Starting phenix.real_space_refine on Mon Jul 28 06:53:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uz3_20951/07_2025/6uz3_20951.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uz3_20951/07_2025/6uz3_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_20951/07_2025/6uz3_20951.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uz3_20951/07_2025/6uz3_20951.map" model { file = "/net/cci-nas-00/data/ceres_data/6uz3_20951/07_2025/6uz3_20951.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uz3_20951/07_2025/6uz3_20951.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2, 'PHE:plan': 3, 'GLU:plan': 6, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 464 Unusual residues: {'6OU': 11, '9Z9': 5, 'NAG': 2} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 344 Unresolved non-hydrogen dihedrals: 329 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'6OU:plan-1': 9, '6OU:plan-2': 2, '6OU:plan-3': 1} Unresolved non-hydrogen planarities: 31 Time building chain proxies: 6.34, per 1000 atoms: 0.67 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: 4.02 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.94 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: 3.16 Time building geometry restraints manager: 3.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 1406 1.27 - 1.40: 2503 1.40 - 1.54: 5535 1.54 - 1.68: 102 1.68 - 1.81: 124 Bond restraints: 9670 Sorted by residual: bond pdb=" C06 9Z9 A3014 " pdb=" C07 9Z9 A3014 " ideal model delta sigma weight residual 1.520 1.131 0.389 2.00e-02 2.50e+03 3.78e+02 bond pdb=" C06 9Z9 A3010 " pdb=" C07 9Z9 A3010 " ideal model delta sigma weight residual 1.520 1.137 0.383 2.00e-02 2.50e+03 3.67e+02 bond pdb=" C06 9Z9 A3011 " pdb=" C07 9Z9 A3011 " ideal model delta sigma weight residual 1.520 1.138 0.382 2.00e-02 2.50e+03 3.65e+02 bond pdb=" C06 9Z9 A3012 " pdb=" C07 9Z9 A3012 " ideal model delta sigma weight residual 1.520 1.157 0.363 2.00e-02 2.50e+03 3.30e+02 bond pdb=" C06 9Z9 A3013 " pdb=" C07 9Z9 A3013 " ideal model delta sigma weight residual 1.520 1.160 0.360 2.00e-02 2.50e+03 3.23e+02 ... (remaining 9665 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 12819 4.09 - 8.18: 240 8.18 - 12.27: 42 12.27 - 16.36: 5 16.36 - 20.45: 2 Bond angle restraints: 13108 Sorted by residual: angle pdb=" N LYS A1616 " pdb=" CA LYS A1616 " pdb=" C LYS A1616 " ideal model delta sigma weight residual 111.36 122.77 -11.41 1.09e+00 8.42e-01 1.09e+02 angle pdb=" N LYS A1302 " pdb=" CA LYS A1302 " pdb=" C LYS A1302 " ideal model delta sigma weight residual 113.18 102.85 10.33 1.21e+00 6.83e-01 7.28e+01 angle pdb=" N PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta sigma weight residual 103.25 111.59 -8.34 1.05e+00 9.07e-01 6.30e+01 angle pdb=" N THR A1622 " pdb=" CA THR A1622 " pdb=" CB THR A1622 " ideal model delta sigma weight residual 110.81 100.46 10.35 1.48e+00 4.57e-01 4.89e+01 angle pdb=" N THR A1622 " pdb=" CA THR A1622 " pdb=" C THR A1622 " ideal model delta sigma weight residual 114.04 105.84 8.20 1.24e+00 6.50e-01 4.37e+01 ... (remaining 13103 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 5829 35.96 - 71.92: 254 71.92 - 107.88: 26 107.88 - 143.83: 12 143.83 - 179.79: 7 Dihedral angle restraints: 6128 sinusoidal: 2849 harmonic: 3279 Sorted by residual: dihedral pdb=" CA ARG A1364 " pdb=" C ARG A1364 " pdb=" N CYS A1365 " pdb=" CA CYS A1365 " ideal model delta harmonic sigma weight residual -180.00 -126.13 -53.87 0 5.00e+00 4.00e-02 1.16e+02 dihedral pdb=" N PRO A1621 " pdb=" C PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta harmonic sigma weight residual 115.10 141.39 -26.29 0 2.50e+00 1.60e-01 1.11e+02 dihedral pdb=" C PRO A1621 " pdb=" N PRO A1621 " pdb=" CA PRO A1621 " pdb=" CB PRO A1621 " ideal model delta harmonic sigma weight residual -120.70 -141.82 21.12 0 2.50e+00 1.60e-01 7.14e+01 ... (remaining 6125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.649: 1532 0.649 - 1.298: 9 1.298 - 1.947: 5 1.947 - 2.596: 0 2.596 - 3.245: 1 Chirality restraints: 1547 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -0.78 -1.62 2.00e-02 2.50e+03 6.56e+03 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-02 2.50e+03 3.98e+02 chirality pdb=" C1 NAG A3009 " pdb=" ND2 ASN A 284 " pdb=" C2 NAG A3009 " pdb=" O5 NAG A3009 " both_signs ideal model delta sigma weight residual False -2.40 0.84 -3.24 2.00e-01 2.50e+01 2.63e+02 ... (remaining 1544 not shown) Planarity restraints: 1546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 1 " 0.361 2.00e-02 2.50e+03 3.10e-01 1.20e+03 pdb=" C7 NAG D 1 " -0.089 2.00e-02 2.50e+03 pdb=" C8 NAG D 1 " 0.143 2.00e-02 2.50e+03 pdb=" N2 NAG D 1 " -0.550 2.00e-02 2.50e+03 pdb=" O7 NAG D 1 " 0.135 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.352 2.00e-02 2.50e+03 3.04e-01 1.16e+03 pdb=" C7 NAG D 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.540 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3009 " -0.260 2.00e-02 2.50e+03 2.23e-01 6.19e+02 pdb=" C7 NAG A3009 " 0.056 2.00e-02 2.50e+03 pdb=" C8 NAG A3009 " 0.028 2.00e-02 2.50e+03 pdb=" N2 NAG A3009 " 0.372 2.00e-02 2.50e+03 pdb=" O7 NAG A3009 " -0.195 2.00e-02 2.50e+03 ... (remaining 1543 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.99: 