Starting phenix.real_space_refine on Fri Sep 11 15:41:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uz3_20951/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.cif" model { file = "/net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uz3_20951/09_2026/6uz3_20951.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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: 232 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: 1.70, per 1000 atoms: 0.18 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: 0.77 Conformation dependent library (CDL) restraints added in 250.2 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: 0.17 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: 1.40 Time building geometry restraints manager: 0.95 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 - 30.25: 5219 30.25 - 60.50: 254 60.50 - 90.74: 16 90.74 - 120.99: 4 120.99 - 151.24: 3 Dihedral angle restraints: 5496 sinusoidal: 2217 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 5493 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: 0.950 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 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 : 17.373 151.241 3367 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/Z covalent geometry : bond 0.02197 / 1.09 ( 9670) covalent geometry : angle 1.32993 / 0.62 (13108) SS BOND : bond 0.00710 / 0.35 ( 3) SS BOND : angle 2.65709 / 1.26 ( 6) hydrogen bonds : bond 0.17140 / 11.39 ( 599) hydrogen bonds : angle 7.18305 / 5.12 ( 1737) Misc. bond : bond 0.27975 / 10.36 ( 3) link_BETA1-4 : bond 0.03272 / 1.72 ( 4) link_BETA1-4 : angle 7.66862 / 3.62 ( 12) link_NAG-ASN : bond 0.05193 / 2.08 ( 5) link_NAG-ASN : angle 18.05642 / 10.46 ( 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 : 0.381 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: 0.0765 time to fit residues: 29.4408 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 : 0.401 ------------------------------------------------------------------------------- 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... A 145 ASN A 195 ASN A 314 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 = 0.4381 r_free = 0.4381 target = 0.173685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.143813 restraints weight = 17066.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.146672 restraints weight = 8717.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.147948 restraints weight = 5502.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.147927 restraints weight = 4901.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.148210 restraints weight = 4792.019| |-----------------------------------------------------------------------------| r_work (final): 0.4092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9685 Z= 0.188 Angle : 0.876 18.044 13141 Z= 0.413 Chirality : 0.047 0.492 1547 Planarity : 0.005 0.045 1541 Dihedral : 14.273 132.837 1423 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.29 % Favored : 91.62 % Rotamer: Outliers : 3.27 % Allowed : 19.28 % Favored : 77.45 % 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: -2.10 (0.24), residues: 1110 helix: -0.93 (0.17), residues: 784 sheet: -2.66 (1.44), residues: 10 loop : -2.20 (0.39), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 384 TYR 0.024 0.002 TYR A 417 PHE 0.036 0.002 PHE A 785 TRP 0.024 0.002 TRP A1423 HIS 0.005 0.002 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 ( 9670) covalent geometry : angle 0.81948 / 0.40 (13108) SS BOND : bond 0.00216 / 0.11 ( 3) SS BOND : angle 1.91803 / 0.99 ( 6) hydrogen bonds : bond 0.05537 / 3.68 ( 599) hydrogen bonds : angle 5.66927 / 4.05 ( 1737) Misc. bond : bond 0.00313 / 0.12 ( 3) link_BETA1-4 : bond 0.00755 / 0.33 ( 4) link_BETA1-4 : angle 2.75249 / 1.47 ( 12) link_NAG-ASN : bond 0.01140 / 0.66 ( 5) link_NAG-ASN : angle 8.83033 / 5.74 ( 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 266 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8620 (tptt) cc_final: 0.7693 (mtpp) REVERT: A 160 TYR cc_start: 0.6950 (OUTLIER) cc_final: 0.5555 (m-80) REVERT: A 404 TYR cc_start: 0.7544 (t80) cc_final: 0.7035 (t80) REVERT: A 809 ARG cc_start: 0.8215 (mpt-90) cc_final: 0.7819 (mpp80) REVERT: A 1265 PHE cc_start: 0.7298 (m-80) cc_final: 0.6697 (t80) REVERT: A 1274 CYS cc_start: 0.8346 (m) cc_final: 0.7982 (m) REVERT: A 1323 ARG cc_start: 0.7268 (ttp80) cc_final: 0.6460 (ttp80) REVERT: A 1496 TYR cc_start: 0.7943 (m-10) cc_final: 0.7558 (m-80) REVERT: A 1497 TYR cc_start: 0.7717 (t80) cc_final: 0.7261 (t80) REVERT: A 