Starting phenix.real_space_refine on Fri Jul 3 00:21:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6l_41071/07_2026/8t6l_41071.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6l_41071/07_2026/8t6l_41071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t6l_41071/07_2026/8t6l_41071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6l_41071/07_2026/8t6l_41071.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6l_41071/07_2026/8t6l_41071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6l_41071/07_2026/8t6l_41071.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.024 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 10 5.49 5 S 74 5.16 5 C 7380 2.51 5 N 1597 2.21 5 O 1927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10988 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 9905 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1237, 9897 Classifications: {'peptide': 1237} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1197} Chain breaks: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 1237, 9897 Classifications: {'peptide': 1237} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 1197} Chain breaks: 4 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 59 Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 10130 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 916 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 916 Unusual residues: {'9Z9': 2, 'LBN': 10, 'NAG': 3, 'Y01': 11, 'YIJ': 2} Classifications: {'undetermined': 28, 'water': 1} Link IDs: {None: 28} Unresolved non-hydrogen bonds: 189 Unresolved non-hydrogen angles: 208 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'LBN:plan-3': 6, 'LBN:plan-1': 1} Unresolved non-hydrogen planarities: 21 Time building chain proxies: 3.21, per 1000 atoms: 0.29 Number of scatterers: 10988 At special positions: 0 Unit cell: (128.778, 128.778, 114.745, 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 74 16.00 P 10 15.00 O 1927 8.00 N 1597 7.00 C 7380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 336 " distance=2.03 Simple disulfide: pdb=" SG CYS A 327 " - pdb=" SG CYS A 342 " distance=2.03 Simple disulfide: pdb=" SG CYS A 909 " - pdb=" SG CYS A 918 " distance=2.03 Simple disulfide: pdb=" SG CYS A1365 " - pdb=" SG CYS A1386 " distance=2.03 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=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA E 3 " - " MAN E 4 " " MAN E 4 " - " MAN E 5 " BETA1-3 " NAG B 1 " - " NAG B 2 " BETA1-4 " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG A3001 " - " ASN A 284 " " NAG A3002 " - " ASN A 319 " " NAG A3003 " - " ASN A1376 " " NAG B 1 " - " ASN A 329 " " NAG C 1 " - " ASN A1367 " " NAG D 1 " - " ASN A1382 " " NAG E 1 " - " ASN A1390 " Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 671.5 milliseconds 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2336 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 4 sheets defined 75.4% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 17 through 32 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 66 through 70 removed outlier: 3.653A pdb=" N TYR A 69 " --> pdb=" O PRO A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 114 Processing helix chain 'A' and resid 119 through 131 Processing helix chain 'A' and resid 131 through 149 removed outlier: 3.503A pdb=" N SER A 135 " --> pdb=" O HIS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 158 through 181 removed outlier: 3.557A pdb=" N GLY A 181 " --> pdb=" O ILE A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.971A pdb=" N ASP A 192 " --> pdb=" O PHE A 189 " (cutoff:3.500A) Proline residue: A 193 - end of helix Processing helix chain 'A' and resid 194 through 210 removed outlier: 4.157A pdb=" N ASP A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 227 removed outlier: 3.570A pdb=" N LEU A 219 " --> pdb=" O VAL A 216 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG A 220 " --> pdb=" O SER A 217 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE A 222 " --> pdb=" O LEU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 234 removed outlier: 3.821A pdb=" N SER A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 250 removed outlier: 3.545A pdb=" N LYS A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 239 " --> pdb=" O SER A 235 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 273 Processing helix chain 'A' and resid 275 through 279 removed outlier: 3.530A pdb=" N ARG A 278 " --> pdb=" O GLY A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 311 