6 1.99 - 2.72: 770 2.72 - 3.44: 14930 3.44 - 4.17: 21633 4.17 - 4.90: 38462 Nonbonded interactions: 75801 Sorted by model distance: nonbonded pdb=" O LEU A 129 " pdb=" CE2 PHE A 134 " model vdw 1.260 3.340 nonbonded pdb=" CD1 ILE A 138 " pdb=" OE2 GLU A 172 " model vdw 1.659 3.460 nonbonded pdb=" O LEU A 129 " pdb=" CZ PHE A 134 " model vdw 1.838 3.340 nonbonded pdb=" O CYS A 342 " pdb=" O7 NAG C 1 " model vdw 1.942 3.040 nonbonded pdb=" O CYS A 342 " pdb=" C7 NAG C 1 " model vdw 1.953 3.270 ... (remaining 75796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 25.940 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.023 0.485 9685 Z= 1.197 Angle : 1.481 38.517 13141 Z= 0.659 Chirality : 0.154 3.245 1547 Planarity : 0.015 0.310 1541 Dihedral : 20.904 179.792 3999 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 32.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.058 0.003 TRP A1423 HIS 0.010 0.002 HIS A 351 PHE 0.030 0.003 PHE A 148 TYR 0.024 0.003 TYR A1201 ARG 0.010 0.001 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.05193 ( 5) link_NAG-ASN : angle 18.05642 ( 15) link_BETA1-4 : bond 0.03272 ( 4) link_BETA1-4 : angle 7.66862 ( 12) hydrogen bonds : bond 0.17140 ( 599) hydrogen bonds : angle 7.18305 ( 1737) SS BOND : bond 0.00710 ( 3) SS BOND : angle 2.65709 ( 6) covalent geometry : bond 0.02197 ( 9670) covalent geometry : angle 1.32993 (13108) Misc. bond : bond 0.27975 ( 3) *********************** 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 : 1.016 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: 0.8145 (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: 0.8601 (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: 0.8233 (tp) REVERT: A 907 TRP cc_start: 0.7849 (m-10) cc_final: 0.7482 (m-90) REVERT: A 1274 CYS cc_start: 0.8066 (m) cc_final: 0.7744 (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: 0.7537 (m-80) REVERT: A 1497 TYR cc_start: 0.7653 (t80) cc_final: 0.7228 (t80) REVERT: A 1500 MET cc_start: 0.6295 (ttm) cc_final: 0.5868 (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: 0.2228 (tpt) REVERT: A 1588 TYR cc_start: 0.6200 (p90) cc_final: 0.5982 (p90) REVERT: A 1622 THR cc_start: 0.7464 (m) cc_final: 0.7251 (t) outliers start: 10 outliers final: 7 residues processed: 264 average time/residue: 0.1974 time to fit residues: 74.4176 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 : 1.017 ------------------------------------------------------------------------------- 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 94 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 101 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 ASN A 314 ASN A 731 ASN A 739 HIS A 780 GLN ** A 860 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 871 HIS ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 930 ASN A1327 ASN A1615 GLN A1767 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.173483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.140494 restraints weight = 16925.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.144467 restraints weight = 8507.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.146936 restraints weight = 5625.334| |-----------------------------------------------------------------------------| r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.1862 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 : 0.881 18.307 13141 Z= 0.413 Chirality : 0.047 0.493 1547 Planarity : 0.005 0.049 1541 Dihedral : 19.898 178.157 2055 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 3.06 % Allowed : 19.07 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.24), residues: 1110 helix: -0.93 (0.17), residues: 782 sheet: -2.68 (1.41), residues: 10 loop : -2.21 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1423 HIS 0.005 0.001 HIS A 871 PHE 0.034 0.002 PHE A 785 TYR 0.024 0.002 TYR A 417 ARG 0.007 0.001 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01162 ( 5) link_NAG-ASN : angle 9.10729 ( 15) link_BETA1-4 : bond 0.01025 ( 4) link_BETA1-4 : angle 3.16300 ( 12) hydrogen bonds : bond 0.05622 ( 599) hydrogen bonds : angle 5.67650 ( 1737) SS BOND : bond 0.00282 ( 3) SS BOND : angle 1.81291 ( 6) covalent geometry : bond 0.00398 ( 9670) covalent geometry : angle 0.81982 (13108) Misc. bond : bond 0.00482 ( 3) *********************** 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 263 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 234 time to evaluate : 1.039 Fit side-chains REVERT: A 159 LYS cc_start: 0.8604 (tptt) cc_final: 0.7714 (mttm) REVERT: A 160 TYR cc_start: 0.6982 (OUTLIER) cc_final: 0.5622 (m-80) REVERT: A 404 TYR cc_start: 0.7539 (t80) cc_final: 0.7087 (t80) REVERT: A 809 ARG cc_start: 0.8231 (mpt-90) cc_final: 0.7810 (mpp80) REVERT: A 1265 PHE cc_start: 0.7310 (m-80) cc_final: 0.6677 (t80) REVERT: A 1274 CYS cc_start: 0.8395 (m) cc_final: 0.8011 (m) REVERT: A 1323 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6419 (ttp80) REVERT: A 1364 ARG cc_start: 0.6898 (pmt-80) cc_final: 0.6687 (pmt-80) REVERT: A 1496 TYR cc_start: 0.7908 (m-10) cc_final: 0.7551 (m-80) REVERT: A 1497 TYR cc_start: 0.7687 (t80) cc_final: 0.7241 (t80) REVERT: A 1500 MET cc_start: 