1500 MET cc_start: 0.6285 (ttm) cc_final: 0.5919 (ttp) REVERT: A 1537 MET cc_start: 0.6855 (tpp) cc_final: 0.6646 (ttt) REVERT: A 1588 TYR cc_start: 0.6106 (p90) cc_final: 0.5678 (p90) REVERT: A 1629 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8387 (tt) REVERT: A 1671 PHE cc_start: 0.7841 (t80) cc_final: 0.7590 (t80) REVERT: A 1703 MET cc_start: 0.7676 (tpt) cc_final: 0.7451 (tpt) REVERT: A 1729 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5530 (p90) outliers start: 31 outliers final: 15 residues processed: 257 average time/residue: 0.0738 time to fit residues: 27.9085 Evaluate side-chains 235 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 217 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 30 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 102 optimal weight: 9.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.0170 chunk 50 optimal weight: 20.0000 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.9824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 ASN A 310 ASN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** 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 = 0.177553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.144986 restraints weight = 17053.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.148948 restraints weight = 8367.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.151491 restraints weight = 5490.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.153099 restraints weight = 4318.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153592 restraints weight = 3754.438| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9685 Z= 0.144 Angle : 0.754 14.095 13141 Z= 0.361 Chirality : 0.043 0.347 1547 Planarity : 0.004 0.047 1541 Dihedral : 12.665 121.192 1412 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 4.00 % Allowed : 20.23 % Favored : 75.76 % 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: -1.08 (0.25), residues: 1110 helix: -0.15 (0.18), residues: 782 sheet: -3.07 (1.29), residues: 10 loop : -1.83 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 384 TYR 0.019 0.002 TYR A 308 PHE 0.017 0.001 PHE A1753 TRP 0.018 0.001 TRP A1423 HIS 0.002 0.001 HIS A 131 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 9670) covalent geometry : angle 0.71579 / 0.35 (13108) SS BOND : bond 0.00326 / 0.17 ( 3) SS BOND : angle 1.45028 / 0.72 ( 6) hydrogen bonds : bond 0.04691 / 3.12 ( 599) hydrogen bonds : angle 5.25681 / 3.75 ( 1737) Misc. bond : bond 0.00096 / 0.05 ( 3) link_BETA1-4 : bond 0.00779 / 0.36 ( 4) link_BETA1-4 : angle 1.77691 / 1.16 ( 12) link_NAG-ASN : bond 0.01222 / 0.59 ( 5) link_NAG-ASN : angle 6.84096 / 4.40 ( 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 286 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.337 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8529 (tptt) cc_final: 0.8100 (mttm) REVERT: A 160 TYR cc_start: 0.6838 (OUTLIER) cc_final: 0.5614 (m-80) REVERT: A 163 TYR cc_start: 0.7385 (m-80) cc_final: 0.7183 (m-80) REVERT: A 174 LEU cc_start: 0.8201 (tt) cc_final: 0.7901 (mt) REVERT: A 394 PHE cc_start: 0.6230 (OUTLIER) cc_final: 0.5954 (m-80) REVERT: A 404 TYR cc_start: 0.7271 (t80) cc_final: 0.7033 (t80) REVERT: A 407 ASN cc_start: 0.8697 (t0) cc_final: 0.8232 (t0) REVERT: A 1215 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6877 (t80) REVERT: A 1265 PHE cc_start: 0.7290 (m-80) cc_final: 0.6698 (t80) REVERT: A 1274 CYS cc_start: 0.8231 (m) cc_final: 0.7895 (m) REVERT: A 1323 ARG cc_start: 0.7120 (ttp80) cc_final: 0.6395 (ttp80) REVERT: A 1364 ARG cc_start: 0.6728 (pmt-80) cc_final: 0.6228 (pmt-80) REVERT: A 1497 TYR cc_start: 0.7678 (t80) cc_final: 0.7217 (t80) REVERT: A 1537 MET cc_start: 0.7000 (tpp) cc_final: 0.6786 (ttt) REVERT: A 1588 TYR cc_start: 0.6127 (p90) cc_final: 0.5752 (p90) REVERT: A 1613 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7128 (mp) REVERT: A 1729 TYR cc_start: 0.6058 (OUTLIER) cc_final: 0.5529 (p90) outliers start: 38 outliers final: 20 residues processed: 272 average time/residue: 0.0762 time to fit residues: 30.4374 Evaluate side-chains 249 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 224 time to evaluate : 0.547 ------------------------------------------------------------------------------- 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 230 THR 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 394 PHE 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 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE 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 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1613 ILE 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: 2.9990 chunk 78 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 72 optimal weight: 30.0000 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.174614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.141632 restraints weight = 17222.