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.956A pdb=" N LEU A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.962A 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 removed outlier: 3.774A pdb=" N PHE A 394 " --> pdb=" O TYR A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 435 removed outlier: 3.502A pdb=" N THR A 428 " --> pdb=" O THR A 424 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 717 removed outlier: 3.535A pdb=" N ASP A 717 " --> pdb=" O PHE A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 735 removed outlier: 3.616A pdb=" N ASP A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 772 removed outlier: 3.735A pdb=" N LEU A 755 " --> pdb=" O GLN A 751 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE A 770 " --> pdb=" O THR A 766 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU A 772 " --> pdb=" O LYS A 768 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 779 removed outlier: 4.204A pdb=" N PHE A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 779 " --> pdb=" O TYR A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 800 Processing helix chain 'A' and resid 807 through 822 removed outlier: 3.561A pdb=" N ARG A 812 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 813 " --> pdb=" O SER A 810 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 821 " --> pdb=" O LYS A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 838 removed outlier: 3.563A pdb=" N ASN A 827 " --> pdb=" O TRP A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 862 removed outlier: 3.561A pdb=" N GLY A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLN A 860 " --> pdb=" O VAL A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 870 through 873 Processing helix chain 'A' and resid 886 through 899 Processing helix chain 'A' and resid 902 through 911 removed outlier: 4.100A pdb=" N ASP A 908 " --> pdb=" O GLU A 904 " (cutoff:3.500A) Processing helix chain 'A' and resid 914 through 944 Processing helix chain 'A' and resid 1191 through 1206 Processing helix chain 'A' and resid 1206 through 1225 removed outlier: 3.914A pdb=" N ALA A1225 " --> pdb=" O SER A1221 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1263 removed outlier: 3.832A pdb=" N VAL A1239 " --> pdb=" O LYS A1235 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LEU A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A1253 " --> pdb=" O THR A1249 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1270 Processing helix chain 'A' and resid 1271 through 1293 Processing helix chain 'A' and resid 1298 through 1307 removed outlier: 3.553A pdb=" N LYS A1302 " --> pdb=" O MET A1298 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N THR A1306 " --> pdb=" O LYS A1302 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1308 through 1316 Proline residue: A1312 - end of helix Processing helix chain 'A' and resid 1319 through 1332 removed outlier: 3.997A pdb=" N VAL A1325 " --> pdb=" O GLY A1321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A1331 " --> pdb=" O ASN A1327 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA A1332 " --> pdb=" O ALA A1328 " (cutoff:3.500A) Processing helix chain 'A' and resid 1332 through 1358 removed outlier: 3.791A pdb=" N PHE A1350 " --> pdb=" O PHE A1346 " (cutoff:3.500A) Processing helix chain 'A' and resid 1382 through 1389 Processing helix chain 'A' and resid 1406 through 1420 removed outlier: 3.946A pdb=" N LEU A1412 " --> pdb=" O GLY A1408 " (cutoff:3.500A) Processing helix chain 'A' and resid 1423 through 1431 removed outlier: 3.598A pdb=" N ALA A1429 " --> pdb=" O ASP A1425 " (cutoff:3.500A) 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 1460 removed outlier: 3.777A pdb=" N PHE A1452 " --> pdb=" O MET A1448 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1482 Processing helix chain 'A' and resid 1490 through 1504 removed outlier: 3.631A pdb=" N LEU A1503 " --> pdb=" O ALA A1499 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY A1504 " --> pdb=" O MET A1500 " (cutoff:3.500A) Processing helix chain 'A' and resid 1518 through 1529 removed outlier: 3.626A pdb=" N LYS A1529 " --> pdb=" O ASP A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1549 removed outlier: 4.025A pdb=" N ASP A1533 " --> pdb=" O LYS A1529 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET A1547 " --> pdb=" O ASN A1543 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N MET A1548 " --> pdb=" O MET A1544 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A1549 " --> pdb=" O VAL A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1555 