0.6273 (ttm) cc_final: 0.5901 (ttp) REVERT: A 1588 TYR cc_start: 0.6092 (p90) cc_final: 0.5879 (p90) REVERT: A 1629 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8415 (tt) REVERT: A 1671 PHE cc_start: 0.7880 (t80) cc_final: 0.7637 (t80) REVERT: A 1703 MET cc_start: 0.7696 (tpt) cc_final: 0.7457 (tpt) REVERT: A 1729 TYR cc_start: 0.6071 (OUTLIER) cc_final: 0.5594 (p90) outliers start: 29 outliers final: 13 residues processed: 255 average time/residue: 0.1985 time to fit residues: 73.2024 Evaluate side-chains 233 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 217 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 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 81 optimal weight: 1.9990 chunk 49 optimal weight: 0.1980 chunk 72 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 92 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.174648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.144779 restraints weight = 17190.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.147972 restraints weight = 8724.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.149205 restraints weight = 5465.853| |-----------------------------------------------------------------------------| r_work (final): 0.4104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2435 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= 0.168 Angle : 0.788 14.204 13141 Z= 0.377 Chirality : 0.045 0.419 1547 Planarity : 0.004 0.050 1541 Dihedral : 18.156 179.701 2044 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.21 % Favored : 92.70 % Rotamer: Outliers : 4.43 % Allowed : 20.23 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.25), residues: 1110 helix: -0.29 (0.18), residues: 788 sheet: -3.11 (1.26), residues: 10 loop : -1.85 (0.40), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1423 HIS 0.003 0.001 HIS A 351 PHE 0.017 0.002 PHE A1278 TYR 0.023 0.002 TYR A 308 ARG 0.006 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01139 ( 5) link_NAG-ASN : angle 7.17056 ( 15) link_BETA1-4 : bond 0.00833 ( 4) link_BETA1-4 : angle 2.64948 ( 12) hydrogen bonds : bond 0.04848 ( 599) hydrogen bonds : angle 5.38556 ( 1737) SS BOND : bond 0.00405 ( 3) SS BOND : angle 1.64435 ( 6) covalent geometry : bond 0.00364 ( 9670) covalent geometry : angle 0.74557 (13108) Misc. bond : bond 0.00265 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 237 time to evaluate : 0.938 Fit side-chains revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8599 (tptt) cc_final: 0.8153 (mttm) REVERT: A 160 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5679 (m-80) REVERT: A 174 LEU cc_start: 0.8243 (tt) cc_final: 0.7767 (mt) REVERT: A 404 TYR cc_start: 0.7418 (t80) cc_final: 0.7037 (t80) REVERT: A 407 ASN cc_start: 0.8774 (t0) cc_final: 0.8340 (t0) REVERT: A 1215 PHE cc_start: 0.7349 (OUTLIER) cc_final: 0.6972 (t80) REVERT: A 1265 PHE cc_start: 0.7319 (m-80) cc_final: 0.6596 (t80) REVERT: A 1274 CYS cc_start: 0.8302 (m) cc_final: 0.7935 (m) REVERT: A 1323 ARG cc_start: 0.7262 (ttp80) cc_final: 0.6449 (ttp80) REVERT: A 1496 TYR cc_start: 0.7988 (m-10) cc_final: 0.7577 (m-80) REVERT: A 1497 TYR cc_start: 0.7830 (t80) cc_final: 0.7407 (t80) REVERT: A 1588 TYR cc_start: 0.6258 (p90) cc_final: 0.5846 (p90) REVERT: A 1613 ILE cc_start: 0.7236 (OUTLIER) cc_final: 0.7026 (mp) REVERT: A 1671 PHE cc_start: 0.7687 (t80) cc_final: 0.7454 (t80) REVERT: A 1729 TYR cc_start: 0.6052 (OUTLIER) cc_final: 0.5445 (p90) REVERT: A 1765 VAL cc_start: 0.7451 (t) cc_final: 0.6939 (p) outliers start: 42 outliers final: 25 residues processed: 262 average time/residue: 0.1790 time to fit residues: 68.4411 Evaluate side-chains 246 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 217 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 849 ILE Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1656 LEU 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 71 optimal weight: 10.0000 chunk 37 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN A 860 GLN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.175278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.143533 restraints weight = 16943.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.148210 restraints weight = 8559.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.148852 restraints weight = 5289.859| |-----------------------------------------------------------------------------| r_work (final): 0.4091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.2782 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= 0.160 Angle : 0.769 12.915 13141 Z= 0.364 Chirality : 0.044 0.400 1547 Planarity : 0.004 0.055 1541 Dihedral : 17.069 176.685 2044 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 15.