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.145423 restraints weight = 8555.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.147969 restraints weight = 5667.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149440 restraints weight = 4463.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.150148 restraints weight = 3913.479| |-----------------------------------------------------------------------------| r_work (final): 0.4117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6963 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9685 Z= 0.188 Angle : 0.790 12.670 13141 Z= 0.375 Chirality : 0.044 0.379 1547 Planarity : 0.004 0.046 1541 Dihedral : 12.246 119.460 1412 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 4.95 % Allowed : 22.55 % Favored : 72.50 % 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: -0.81 (0.25), residues: 1110 helix: 0.03 (0.18), residues: 783 sheet: -3.07 (1.33), residues: 10 loop : -1.67 (0.40), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.026 0.002 TYR A 308 PHE 0.015 0.002 PHE A1753 TRP 0.012 0.001 TRP A1442 HIS 0.006 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 ( 9670) covalent geometry : angle 0.75560 / 0.37 (13108) SS BOND : bond 0.00433 / 0.22 ( 3) SS BOND : angle 1.60861 / 0.79 ( 6) hydrogen bonds : bond 0.04672 / 3.13 ( 599) hydrogen bonds : angle 5.30328 / 3.77 ( 1737) Misc. bond : bond 0.00096 / 0.05 ( 3) link_BETA1-4 : bond 0.00591 / 0.26 ( 4) link_BETA1-4 : angle 1.75337 / 1.20 ( 12) link_NAG-ASN : bond 0.01179 / 0.56 ( 5) link_NAG-ASN : angle 6.63176 / 4.21 ( 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 277 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 230 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8631 (tptt) cc_final: 0.8182 (mttm) REVERT: A 160 TYR cc_start: 0.6882 (OUTLIER) cc_final: 0.5676 (m-80) REVERT: A 174 LEU cc_start: 0.8193 (tt) cc_final: 0.7764 (mt) REVERT: A 404 TYR cc_start: 0.7570 (t80) cc_final: 0.7068 (t80) REVERT: A 422 GLN cc_start: 0.7022 (mt0) cc_final: 0.6770 (pp30) REVERT: A 906 MET cc_start: 0.7811 (tpp) cc_final: 0.7195 (mmm) REVERT: A 1215 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6965 (t80) REVERT: A 1265 PHE cc_start: 0.7270 (m-80) cc_final: 0.6678 (t80) REVERT: A 1274 CYS cc_start: 0.8197 (m) cc_final: 0.7832 (m) REVERT: A 1323 ARG cc_start: 0.7040 (ttp80) cc_final: 0.6375 (ttp80) REVERT: A 1364 ARG cc_start: 0.6789 (pmt-80) cc_final: 0.6538 (pmt-80) REVERT: A 1496 TYR cc_start: 0.7565 (m-80) cc_final: 0.7185 (m-80) REVERT: A 1497 TYR cc_start: 0.7688 (t80) cc_final: 0.7227 (t80) REVERT: A 1537 MET cc_start: 0.6835 (tpp) cc_final: 0.6557 (ttt) REVERT: A 1538 PHE cc_start: 0.7089 (m-10) cc_final: 0.6886 (m-10) REVERT: A 1729 TYR cc_start: 0.6050 (OUTLIER) cc_final: 0.5479 (p90) outliers start: 47 outliers final: 27 residues processed: 257 average time/residue: 0.0749 time to fit residues: 28.7098 Evaluate side-chains 248 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 218 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 722 LEU Chi-restraints excluded: chain A residue 826 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 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 1503 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1711 THR 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: 1.9990 chunk 3 optimal weight: 0.3980 chunk 14 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN A1465 ASN A1586 HIS A1736 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.177907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.145633 restraints weight = 17046.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149608 restraints weight = 8291.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.152212 restraints weight = 5397.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.153836 restraints weight = 4217.