through 1585 Processing helix chain 'A' and resid 1592 through 1617 removed outlier: 3.557A pdb=" N PHE A1596 " --> pdb=" O SER A1592 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A1597 " --> pdb=" O TRP A1593 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A1598 " --> pdb=" O ASN A1594 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ASP A1612 " --> pdb=" O THR A1608 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1630 removed outlier: 3.730A pdb=" N VAL A1626 " --> pdb=" O THR A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1631 through 1636 removed outlier: 4.339A pdb=" N ILE A1635 " --> pdb=" O ARG A1631 " (cutoff:3.500A) Processing helix chain 'A' and resid 1637 through 1640 removed outlier: 3.654A pdb=" N ARG A1640 " --> pdb=" O ARG A1637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1637 through 1640' Processing helix chain 'A' and resid 1642 through 1681 Proline residue: A1657 - end of helix removed outlier: 3.542A pdb=" N LEU A1665 " --> pdb=" O ASN A1661 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1711 removed outlier: 3.939A pdb=" N THR A1711 " --> pdb=" O PHE A1707 " (cutoff:3.500A) Processing helix chain 'A' and resid 1714 through 1724 removed outlier: 3.554A pdb=" N LEU A1718 " --> pdb=" O GLY A1714 " (cutoff:3.500A) Proline residue: A1721 - end of helix removed outlier: 3.529A pdb=" N ASN A1724 " --> pdb=" O SER A1720 " (cutoff:3.500A) Processing helix chain 'A' and resid 1746 through 1780 removed outlier: 3.511A pdb=" N LEU A1752 " --> pdb=" O ALA A1748 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE A1772 " --> pdb=" O MET A1768 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE A1773 " --> pdb=" O TYR A1769 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 63 through 64 removed outlier: 4.118A pdb=" N LYS A 63 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 94 " --> pdb=" O PHE A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 280 through 283 Processing sheet with id=AA3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AA4, first strand: chain 'A' and resid 1371 through 1374 removed outlier: 4.197A pdb=" N ASN A1367 " --> pdb=" O GLY A1371 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LEU A1373 " --> pdb=" O CYS A1365 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N CYS A1365 " --> pdb=" O LEU A1373 " (cutoff:3.500A) 641 hydrogen bonds defined for protein. 1820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 0.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1594 1.32 - 1.44: 3026 1.44 - 1.57: 6513 1.57 - 1.69: 21 1.69 - 1.81: 123 Bond restraints: 11277 Sorted by residual: bond pdb=" C9 LBN A3010 " pdb=" O2 LBN A3010 " ideal model delta sigma weight residual 1.409 1.457 -0.048 2.00e-02 2.50e+03 5.87e+00 bond pdb=" C1 LBN A3012 " pdb=" O1 LBN A3012 " ideal model delta sigma weight residual 1.410 1.458 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C9 LBN A3008 " pdb=" O2 LBN A3008 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C9 LBN A3007 " pdb=" O2 LBN A3007 " ideal model delta sigma weight residual 1.409 1.456 -0.047 2.00e-02 2.50e+03 5.41e+00 bond pdb=" C9 LBN A3009 " pdb=" O2 LBN A3009 " ideal model delta sigma weight residual 1.409 1.455 -0.046 2.00e-02 2.50e+03 5.28e+00 ... (remaining 11272 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 14968 2.05 - 4.10: 314 4.10 - 6.16: 52 6.16 - 8.21: 6 8.21 - 10.26: 13 Bond angle restraints: 15353 Sorted by residual: angle pdb=" CA GLU A 30 " pdb=" CB GLU A 30 " pdb=" CG GLU A 30 " ideal model delta sigma weight residual 114.10 121.67 -7.57 2.00e+00 2.50e-01 1.43e+01 angle pdb=" CA GLN A 780 " pdb=" CB GLN A 780 " pdb=" CG GLN A 780 " ideal model delta sigma weight residual 114.10 121.14 -7.04 2.00e+00 2.50e-01 1.24e+01 angle pdb=" O1 LBN A3006 " pdb=" P1 LBN A3006 " pdb=" O2 LBN A3006 " ideal model delta sigma weight residual 93.45 103.71 -10.26 3.00e+00 1.11e-01 1.17e+01 angle pdb=" O1 LBN A3004 " pdb=" P1 LBN A3004 " pdb=" O2 LBN A3004 " ideal model delta sigma weight residual 93.45 103.62 -10.17 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O1 LBN A3012 " pdb=" P1 LBN A3012 " pdb=" O2 LBN A3012 " ideal model delta sigma weight residual 93.45 103.04 -9.59 3.00e+00 1.11e-01 1.02e+01 ... (remaining 15348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.77: 7315 34.77 - 69.54: 316 69.54 - 104.31: 48 104.31 - 139.07: 45 139.07 - 173.84: 8 Dihedral angle restraints: 7732 sinusoidal: 4117 harmonic: 3615 Sorted by residual: dihedral pdb=" CB CYS A 909 " pdb=" SG CYS A 909 " pdb=" SG