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 5.48 % Allowed : 22.13 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1110 helix: -0.04 (0.18), residues: 804 sheet: -3.02 (1.34), residues: 10 loop : -1.73 (0.42), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 375 HIS 0.006 0.001 HIS A 279 PHE 0.015 0.001 PHE A1753 TYR 0.025 0.002 TYR A 308 ARG 0.005 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01181 ( 5) link_NAG-ASN : angle 6.72412 ( 15) link_BETA1-4 : bond 0.00884 ( 4) link_BETA1-4 : angle 2.65503 ( 12) hydrogen bonds : bond 0.04598 ( 599) hydrogen bonds : angle 5.23016 ( 1737) SS BOND : bond 0.00379 ( 3) SS BOND : angle 1.53591 ( 6) covalent geometry : bond 0.00346 ( 9670) covalent geometry : angle 0.73089 (13108) Misc. bond : bond 0.00182 ( 3) *********************** 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 281 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 229 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8645 (tptt) cc_final: 0.8170 (mttm) REVERT: A 160 TYR cc_start: 0.6865 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: A 174 LEU cc_start: 0.7998 (tt) cc_final: 0.7577 (mt) REVERT: A 400 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7203 (mm) REVERT: A 404 TYR cc_start: 0.7483 (t80) cc_final: 0.6972 (t80) REVERT: A 422 GLN cc_start: 0.7421 (mt0) cc_final: 0.6934 (pp30) REVERT: A 1215 PHE cc_start: 0.7413 (OUTLIER) cc_final: 0.7003 (t80) REVERT: A 1237 ILE cc_start: 0.7759 (OUTLIER) cc_final: 0.7544 (tp) REVERT: A 1265 PHE cc_start: 0.7317 (m-80) cc_final: 0.6601 (t80) REVERT: A 1274 CYS cc_start: 0.8293 (m) cc_final: 0.7908 (m) REVERT: A 1323 ARG cc_start: 0.7018 (ttp80) cc_final: 0.6323 (ttp80) REVERT: A 1348 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7711 (tp) REVERT: A 1364 ARG cc_start: 0.7026 (pmt-80) cc_final: 0.6745 (pmt-80) REVERT: A 1444 ASP cc_start: 0.7940 (t70) cc_final: 0.7655 (t70) REVERT: A 1496 TYR cc_start: 0.8091 (m-10) cc_final: 0.7736 (m-80) REVERT: A 1497 TYR cc_start: 0.7895 (t80) cc_final: 0.7342 (t80) REVERT: A 1588 TYR cc_start: 0.6217 (p90) cc_final: 0.5759 (p90) REVERT: A 1729 TYR cc_start: 0.6115 (OUTLIER) cc_final: 0.5517 (p90) outliers start: 52 outliers final: 29 residues processed: 259 average time/residue: 0.2017 time to fit residues: 76.3782 Evaluate side-chains 252 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 217 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 HIS Chi-restraints excluded: chain A residue 160 TYR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 239 THR Chi-restraints excluded: chain A residue 306 ASP Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 395 MET Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 733 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1348 LEU 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 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1544 MET Chi-restraints excluded: chain A residue 1597 ASP Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1626 VAL Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 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 40 optimal weight: 0.5980 chunk 13 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 43 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 7 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 731 ASN ** A 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1327 ASN ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.177193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.144376 restraints weight = 17214.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4101 r_free = 0.4101 target = 0.148324 restraints weight = 8453.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.150923 restraints weight = 5562.073| |-----------------------------------------------------------------------------| r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.3069 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= 0.143 Angle : 0.780 13.103 13141 Z= 0.363 Chirality : 0.044 0.371 1547 Planarity : 0.004 0.044 1541 Dihedral : 16.257 174.155 2044 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.49 % Favored : 93.42 % Rotamer: Outliers : 5.16 % Allowed : 24.13 % Favored : 70.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.26), residues: 1110 helix: 0.22 (0.18), residues: 800 sheet: -3.11 (1.35), residues: 10 loop : -1.69 (0.40), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1442 HIS 0.002 0.001 HIS A 279 PHE 0.019 0.001 PHE A1762 TYR 0.017 0.001 TYR A 308 ARG 0.004 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01185 ( 5) link_NAG-ASN : angle 6.43221 ( 15) link_BETA1-4 : bond 0.00907 ( 4) link_BETA1-4 : angle 2.67819 ( 12) hydrogen bonds : bond 0.04341 ( 599) hydrogen bonds : angle 5.12747 ( 1737) SS BOND : bond 0.00324 ( 3) SS BOND : angle 1.65543 ( 6) covalent geometry : bond 0.00306 ( 9670) covalent geometry : angle 0.74505 (13108) Misc. bond : bond 0.00104 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2220 Ramachandran restraints generated. 