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154810 restraints weight = 3662.178| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3130 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= 0.139 Angle : 0.771 13.192 13141 Z= 0.360 Chirality : 0.043 0.329 1547 Planarity : 0.004 0.043 1541 Dihedral : 11.516 115.888 1411 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.40 % Favored : 93.51 % Rotamer: Outliers : 4.21 % Allowed : 24.13 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % 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: -0.45 (0.25), residues: 1110 helix: 0.32 (0.18), residues: 785 sheet: -2.95 (1.39), residues: 10 loop : -1.62 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1640 TYR 0.021 0.001 TYR A1588 PHE 0.015 0.001 PHE A1753 TRP 0.011 0.001 TRP A1442 HIS 0.003 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 ( 9670) covalent geometry : angle 0.73919 / 0.35 (13108) SS BOND : bond 0.00302 / 0.16 ( 3) SS BOND : angle 1.75085 / 0.79 ( 6) hydrogen bonds : bond 0.04311 / 2.89 ( 599) hydrogen bonds : angle 5.13155 / 3.66 ( 1737) Misc. bond : bond 0.00101 / 0.05 ( 3) link_BETA1-4 : bond 0.00662 / 0.30 ( 4) link_BETA1-4 : angle 1.59594 / 1.08 ( 12) link_NAG-ASN : bond 0.01219 / 0.59 ( 5) link_NAG-ASN : angle 6.31361 / 4.02 ( 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 276 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8553 (tptt) cc_final: 0.8145 (mttm) REVERT: A 160 TYR cc_start: 0.6826 (OUTLIER) cc_final: 0.5680 (m-80) REVERT: A 174 LEU cc_start: 0.7975 (tt) cc_final: 0.7503 (mt) REVERT: A 369 LEU cc_start: 0.7978 (mp) cc_final: 0.7763 (mt) REVERT: A 404 TYR cc_start: 0.7365 (t80) cc_final: 0.7034 (t80) REVERT: A 422 GLN cc_start: 0.6936 (mt0) cc_final: 0.6725 (pp30) REVERT: A 1215 PHE cc_start: 0.7322 (OUTLIER) cc_final: 0.6767 (t80) REVERT: A 1265 PHE cc_start: 0.7216 (m-80) cc_final: 0.6698 (t80) REVERT: A 1274 CYS cc_start: 0.8100 (m) cc_final: 0.7759 (m) REVERT: A 1364 ARG cc_start: 0.6625 (pmt-80) cc_final: 0.6393 (pmt-80) REVERT: A 1489 MET cc_start: 0.7359 (mtm) cc_final: 0.7139 (mtm) REVERT: A 1496 TYR cc_start: 0.7577 (m-80) cc_final: 0.7108 (m-80) REVERT: A 1497 TYR cc_start: 0.7679 (t80) cc_final: 0.7200 (t80) REVERT: A 1581 MET cc_start: 0.3654 (tpt) cc_final: 0.3358 (tpt) REVERT: A 1588 TYR cc_start: 0.5669 (p90) cc_final: 0.5397 (p90) REVERT: A 1613 ILE cc_start: 0.7263 (OUTLIER) cc_final: 0.6980 (mp) REVERT: A 1729 TYR cc_start: 0.6049 (OUTLIER) cc_final: 0.5494 (p90) outliers start: 40 outliers final: 25 residues processed: 261 average time/residue: 0.0716 time to fit residues: 27.9666 Evaluate side-chains 252 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 223 time to evaluate : 0.262 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 37 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 20.0000 chunk 27 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 99 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1406 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 = 0.4390 r_free = 0.4390 target = 0.174598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.141877 restraints weight = 17036.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.145718 restraints weight = 8399.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.148210 restraints weight = 5523.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.149728 restraints weight = 4348.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.150488 restraints weight = 3805.641| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3099 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= 0.188 Angle : 0.795 14.745 13141 Z= 0.375 Chirality : 0.045 0.369 1547 Planarity : 0.004 0.044 1541 Dihedral : 11.460 113.084 1411 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.70 % Rotamer: Outliers : 5.48 % Allowed : 25.61 % Favored : 68.91 % 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: -0.44 (0.26), residues: 1110 helix: 0.31 (0.18), residues: 788 sheet: -3.05 (1.30), residues: 10 loop : -1.55 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 384 TYR 0.015 0.002 TYR A 379 PHE 0.015 0.002 PHE A 393 TRP 0.010 0.001 TRP A1442 HIS 0.005 0.001 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.19 ( 9670) covalent geometry : angle 0.76495 / 0.37 (13108) SS BOND : bond 0.00447 / 0.23 ( 3) SS BOND : angle 1.62385 / 0.79 ( 6) hydrogen bonds : bond 0.04472 / 3.01 ( 599) hydrogen bonds : angle 5.21033 / 3.70 ( 1737) Misc. bond : bond 0.00095 / 0.04 ( 3) link_BETA1-4 : bond 0.00631 / 0.27 ( 4) link_BETA1-4 : angle 1.74440 / 1.20 ( 12) link_NAG-ASN : bond 0.01165 / 0.55 ( 5) link_NAG-ASN : angle 6.22738 / 3.92 ( 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 281 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8651 (tptt) cc_final: 0.8245 (mttm) REVERT: A 160 TYR cc_start: 0.6855 (OUTLIER) cc_final: 0.5620 (m-80) REVERT: A 