start: 45 outliers final: 26 residues processed: 255 average time/residue: 0.0773 time to fit residues: 29.6200 Evaluate side-chains 250 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 217 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1581 MET Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 1 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 104 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS ** A1736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.174964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.142800 restraints weight = 17060.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.146635 restraints weight = 8379.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.149155 restraints weight = 5492.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150638 restraints weight = 4314.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.151094 restraints weight = 3779.151| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.3343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9685 Z= 0.185 Angle : 0.806 14.808 13141 Z= 0.382 Chirality : 0.046 0.394 1547 Planarity : 0.004 0.043 1541 Dihedral : 15.131 168.930 2043 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.48 % Favored : 92.43 % Rotamer: Outliers : 5.16 % Allowed : 26.03 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.42 (0.26), residues: 1110 helix: 0.32 (0.18), residues: 796 sheet: -3.15 (1.26), residues: 10 loop : -1.60 (0.40), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 384 TYR 0.014 0.002 TYR A1449 PHE 0.015 0.002 PHE A1404 TRP 0.013 0.001 TRP A1442 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9670) covalent geometry : angle 0.77462 (13108) SS BOND : bond 0.00453 ( 3) SS BOND : angle 1.55678 ( 6) hydrogen bonds : bond 0.04478 ( 599) hydrogen bonds : angle 5.17925 ( 1737) Misc. bond : bond 0.00098 ( 3) link_BETA1-4 : bond 0.00970 ( 4) link_BETA1-4 : angle 2.83642 ( 12) link_NAG-ASN : bond 0.01122 ( 5) link_NAG-ASN : angle 6.16445 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 0.207 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8636 (tptt) cc_final: 0.8180 (mttm) REVERT: A 160 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5587 (m-10) REVERT: A 174 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7786 (mt) REVERT: A 404 TYR cc_start: 0.7523 (t80) cc_final: 0.7137 (t80) REVERT: A 734 PHE cc_start: 0.7654 (t80) cc_final: 0.7402 (t80) REVERT: A 1215 PHE cc_start: 0.7267 (OUTLIER) cc_final: 0.6664 (t80) REVERT: A 1265 PHE cc_start: 0.7243 (m-80) cc_final: 0.6720 (t80) REVERT: A 1274 CYS cc_start: 0.8104 (m) cc_final: 0.7759 (m) REVERT: A 1364 ARG cc_start: 0.6521 (pmt-80) cc_final: 0.6288 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8871 (tt) cc_final: 0.8608 (mt) REVERT: A 1496 TYR cc_start: 0.7599 (m-80) cc_final: 0.7148 (m-80) REVERT: A 1497 TYR cc_start: 0.7707 (t80) cc_final: 0.7229 (t80) REVERT: A 1613 ILE cc_start: 0.7377 (OUTLIER) cc_final: 0.7076 (mp) REVERT: A 1640 ARG cc_start: 0.8059 (ttp80) cc_final: 0.7844 (ttp80) REVERT: A 1656 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7870 (mm) REVERT: A 1729 TYR cc_start: 0.6126 (OUTLIER) cc_final: 0.5562 (p90) outliers start: 49 outliers final: 34 residues processed: 255 average time/residue: 0.0748 time to fit residues: 28.6049 Evaluate side-chains 259 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 219 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1333 ILE Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1419 THR Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1544 MET Chi-restraints excluded: chain A residue 1581 MET Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1465 ASN A1586 HIS ** A1736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.179675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.148214 restraints weight = 16944.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.152222 restraints weight = 8116.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.154829 restraints weight = 5247.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.156441 restraints weight = 4092.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.157395 restraints weight = 3551.501| |-----------------------------------------------------------------------------| r_work (final): 0.4208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9685 Z= 0.134 Angle : 0.784 15.154 13141 Z= 0.365 Chirality : 0.044 0.342 1547 Planarity : 0.004 0.042 1541 Dihedral : 14.435 169.176 2043 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 4.21 % Allowed : 27.92 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.29 (0.25), residues: 1110 helix: 0.48 (0.18), residues: 793 sheet: -3.21 (1.19), residues: 10 loop : -1.72 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 815 TYR 0.013 0.001 TYR A 379 PHE 0.026 0.001 PHE A1762 TRP 0.011 0.001 TRP A1442 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 9670) covalent geometry : angle 0.75344 (13108) SS BOND : bond 0.00272 ( 3) SS BOND : angle 1.25962 ( 6) hydrogen bonds : bond 0.04263 ( 599) hydrogen bonds : angle 5.06538 ( 