1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 234 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8580 (tptt) cc_final: 0.8162 (mttm) REVERT: A 160 TYR cc_start: 0.6874 (OUTLIER) cc_final: 0.5744 (m-80) REVERT: A 174 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7542 (mt) REVERT: A 382 THR cc_start: 0.8341 (m) cc_final: 0.8102 (m) REVERT: A 400 LEU cc_start: 0.7387 (OUTLIER) cc_final: 0.6785 (mm) REVERT: A 404 TYR cc_start: 0.7329 (t80) cc_final: 0.7021 (t80) REVERT: A 422 GLN cc_start: 0.7150 (mt0) cc_final: 0.6809 (pp30) REVERT: A 1215 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6749 (t80) REVERT: A 1265 PHE cc_start: 0.7287 (m-80) cc_final: 0.6655 (t80) REVERT: A 1274 CYS cc_start: 0.8189 (m) cc_final: 0.7824 (m) REVERT: A 1348 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7596 (tp) REVERT: A 1364 ARG cc_start: 0.6916 (pmt-80) cc_final: 0.6593 (pmt-80) REVERT: A 1497 TYR cc_start: 0.7771 (t80) cc_final: 0.7259 (t80) REVERT: A 1596 PHE cc_start: 0.8954 (t80) cc_final: 0.8505 (t80) REVERT: A 1613 ILE cc_start: 0.7303 (OUTLIER) cc_final: 0.7026 (mp) REVERT: A 1729 TYR cc_start: 0.6094 (OUTLIER) cc_final: 0.5531 (p90) outliers start: 49 outliers final: 29 residues processed: 262 average time/residue: 0.1927 time to fit residues: 73.0163 Evaluate side-chains 251 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 215 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 733 LEU Chi-restraints excluded: chain A residue 737 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1544 MET 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 1708 GLN 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 2 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 107 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 94 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** A1736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.178192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.146172 restraints weight = 16811.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.150199 restraints weight = 8224.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.152780 restraints weight = 5377.834| |-----------------------------------------------------------------------------| r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6914 moved from start: 0.3311 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= 0.140 Angle : 0.762 12.675 13141 Z= 0.357 Chirality : 0.044 0.358 1547 Planarity : 0.004 0.041 1541 Dihedral : 15.449 170.469 2043 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.22 % Favored : 93.69 % Rotamer: Outliers : 5.06 % Allowed : 24.97 % Favored : 69.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1110 helix: 0.44 (0.18), residues: 797 sheet: -3.06 (1.29), residues: 10 loop : -1.59 (0.39), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1442 HIS 0.002 0.001 HIS A1586 PHE 0.014 0.001 PHE A 393 TYR 0.019 0.002 TYR A1588 ARG 0.007 0.000 ARG A1640 Details of bonding type rmsd link_NAG-ASN : bond 0.01200 ( 5) link_NAG-ASN : angle 6.23821 ( 15) link_BETA1-4 : bond 0.00998 ( 4) link_BETA1-4 : angle 2.76906 ( 12) hydrogen bonds : bond 0.04231 ( 599) hydrogen bonds : angle 5.02790 ( 1737) SS BOND : bond 0.00296 ( 3) SS BOND : angle 1.37205 ( 6) covalent geometry : bond 0.00296 ( 9670) covalent geometry : angle 0.72831 (13108) Misc. bond : bond 0.00102 ( 3) *********************** 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 275 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8599 (tptt) cc_final: 0.8140 (mttm) REVERT: A 160 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5625 (m-80) REVERT: A 174 LEU cc_start: 0.7983 (tt) cc_final: 0.7688 (mt) REVERT: A 400 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7055 (mm) REVERT: A 404 TYR cc_start: 0.7471 (t80) cc_final: 0.7044 (t80) REVERT: A 422 GLN cc_start: 0.7088 (mt0) cc_final: 0.6786 (pp30) REVERT: A 1215 PHE cc_start: 0.7317 (OUTLIER) cc_final: 0.6739 (t80) REVERT: A 1265 PHE cc_start: 0.7228 (m-80) cc_final: 0.6677 (t80) REVERT: A 1274 CYS cc_start: 0.8165 (m) cc_final: 0.7813 (m) REVERT: A 1348 LEU cc_start: 0.7871 (OUTLIER) cc_final: 0.7602 (tp) REVERT: A 1364 ARG cc_start: 0.6751 (pmt-80) cc_final: 0.6395 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8540 (mt) REVERT: A 1472 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7829 (tt) REVERT: A 1497 TYR cc_start: 0.7731 (t80) cc_final: 0.7231 (t80) REVERT: A 1581 MET cc_start: 0.2991 (tpt) cc_final: 0.1471 (ttt) REVERT: A 1685 LYS cc_start: 0.7730 (OUTLIER) cc_final: 0.7487 (ttmt) REVERT: A 1729 TYR cc_start: 0.6062 (OUTLIER) cc_final: 0.5543 (p90) outliers start: 48 outliers final: 27 residues processed: 256 average time/residue: 0.1778 time to fit residues: 67.3402 Evaluate side-chains 247 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.946 ------------------------------------------------------------------------------- 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 254 VAL 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 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 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1472 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 1624 PHE Chi-restraints excluded: chain A residue 1685 LYS Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 41 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 chunk 73 optimal weight: 0.0060 chunk 62 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 overall best weight: 0.6998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.180576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.149212 restraints weight = 16906.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153343 restraints weight = 8179.