174 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7577 (mt) REVERT: A 404 TYR cc_start: 0.7624 (t80) cc_final: 0.6978 (t80) REVERT: A 422 GLN cc_start: 0.6962 (mt0) cc_final: 0.6738 (pp30) REVERT: A 862 PHE cc_start: 0.7618 (m-80) cc_final: 0.7376 (m-80) REVERT: A 1215 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6617 (t80) REVERT: A 1265 PHE cc_start: 0.7269 (m-80) cc_final: 0.6722 (t80) REVERT: A 1274 CYS cc_start: 0.8144 (m) cc_final: 0.7785 (m) REVERT: A 1364 ARG cc_start: 0.6676 (pmt-80) cc_final: 0.6399 (pmt-80) REVERT: A 1496 TYR cc_start: 0.7559 (m-80) cc_final: 0.7073 (m-80) REVERT: A 1497 TYR cc_start: 0.7713 (t80) cc_final: 0.7230 (t80) REVERT: A 1581 MET cc_start: 0.3535 (tpt) cc_final: 0.1835 (ttt) REVERT: A 1613 ILE cc_start: 0.7348 (OUTLIER) cc_final: 0.7051 (mp) REVERT: A 1656 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7876 (mm) REVERT: A 1729 TYR cc_start: 0.6033 (OUTLIER) cc_final: 0.5439 (p90) outliers start: 52 outliers final: 32 residues processed: 260 average time/residue: 0.0707 time to fit residues: 27.6625 Evaluate side-chains 259 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 221 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 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 722 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 940 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 1333 ILE 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 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1544 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 1708 GLN Chi-restraints excluded: chain A residue 1711 THR 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: 6.9990 chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 chunk 93 optimal weight: 20.0000 chunk 86 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1406 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 = 0.4390 r_free = 0.4390 target = 0.174566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.141888 restraints weight = 17047.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.145860 restraints weight = 8353.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.148398 restraints weight = 5428.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.149966 restraints weight = 4253.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.150553 restraints weight = 3711.220| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6952 moved from start: 0.3218 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= 0.183 Angle : 0.815 14.638 13141 Z= 0.383 Chirality : 0.045 0.364 1547 Planarity : 0.004 0.042 1541 Dihedral : 11.349 109.562 1411 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.03 % Favored : 92.88 % Rotamer: Outliers : 5.69 % Allowed : 25.82 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.09 % 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: -0.41 (0.26), residues: 1110 helix: 0.32 (0.18), residues: 790 sheet: -3.11 (1.24), residues: 10 loop : -1.54 (0.40), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1640 TYR 0.016 0.002 TYR A 379 PHE 0.016 0.002 PHE A1458 TRP 0.012 0.001 TRP A 782 HIS 0.004 0.001 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 ( 9670) covalent geometry : angle 0.78694 / 0.38 (13108) SS BOND : bond 0.00464 / 0.24 ( 3) SS BOND : angle 1.68101 / 0.81 ( 6) hydrogen bonds : bond 0.04513 / 3.03 ( 599) hydrogen bonds : angle 5.20327 / 3.70 ( 1737) Misc. bond : bond 0.00096 / 0.05 ( 3) link_BETA1-4 : bond 0.00602 / 0.27 ( 4) link_BETA1-4 : angle 1.69187 / 1.17 ( 12) link_NAG-ASN : bond 0.01123 / 0.54 ( 5) link_NAG-ASN : angle 6.05313 / 3.79 ( 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 283 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8667 (tptt) cc_final: 0.8241 (mttm) REVERT: A 160 TYR cc_start: 0.6885 (OUTLIER) cc_final: 0.5590 (m-10) REVERT: A 174 LEU cc_start: 0.7932 (tt) cc_final: 0.7585 (mt) REVERT: A 404 TYR cc_start: 0.7566 (t80) cc_final: 0.7150 (t80) REVERT: A 422 GLN cc_start: 0.6984 (mt0) cc_final: 0.6744 (pp30) REVERT: A 862 PHE cc_start: 0.7569 (m-80) cc_final: 0.7346 (m-80) REVERT: A 1215 PHE cc_start: 0.7202 (OUTLIER) cc_final: 0.6466 (t80) REVERT: A 1265 PHE cc_start: 0.7225 (m-80) cc_final: 0.6673 (t80) REVERT: A 1274 CYS cc_start: 0.8134 (m) cc_final: 0.7775 (m) REVERT: A 1496 TYR cc_start: 0.7623 (m-80) cc_final: 0.7160 (m-80) REVERT: A 1497 TYR cc_start: 0.7729 (t80) cc_final: 0.7284 (t80) REVERT: A 1581 MET cc_start: 0.3584 (tpt) cc_final: 0.1824 (ttt) REVERT: A 1613 ILE cc_start: 0.7321 (OUTLIER) cc_final: 0.7008 (mp) REVERT: A 