1737) Misc. bond : bond 0.00111 ( 3) link_BETA1-4 : bond 0.01041 ( 4) link_BETA1-4 : angle 2.87006 ( 12) link_NAG-ASN : bond 0.01142 ( 5) link_NAG-ASN : angle 5.96106 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 230 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8591 (tptt) cc_final: 0.8144 (mttm) REVERT: A 160 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.5542 (m-10) REVERT: A 174 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7724 (mt) REVERT: A 382 THR cc_start: 0.8318 (m) cc_final: 0.8055 (m) REVERT: A 926 MET cc_start: 0.7823 (tpt) cc_final: 0.7024 (tpt) REVERT: A 1215 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6483 (t80) REVERT: A 1265 PHE cc_start: 0.7169 (m-80) cc_final: 0.6694 (t80) REVERT: A 1274 CYS cc_start: 0.8077 (m) cc_final: 0.7748 (m) REVERT: A 1348 LEU cc_start: 0.8096 (OUTLIER) cc_final: 0.7831 (tp) REVERT: A 1364 ARG cc_start: 0.6402 (pmt-80) cc_final: 0.6202 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8827 (tt) cc_final: 0.8556 (mt) REVERT: A 1472 ILE cc_start: 0.7952 (mp) cc_final: 0.7701 (tt) REVERT: A 1496 TYR cc_start: 0.7596 (m-80) cc_final: 0.7150 (m-80) REVERT: A 1497 TYR cc_start: 0.7681 (t80) cc_final: 0.7206 (t80) REVERT: A 1613 ILE cc_start: 0.7304 (OUTLIER) cc_final: 0.6994 (mp) REVERT: A 1640 ARG cc_start: 0.7991 (ttp80) cc_final: 0.7772 (ttp80) REVERT: A 1656 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7893 (mm) REVERT: A 1685 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7429 (ttmt) REVERT: A 1729 TYR cc_start: 0.6377 (OUTLIER) cc_final: 0.5851 (p90) outliers start: 40 outliers final: 27 residues processed: 253 average time/residue: 0.0831 time to fit residues: 31.0090 Evaluate side-chains 256 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 221 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1656 LEU Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 45 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS A1736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.177363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145440 restraints weight = 16801.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.149322 restraints weight = 8220.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.151863 restraints weight = 5369.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.153131 restraints weight = 4226.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.154235 restraints weight = 3738.183| |-----------------------------------------------------------------------------| r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9685 Z= 0.161 Angle : 0.813 14.895 13141 Z= 0.381 Chirality : 0.045 0.372 1547 Planarity : 0.004 0.041 1541 Dihedral : 14.101 169.547 2043 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.94 % Favored : 92.97 % Rotamer: Outliers : 4.53 % Allowed : 28.56 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.28 (0.25), residues: 1110 helix: 0.47 (0.18), residues: 796 sheet: -3.19 (1.18), residues: 10 loop : -1.68 (0.38), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.013 0.001 TYR A 417 PHE 0.016 0.001 PHE A 393 TRP 0.023 0.001 TRP A1347 HIS 0.003 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9670) covalent geometry : angle 0.78389 (13108) SS BOND : bond 0.00378 ( 3) SS BOND : angle 1.37474 ( 6) hydrogen bonds : bond 0.04319 ( 599) hydrogen bonds : angle 5.08013 ( 1737) Misc. bond : bond 0.00085 ( 3) link_BETA1-4 : bond 0.01065 ( 4) link_BETA1-4 : angle 3.00382 ( 12) link_NAG-ASN : bond 0.01048 ( 5) link_NAG-ASN : angle 5.82681 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 230 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8609 (tptt) cc_final: 0.8173 (mttm) REVERT: A 160 TYR cc_start: 0.6848 (OUTLIER) cc_final: 0.5531 (m-10) REVERT: A 174 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7657 (mt) REVERT: A 1215 PHE cc_start: 0.7071 (OUTLIER) cc_final: 0.6392 (t80) REVERT: A 1265 PHE cc_start: 0.7162 (m-80) cc_final: 0.6697 (t80) REVERT: A 1274 CYS cc_start: 0.8014 (m) cc_final: 0.7681 (m) REVERT: A 1348 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7826 (tp) REVERT: A 1364 ARG cc_start: 0.6452 (pmt-80) cc_final: 0.6130 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8870 (tt) cc_final: 0.8576 (mt) REVERT: A 1472 ILE cc_start: 0.7947 (mp) cc_final: 0.7734 (tt) REVERT: A 1496 TYR cc_start: 0.7629 (m-80) cc_final: 0.7205 (m-80) REVERT: A 1497 TYR cc_start: 0.7684 (t80) cc_final: 0.7238 (t80) REVERT: A 1613 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7016 (mp) REVERT: A 1640 ARG cc_start: 0.8029 (ttp80) cc_final: 0.7812 (ttp80) REVERT: A 1685 LYS cc_start: 0.7705 (OUTLIER) cc_final: 0.7445 (ttmt) REVERT: A 1729 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5773 (p90) outliers start: 43 outliers final: 30 residues processed: 256 average time/residue: 0.0774 time to fit residues: 29.6734 Evaluate side-chains 259 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 222 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1581 MET Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1649 LEU Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 0.6980 chunk 35 optimal weight: 20.0000 chunk 110 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS A1736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.177995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146135 restraints weight = 16863.