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.155976 restraints weight = 5290.843| |-----------------------------------------------------------------------------| r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3673 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= 0.134 Angle : 0.779 13.717 13141 Z= 0.364 Chirality : 0.044 0.339 1547 Planarity : 0.004 0.040 1541 Dihedral : 14.507 168.503 2043 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.77 % Favored : 94.14 % Rotamer: Outliers : 4.32 % Allowed : 27.08 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1110 helix: 0.59 (0.18), residues: 793 sheet: -3.19 (1.24), residues: 10 loop : -1.68 (0.38), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 782 HIS 0.002 0.001 HIS A 279 PHE 0.035 0.001 PHE A 785 TYR 0.052 0.002 TYR A1496 ARG 0.004 0.000 ARG A 815 Details of bonding type rmsd link_NAG-ASN : bond 0.01146 ( 5) link_NAG-ASN : angle 5.94638 ( 15) link_BETA1-4 : bond 0.00943 ( 4) link_BETA1-4 : angle 2.79468 ( 12) hydrogen bonds : bond 0.04207 ( 599) hydrogen bonds : angle 4.98074 ( 1737) SS BOND : bond 0.00232 ( 3) SS BOND : angle 1.25457 ( 6) covalent geometry : bond 0.00275 ( 9670) covalent geometry : angle 0.74792 (13108) Misc. bond : bond 0.00122 ( 3) *********************** 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 284 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 243 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8530 (tptt) cc_final: 0.8095 (mttm) REVERT: A 160 TYR cc_start: 0.6625 (OUTLIER) cc_final: 0.5516 (m-80) REVERT: A 174 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7736 (mt) REVERT: A 404 TYR cc_start: 0.7293 (t80) cc_final: 0.6986 (t80) REVERT: A 422 GLN cc_start: 0.7081 (mt0) cc_final: 0.6789 (pp30) REVERT: A 794 LEU cc_start: 0.8736 (mt) cc_final: 0.7932 (tp) REVERT: A 926 MET cc_start: 0.7797 (tpt) cc_final: 0.7021 (tpt) REVERT: A 1215 PHE cc_start: 0.7305 (OUTLIER) cc_final: 0.6707 (t80) REVERT: A 1265 PHE cc_start: 0.7193 (m-80) cc_final: 0.6660 (t80) REVERT: A 1274 CYS cc_start: 0.8134 (m) cc_final: 0.7799 (m) REVERT: A 1348 LEU cc_start: 0.7863 (OUTLIER) cc_final: 0.7602 (tp) REVERT: A 1364 ARG cc_start: 0.6650 (pmt-80) cc_final: 0.6086 (pmt-80) REVERT: A 1446 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8544 (mt) REVERT: A 1472 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.7854 (tt) REVERT: A 1497 TYR cc_start: 0.7796 (t80) cc_final: 0.7313 (t80) REVERT: A 1581 MET cc_start: 0.2908 (tpt) cc_final: 0.1327 (ttt) REVERT: A 1603 LEU cc_start: 0.9047 (mm) cc_final: 0.8759 (mm) REVERT: A 1613 ILE cc_start: 0.7232 (OUTLIER) cc_final: 0.6948 (mp) REVERT: A 1656 LEU cc_start: 0.8105 (OUTLIER) cc_final: 0.7867 (mm) REVERT: A 1729 TYR cc_start: 0.6199 (OUTLIER) cc_final: 0.5638 (p90) outliers start: 41 outliers final: 21 residues processed: 265 average time/residue: 0.1860 time to fit residues: 71.1149 Evaluate side-chains 254 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 224 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 327 CYS Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 722 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 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1348 LEU Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1424 MET Chi-restraints excluded: chain A residue 1446 LEU Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1472 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 50 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.175978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.143748 restraints weight = 17122.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.147692 restraints weight = 8337.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4123 r_free = 0.4123 target = 0.150262 restraints weight = 5436.150| |-----------------------------------------------------------------------------| r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.3531 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= 0.186 Angle : 0.814 13.830 13141 Z= 0.384 Chirality : 0.048 0.455 1547 Planarity : 0.004 0.038 1541 Dihedral : 14.364 169.441 2043 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.85 % Favored : 93.06 % Rotamer: Outliers : 4.32 % Allowed : 28.35 % Favored : 67.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.26), residues: 1110 helix: 0.51 (0.18), residues: 795 sheet: -3.19 (1.22), residues: 10 loop : -1.51 (0.40), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1442 HIS 0.005 0.001 HIS A 351 PHE 0.025 0.002 PHE A 785 TYR 0.018 0.002 TYR A 163 ARG 0.008 0.001 ARG A1640 Details of bonding type rmsd link_NAG-ASN : bond 0.01375 ( 5) link_NAG-ASN : angle 5.97814 ( 15) link_BETA1-4 : bond 0.00619 ( 4) link_BETA1-4 : angle 2.79373 ( 12) hydrogen bonds : bond 0.04395 ( 599) hydrogen bonds : angle 5.09288 ( 1737) SS BOND : bond 0.00387 ( 3) SS BOND : angle 1.52615 ( 6) covalent geometry : bond 0.00419 ( 9670) covalent geometry : angle 0.78482 (13108) Misc. bond : bond 0.00091 ( 3) *********************** 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: 41 poor density : 236 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8614 (tptt) cc_final: 0.8125 (mttm) REVERT: A 160 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.5269 (m-80) REVERT: A 174 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7768 (mt) REVERT: A 400 