1656 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7873 (mm) REVERT: A 1729 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.5751 (p90) outliers start: 54 outliers final: 37 residues processed: 258 average time/residue: 0.0698 time to fit residues: 26.7898 Evaluate side-chains 263 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 395 MET Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 940 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 1333 ILE 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 1471 ILE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1544 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 1708 GLN Chi-restraints excluded: chain A residue 1711 THR 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: 0.6980 chunk 23 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 24 optimal weight: 0.4980 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 36 optimal weight: 30.0000 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4425 r_free = 0.4425 target = 0.178020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.146139 restraints weight = 16920.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.150113 restraints weight = 8180.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.152691 restraints weight = 5313.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.154271 restraints weight = 4156.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.154933 restraints weight = 3627.331| |-----------------------------------------------------------------------------| r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3503 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= 0.139 Angle : 0.799 15.798 13141 Z= 0.370 Chirality : 0.043 0.321 1547 Planarity : 0.004 0.042 1541 Dihedral : 10.764 102.660 1411 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.76 % Favored : 93.15 % Rotamer: Outliers : 4.53 % Allowed : 26.98 % Favored : 68.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.26), residues: 1110 helix: 0.48 (0.18), residues: 797 sheet: -3.22 (1.17), residues: 10 loop : -1.55 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1314 TYR 0.015 0.001 TYR A 353 PHE 0.015 0.001 PHE A 393 TRP 0.011 0.001 TRP A 375 HIS 0.002 0.001 HIS A 279 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 ( 9670) covalent geometry : angle 0.77381 / 0.36 (13108) SS BOND : bond 0.00315 / 0.16 ( 3) SS BOND : angle 1.39340 / 0.67 ( 6) hydrogen bonds : bond 0.04292 / 2.88 ( 599) hydrogen bonds : angle 5.09245 / 3.63 ( 1737) Misc. bond : bond 0.00097 / 0.05 ( 3) link_BETA1-4 : bond 0.00644 / 0.28 ( 4) link_BETA1-4 : angle 1.57976 / 1.08 ( 12) link_NAG-ASN : bond 0.01144 / 0.55 ( 5) link_NAG-ASN : angle 5.80959 / 3.66 ( 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 277 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 234 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8582 (tptt) cc_final: 0.8162 (mttm) REVERT: A 160 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.5503 (m-10) REVERT: A 174 LEU cc_start: 0.8100 (OUTLIER) cc_final: 0.7781 (mt) REVERT: A 404 TYR cc_start: 0.7311 (t80) cc_final: 0.7094 (t80) REVERT: A 926 MET cc_start: 0.7927 (tpt) cc_final: 0.7090 (tpt) REVERT: A 1215 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.6180 (t80) REVERT: A 1265 PHE cc_start: 0.7180 (m-80) cc_final: 0.6684 (t80) REVERT: A 1274 CYS cc_start: 0.8076 (m) cc_final: 0.7751 (m) REVERT: A 1472 ILE cc_start: 0.7947 (mp) cc_final: 0.7724 (tt) REVERT: A 1496 TYR cc_start: 0.7609 (m-80) cc_final: 0.7256 (m-80) REVERT: A 1497 TYR cc_start: 0.7686 (t80) cc_final: 0.7207 (t80) REVERT: A 1581 MET cc_start: 0.3123 (tpt) cc_final: 0.1475 (ttt) REVERT: A 1613 ILE cc_start: 0.7277 (OUTLIER) cc_final: 0.6956 (mp) REVERT: A 1656 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7879 (mm) REVERT: A 1729 TYR cc_start: 0.6338 (OUTLIER) cc_final: 0.5762 (p90) outliers start: 43 outliers final: 29 residues processed: 257 average time/residue: 0.0707 time to fit residues: 27.3777 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 : 0.245 ------------------------------------------------------------------------------- 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 940 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 1333 ILE Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER 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 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 1649 LEU Chi-restraints excluded: chain A residue 1656 LEU 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: 9.9990 chunk 42 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 71 optimal weight: 0.0040 chunk 27 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 3 optimal weight: 0.0040 overall best weight: 2.2010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 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 = 0.4417 r_free = 0.4417 target = 0.177319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.145403 restraints weight = 16851.