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.150022 restraints weight = 8219.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152540 restraints weight = 5379.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.154115 restraints weight = 4223.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.154680 restraints weight = 3681.071| |-----------------------------------------------------------------------------| r_work (final): 0.4175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9685 Z= 0.155 Angle : 0.831 15.529 13141 Z= 0.387 Chirality : 0.045 0.363 1547 Planarity : 0.004 0.040 1541 Dihedral : 13.849 169.579 2043 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 4.11 % Allowed : 29.08 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.31 (0.25), residues: 1110 helix: 0.43 (0.18), residues: 798 sheet: -3.21 (1.15), residues: 10 loop : -1.65 (0.39), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 384 TYR 0.013 0.001 TYR A 379 PHE 0.017 0.001 PHE A1346 TRP 0.017 0.001 TRP A1347 HIS 0.003 0.001 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 9670) covalent geometry : angle 0.80273 (13108) SS BOND : bond 0.00338 ( 3) SS BOND : angle 1.35426 ( 6) hydrogen bonds : bond 0.04412 ( 599) hydrogen bonds : angle 5.06344 ( 1737) Misc. bond : bond 0.00093 ( 3) link_BETA1-4 : bond 0.01035 ( 4) link_BETA1-4 : angle 3.03348 ( 12) link_NAG-ASN : bond 0.01029 ( 5) link_NAG-ASN : angle 5.77355 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8601 (tptt) cc_final: 0.8172 (mttm) REVERT: A 160 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.5534 (m-10) REVERT: A 174 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7646 (mt) REVERT: A 734 PHE cc_start: 0.7511 (t80) cc_final: 0.7307 (t80) REVERT: A 1215 PHE cc_start: 0.7174 (OUTLIER) cc_final: 0.6471 (t80) REVERT: A 1265 PHE cc_start: 0.7153 (m-80) cc_final: 0.6683 (t80) REVERT: A 1274 CYS cc_start: 0.7984 (m) cc_final: 0.7658 (m) REVERT: A 1364 ARG cc_start: 0.6390 (pmt-80) cc_final: 0.6159 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8850 (tt) cc_final: 0.8577 (mt) REVERT: A 1472 ILE cc_start: 0.7938 (mp) cc_final: 0.7723 (tt) REVERT: A 1496 TYR cc_start: 0.7702 (m-80) cc_final: 0.7307 (m-80) REVERT: A 1497 TYR cc_start: 0.7728 (t80) cc_final: 0.7243 (t80) REVERT: A 1613 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.7004 (mp) REVERT: A 1640 ARG cc_start: 0.8088 (ttp80) cc_final: 0.7884 (ttp80) REVERT: A 1729 TYR cc_start: 0.6345 (OUTLIER) cc_final: 0.5782 (p90) outliers start: 39 outliers final: 29 residues processed: 249 average time/residue: 0.0722 time to fit residues: 27.3086 Evaluate side-chains 256 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ARG Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1581 MET Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1736 ASN Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 0.0980 chunk 20 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 19 optimal weight: 30.0000 chunk 47 optimal weight: 10.0000 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1586 HIS A1736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.180036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.148565 restraints weight = 16765.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.152476 restraints weight = 8162.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.155100 restraints weight = 5314.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.156696 restraints weight = 4141.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157436 restraints weight = 3585.428| |-----------------------------------------------------------------------------| r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6864 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9685 Z= 0.141 Angle : 0.835 16.839 13141 Z= 0.386 Chirality : 0.044 0.346 1547 Planarity : 0.004 0.040 1541 Dihedral : 13.370 169.752 2043 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 3.69 % Allowed : 29.19 % Favored : 67.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.22 (0.25), residues: 1110 helix: 0.53 (0.18), residues: 791 sheet: -3.21 (1.13), residues: 10 loop : -1.67 (0.37), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1314 TYR 0.023 0.001 TYR A1683 PHE 0.016 0.001 PHE A1346 TRP 0.020 0.001 TRP A1347 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 9670) covalent geometry : angle 0.80787 (13108) SS BOND : bond 0.00270 ( 3) SS BOND : angle 1.23531 ( 6) hydrogen bonds : bond 0.04321 ( 599) hydrogen bonds : angle 4.99184 ( 1737) Misc. bond : bond 0.00096 ( 3) link_BETA1-4 : bond 0.01084 ( 4) link_BETA1-4 : angle 3.11265 ( 12) link_NAG-ASN : bond 0.01027 ( 5) link_NAG-ASN : angle 5.65318 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1890.71 seconds wall clock time: 33 minutes 12.08 seconds (1992.08 seconds total)