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7186 (mm) REVERT: A 404 TYR cc_start: 0.7521 (t80) cc_final: 0.7160 (t80) REVERT: A 422 GLN cc_start: 0.7083 (mt0) cc_final: 0.6786 (pp30) REVERT: A 705 MET cc_start: 0.8028 (mmm) cc_final: 0.7754 (mmp) REVERT: A 1215 PHE cc_start: 0.7205 (OUTLIER) cc_final: 0.6529 (t80) REVERT: A 1265 PHE cc_start: 0.7197 (m-80) cc_final: 0.6627 (t80) REVERT: A 1274 CYS cc_start: 0.8162 (m) cc_final: 0.7810 (m) REVERT: A 1313 LEU cc_start: 0.8669 (mp) cc_final: 0.8464 (mp) REVERT: A 1446 LEU cc_start: 0.8873 (tt) cc_final: 0.8604 (mt) REVERT: A 1472 ILE cc_start: 0.8032 (OUTLIER) cc_final: 0.7807 (tt) REVERT: A 1497 TYR cc_start: 0.7849 (t80) cc_final: 0.7364 (t80) REVERT: A 1656 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7980 (mm) REVERT: A 1708 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7980 (pt0) REVERT: A 1729 TYR cc_start: 0.6543 (OUTLIER) cc_final: 0.5841 (p90) outliers start: 41 outliers final: 26 residues processed: 262 average time/residue: 0.2173 time to fit residues: 83.7885 Evaluate side-chains 256 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 222 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1275 TRP Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 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 1472 ILE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1624 PHE 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 26 optimal weight: 0.6980 chunk 31 optimal weight: 8.9990 chunk 111 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 0.0010 overall best weight: 0.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.180439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.150107 restraints weight = 16878.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.152817 restraints weight = 9707.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.156044 restraints weight = 5868.861| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.3897 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= 0.136 Angle : 0.796 15.836 13141 Z= 0.373 Chirality : 0.045 0.366 1547 Planarity : 0.004 0.040 1541 Dihedral : 13.791 169.404 2043 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.86 % Favored : 94.05 % Rotamer: Outliers : 3.69 % Allowed : 29.82 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.26), residues: 1110 helix: 0.71 (0.18), residues: 787 sheet: -3.17 (1.17), residues: 10 loop : -1.53 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1347 HIS 0.003 0.001 HIS A 152 PHE 0.024 0.001 PHE A 785 TYR 0.016 0.001 TYR A 163 ARG 0.003 0.000 ARG A 881 Details of bonding type rmsd link_NAG-ASN : bond 0.01237 ( 5) link_NAG-ASN : angle 5.80571 ( 15) link_BETA1-4 : bond 0.00939 ( 4) link_BETA1-4 : angle 2.86230 ( 12) hydrogen bonds : bond 0.04264 ( 599) hydrogen bonds : angle 4.98555 ( 1737) SS BOND : bond 0.00255 ( 3) SS BOND : angle 1.24290 ( 6) covalent geometry : bond 0.00279 ( 9670) covalent geometry : angle 0.76752 (13108) Misc. bond : bond 0.00102 ( 3) *********************** 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 266 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 159 LYS cc_start: 0.8543 (tptt) cc_final: 0.8126 (mttm) REVERT: A 160 TYR cc_start: 0.6118 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: A 174 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7595 (mt) REVERT: A 382 THR cc_start: 0.8282 (m) cc_final: 0.8038 (m) REVERT: A 422 GLN cc_start: 0.7305 (mt0) cc_final: 0.6894 (pp30) REVERT: A 705 MET cc_start: 0.8127 (mmm) cc_final: 0.7856 (mmp) REVERT: A 794 LEU cc_start: 0.8786 (mt) cc_final: 0.8022 (tp) REVERT: A 1211 THR cc_start: 0.7756 (m) cc_final: 0.7413 (t) REVERT: A 1215 PHE cc_start: 0.7159 (OUTLIER) cc_final: 0.6478 (t80) REVERT: A 1265 PHE cc_start: 0.7076 (m-80) cc_final: 0.6512 (t80) REVERT: A 1274 CYS cc_start: 0.8135 (m) cc_final: 0.7793 (m) REVERT: A 1313 LEU cc_start: 0.8616 (mp) cc_final: 0.8344 (tt) REVERT: A 1446 LEU cc_start: 0.8816 (tt) cc_final: 0.8539 (mt) REVERT: A 1472 ILE cc_start: 0.7949 (OUTLIER) cc_final: 0.7733 (tt) REVERT: A 1497 TYR cc_start: 0.7880 (t80) cc_final: 0.7336 (t80) REVERT: A 1603 LEU cc_start: 0.8869 (mm) cc_final: 0.8633 (mm) REVERT: A 1613 ILE cc_start: 0.7173 (OUTLIER) cc_final: 0.6894 (mp) REVERT: A 1729 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.5831 (p90) outliers start: 35 outliers final: 23 residues processed: 255 average time/residue: 0.2094 time to fit residues: 78.8119 Evaluate side-chains 251 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 222 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1226 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 1293 LEU Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1366 ILE Chi-restraints excluded: chain A residue 1384 SER Chi-restraints excluded: chain A residue 1452 PHE Chi-restraints excluded: chain A residue 1472 ILE Chi-restraints excluded: chain A residue 1487 ILE Chi-restraints excluded: chain A residue 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 64 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 74 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.178845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.146808 restraints weight = 17137.