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.149340 restraints weight = 8223.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151899 restraints weight = 5341.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.153455 restraints weight = 4192.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.154240 restraints weight = 3655.656| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3617 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= 0.151 Angle : 0.803 15.814 13141 Z= 0.376 Chirality : 0.044 0.334 1547 Planarity : 0.004 0.041 1541 Dihedral : 10.530 96.528 1411 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.31 % Favored : 93.60 % Rotamer: Outliers : 4.43 % Allowed : 28.03 % Favored : 67.54 % 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: -0.20 (0.26), residues: 1110 helix: 0.49 (0.18), residues: 795 sheet: -3.26 (1.13), residues: 10 loop : -1.52 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1640 TYR 0.019 0.001 TYR A 417 PHE 0.022 0.001 PHE A1762 TRP 0.008 0.001 TRP A 375 HIS 0.003 0.001 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 9670) covalent geometry : angle 0.77928 / 0.37 (13108) SS BOND : bond 0.00343 / 0.18 ( 3) SS BOND : angle 1.39443 / 0.68 ( 6) hydrogen bonds : bond 0.04288 / 2.88 ( 599) hydrogen bonds : angle 5.09464 / 3.63 ( 1737) Misc. bond : bond 0.00092 / 0.04 ( 3) link_BETA1-4 : bond 0.00618 / 0.28 ( 4) link_BETA1-4 : angle 1.60563 / 1.10 ( 12) link_NAG-ASN : bond 0.01082 / 0.52 ( 5) link_NAG-ASN : angle 5.64102 / 3.54 ( 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 265 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 223 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8602 (tptt) cc_final: 0.8195 (mttm) REVERT: A 160 TYR cc_start: 0.6824 (OUTLIER) cc_final: 0.5515 (m-10) REVERT: A 174 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7709 (mt) REVERT: A 926 MET cc_start: 0.7809 (tpt) cc_final: 0.6966 (tpt) REVERT: A 1215 PHE cc_start: 0.6872 (OUTLIER) cc_final: 0.6152 (t80) REVERT: A 1265 PHE cc_start: 0.7124 (m-80) cc_final: 0.6667 (t80) REVERT: A 1274 CYS cc_start: 0.8049 (m) cc_final: 0.7733 (m) REVERT: A 1472 ILE cc_start: 0.7964 (mp) cc_final: 0.7728 (tt) REVERT: A 1496 TYR cc_start: 0.7609 (m-80) cc_final: 0.7287 (m-80) REVERT: A 1497 TYR cc_start: 0.7682 (t80) cc_final: 0.7249 (t80) REVERT: A 1581 MET cc_start: 0.3062 (tpt) cc_final: 0.1619 (ttt) REVERT: A 1613 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6919 (mp) REVERT: A 1729 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.5776 (p90) outliers start: 42 outliers final: 31 residues processed: 248 average time/residue: 0.0710 time to fit residues: 26.3322 Evaluate side-chains 254 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 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 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 1424 MET 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 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 1649 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 34 optimal weight: 8.9990 chunk 16 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 84 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 0.3980 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 421 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.176439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.144301 restraints weight = 16959.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.148200 restraints weight = 8223.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.150742 restraints weight = 5378.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.152186 restraints weight = 4236.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.153149 restraints weight = 3715.123| |-----------------------------------------------------------------------------| r_work (final): 0.4155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6920 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9685 Z= 0.169 Angle : 0.823 15.524 13141 Z= 0.386 Chirality : 0.045 0.346 1547 Planarity : 0.004 0.039 1541 Dihedral : 10.494 90.647 1411 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.24 % Rotamer: Outliers : 4.21 % Allowed : 28.03 % Favored : 67.76 % 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: -0.26 (0.26), residues: 1110 helix: 0.44 (0.18), residues: 798 sheet: -3.27 (1.12), residues: 10 loop : -1.53 (0.40), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 815 TYR 0.020 0.002 TYR A 417 PHE 0.016 0.002 PHE A 393 TRP 0.008 0.001 TRP A1442 HIS 0.003 0.001 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9670) covalent geometry : angle 0.79935 / 0.38 (13108) SS BOND : bond 0.00366 / 0.19 ( 3) SS BOND : angle 1.44378 / 0.71 ( 6) hydrogen bonds : bond 0.04441 / 2.99 ( 599) hydrogen bonds : angle 5.12811 / 3.65 ( 1737) Misc. bond : bond 0.00090 / 0.04 ( 3) link_BETA1-4 : bond 0.00611 / 0.27 ( 4) link_BETA1-4 : angle 1.62704 / 1.13 ( 12) link_NAG-ASN : bond 0.01045 / 0.50 ( 5) link_NAG-ASN : angle 5.59914 / 3.49 ( 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: 40 poor density : 223 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8624 (tptt) cc_final: 0.8222 (mttm) REVERT: A 160 TYR cc_start: 0.6851 (OUTLIER) cc_final: 0.5504 (m-10) REVERT: A 174 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7666 (mt) REVERT: A 1215 PHE cc_start: 0.7060 (OUTLIER) cc_final: 0.6263 (t80) REVERT: A 1265 PHE cc_start: 0.7137 (m-80) cc_final: 0.6667 (t80) REVERT: A 1274 CYS cc_start: 0.8056 (m) cc_final: 0.7733 (m) REVERT: A 1472 ILE cc_start: 0.7967 (mp) cc_final: 0.7734 (tt) REVERT: A 1496 TYR cc_start: 0.7638 (m-80) cc_final: 0.7301 (m-80) REVERT: A 1497 TYR cc_start: 0.7728 (t80) cc_final: 0.7296 (t80) REVERT: A 1581 MET cc_start: 0.3274 (tpt) cc_final: 0.1619 (ttt) REVERT: A 1613 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.6931 (mp) REVERT: A 1729 TYR cc_start: 0.6358 (OUTLIER) cc_final: 0.5795 (p90) outliers start: 40 outliers final: 32 residues processed: 249 average time/residue: 0.0719 time to fit residues: 26.9545 Evaluate side-chains 257 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.230 ------------------------------------------------------------------------------- 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 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 878 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 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 1424 MET 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 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 1649 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 102 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 19 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 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 = 0.4421 r_free = 0.4421 target = 0.177517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.145531 restraints weight = 16869.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.149470 restraints weight = 8170.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.151973 restraints weight = 5339.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.153519 restraints weight = 4201.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.154229 restraints weight = 3673.584| |-----------------------------------------------------------------------------| r_work (final): 0.4169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6901 moved from start: 0.3752 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= 0.154 Angle : 0.825 15.421 13141 Z= 0.385 Chirality : 0.045 0.332 1547 Planarity : 0.004 0.038 1541 Dihedral : 10.268 80.418 1411 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.24 % Rotamer: Outliers : 3.79 % Allowed : 28.66 % Favored : 67.54 % 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: -0.17 (0.26), residues: 1110 helix: 0.50 (0.18), residues: 791 sheet: -3.25 (1.12), residues: 10 loop : -1.45 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1640 TYR 0.015 0.001 TYR A 353 PHE 0.016 0.001 PHE A 393 TRP 0.008 0.001 TRP A 375 HIS 0.002 0.001 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 ( 9670) covalent geometry : angle 0.80250 / 0.38 (13108) SS BOND : bond 0.00332 / 0.17 ( 3) SS BOND : angle 1.36339 / 0.68 ( 6) hydrogen bonds : bond 0.04412 / 2.97 ( 599) hydrogen bonds : angle 5.08233 / 3.62 ( 1737) Misc. bond : bond 0.00091 / 0.04 ( 3) link_BETA1-4 : bond 0.00663 / 0.29 ( 4) link_BETA1-4 : angle 1.60394 / 1.10 ( 12) link_NAG-ASN : bond 0.01042 / 0.50 ( 5) link_NAG-ASN : angle 5.48863 / 3.42 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1757.83 seconds wall clock time: 30 minutes 54.25 seconds (1854.25 seconds total)