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.150824 restraints weight = 8277.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.153422 restraints weight = 5367.219| |-----------------------------------------------------------------------------| r_work (final): 0.4162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9685 Z= 0.153 Angle : 0.806 14.919 13141 Z= 0.379 Chirality : 0.046 0.360 1547 Planarity : 0.004 0.038 1541 Dihedral : 13.429 169.768 2043 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.13 % Favored : 93.78 % Rotamer: Outliers : 3.27 % Allowed : 30.24 % Favored : 66.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1110 helix: 0.69 (0.18), residues: 787 sheet: -3.16 (1.16), residues: 10 loop : -1.51 (0.38), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1347 HIS 0.003 0.001 HIS A 883 PHE 0.025 0.001 PHE A 785 TYR 0.024 0.002 TYR A 163 ARG 0.008 0.000 ARG A1640 Details of bonding type rmsd link_NAG-ASN : bond 0.01168 ( 5) link_NAG-ASN : angle 5.73393 ( 15) link_BETA1-4 : bond 0.00863 ( 4) link_BETA1-4 : angle 2.90231 ( 12) hydrogen bonds : bond 0.04335 ( 599) hydrogen bonds : angle 5.01218 ( 1737) SS BOND : bond 0.00318 ( 3) SS BOND : angle 1.26089 ( 6) covalent geometry : bond 0.00340 ( 9670) covalent geometry : angle 0.77748 (13108) Misc. bond : bond 0.00088 ( 3) ********************** 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 258 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 227 time to evaluate : 2.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 TYR cc_start: 0.6409 (OUTLIER) cc_final: 0.5170 (m-80) REVERT: A 162 GLU cc_start: 0.8778 (pt0) cc_final: 0.8567 (pt0) REVERT: A 174 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7406 (mt) REVERT: A 422 GLN cc_start: 0.7111 (mt0) cc_final: 0.6749 (pp30) REVERT: A 705 MET cc_start: 0.8055 (mmm) cc_final: 0.7826 (mmp) REVERT: A 1211 THR cc_start: 0.7750 (m) cc_final: 0.7394 (t) REVERT: A 1215 PHE cc_start: 0.7276 (OUTLIER) cc_final: 0.6554 (t80) REVERT: A 1265 PHE cc_start: 0.7159 (m-80) cc_final: 0.6642 (t80) REVERT: A 1274 CYS cc_start: 0.8125 (m) cc_final: 0.7792 (m) REVERT: A 1313 LEU cc_start: 0.8692 (mp) cc_final: 0.8442 (mp) REVERT: A 1446 LEU cc_start: 0.8891 (tt) cc_final: 0.8630 (mt) REVERT: A 1497 TYR cc_start: 0.7804 (t80) cc_final: 0.7277 (t80) REVERT: A 1613 ILE cc_start: 0.7149 (OUTLIER) cc_final: 0.6849 (mp) REVERT: A 1729 TYR cc_start: 0.6416 (OUTLIER) cc_final: 0.5834 (p90) outliers start: 31 outliers final: 23 residues processed: 249 average time/residue: 0.1968 time to fit residues: 73.0584 Evaluate side-chains 253 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 1.005 ------------------------------------------------------------------------------- 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 325 LEU Chi-restraints excluded: chain A residue 327 CYS Chi-restraints excluded: chain A residue 330 SER Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 816 VAL Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 1215 PHE Chi-restraints excluded: chain A residue 1260 TRP Chi-restraints excluded: chain A residue 1261 VAL Chi-restraints excluded: chain A residue 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 1613 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1708 GLN Chi-restraints excluded: chain A residue 1729 TYR Chi-restraints excluded: chain A residue 1744 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 43 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 103 optimal weight: 1.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** A1465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.177464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.146929 restraints weight = 17028.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.149480 restraints weight = 9501.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.149845 restraints weight = 5882.352| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3861 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= 0.169 Angle : 0.815 15.072 13141 Z= 0.384 Chirality : 0.047 0.371 1547 Planarity : 0.004 0.040 1541 Dihedral : 13.130 169.442 2043 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.67 % Favored : 93.24 % Rotamer: Outliers : 4.00 % Allowed : 30.35 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.09 % Twisted Proline : 3.45 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.26), residues: 1110 helix: 0.61 (0.18), residues: 787 sheet: -3.22 (1.16), residues: 10 loop : -1.46 (0.39), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.003 0.001 HIS A 351 PHE 0.025 0.002 PHE A 785 TYR 0.017 0.001 TYR A 417 ARG 0.004 0.000 ARG A 384 Details of bonding type rmsd link_NAG-ASN : bond 0.01132 ( 5) link_NAG-ASN : angle 5.70413 ( 15) link_BETA1-4 : bond 0.00926 ( 4) link_BETA1-4 : angle 2.99967 ( 12) hydrogen bonds : bond 0.04413 ( 599) hydrogen bonds : angle 5.02994 ( 1737) SS BOND : bond 0.00353 ( 3) SS BOND : angle 1.36119 ( 6) covalent geometry : bond 0.00380 ( 9670) covalent geometry : angle 0.78745 (13108) Misc. bond : bond 0.00090 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3644.33 seconds wall clock time: 65 minutes 48.54 seconds (3948.54 seconds total)