CYS A 918 " pdb=" CB CYS A 918 " ideal model delta sinusoidal sigma weight residual 93.00 144.35 -51.35 1 1.00e+01 1.00e-02 3.60e+01 dihedral pdb=" C13 YIJ A3027 " pdb=" C30 YIJ A3027 " pdb=" O6 YIJ A3027 " pdb=" C29 YIJ A3027 " ideal model delta sinusoidal sigma weight residual 99.76 -86.40 -173.84 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C1 YIJ A3027 " pdb=" C6 YIJ A3027 " pdb=" C7 YIJ A3027 " pdb=" O2 YIJ A3027 " ideal model delta sinusoidal sigma weight residual -156.57 6.40 -162.97 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 7729 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1560 0.056 - 0.112: 216 0.112 - 0.168: 15 0.168 - 0.224: 8 0.224 - 0.279: 4 Chirality restraints: 1803 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O3 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-02 2.50e+03 7.30e+01 chirality pdb=" C16 YIJ A3027 " pdb=" C15 YIJ A3027 " pdb=" C17 YIJ A3027 " pdb=" O3 YIJ A3027 " both_signs ideal model delta sigma weight residual False 2.66 2.38 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CBB Y01 A3019 " pdb=" CAC Y01 A3019 " pdb=" CAO Y01 A3019 " pdb=" CBE Y01 A3019 " both_signs ideal model delta sigma weight residual False 2.58 2.33 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1800 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A3001 " 0.334 2.00e-02 2.50e+03 2.84e-01 1.00e+03 pdb=" C7 NAG A3001 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG A3001 " 0.181 2.00e-02 2.50e+03 pdb=" N2 NAG A3001 " -0.496 2.00e-02 2.50e+03 pdb=" O7 NAG A3001 " 0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 2 " 0.323 2.00e-02 2.50e+03 2.78e-01 9.67e+02 pdb=" C7 NAG C 2 " -0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG C 2 " -0.482 2.00e-02 2.50e+03 pdb=" O7 NAG C 2 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.327 2.00e-02 2.50e+03 2.77e-01 9.56e+02 pdb=" C7 NAG B 1 " 0.084 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.186 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.481 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.053 2.00e-02 2.50e+03 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 263 2.71 - 3.26: 11276 3.26 - 3.81: 16726 3.81 - 4.35: 21216 4.35 - 4.90: 35688 Nonbonded interactions: 85169 Sorted by model distance: nonbonded pdb=" OE1 GLN A 780 " pdb=" N GLY A 781 " model vdw 2.167 3.120 nonbonded pdb=" O VAL A 807 " pdb=" OG SER A 810 " model vdw 2.276 3.040 nonbonded pdb=" OH TYR A 740 " pdb=" OE2 GLU A1437 " model vdw 2.278 3.040 nonbonded pdb=" O SER A 62 " pdb=" OG SER A 62 " model vdw 2.278 3.040 nonbonded pdb=" ND2 ASN A1591 " pdb=" OD1 ASN A1594 " model vdw 2.295 3.120 ... (remaining 85164 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 'C' 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.710 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.780 Find NCS groups from input model: 0.070 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: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.005 0.048 11298 Z= 0.250 Angle : 0.711 10.259 15411 Z= 0.292 Chirality : 0.041 0.279 1803 Planarity : 0.020 0.284 1756 Dihedral : 21.675 173.843 5381 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.09 % Allowed : 29.71 % Favored : 70.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.24), residues: 1228 helix: 0.89 (0.18), residues: 809 sheet: -2.79 (0.81), residues: 34 loop : -0.53 (0.34), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1628 TYR 0.017 0.001 TYR A 417 PHE 0.017 0.001 PHE A 106 TRP 0.021 0.001 TRP A 157 HIS 0.002 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.25 (11277) covalent geometry : angle 0.70470 / 0.29 (15353) SS BOND : bond 0.00226 / 0.13 ( 5) SS BOND : angle 0.62584 / 0.38 ( 10) hydrogen bonds : bond 0.23798 / 15.37 ( 641) hydrogen bonds : angle 6.57100 / 4.67 ( 1820) link_ALPHA1-3 : bond 0.00149 / 0.08 ( 1) link_ALPHA1-3 : angle 0.71867 / 0.38 ( 3) link_ALPHA1-6 : bond 0.00599 / 0.31 ( 2) link_ALPHA1-6 : angle 1.04526 / 0.56 ( 6) link_BETA1-3 : bond 0.00261 / 0.14 ( 1) link_BETA1-3 : angle 1.84483 / 1.01 ( 3) link_BETA1-4 : bond 0.00526 / 0.27 ( 5) link_BETA1-4 : angle 2.05340 / 1.36 ( 15) link_NAG-ASN : bond 0.00292 / 0.22 ( 7) link_NAG-ASN : angle 1.82814 / 1.39 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 112 time to evaluate : 0.228 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 112 average time/residue: 0.0722 time to fit residues: 12.2905 Evaluate side-chains 112 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 111 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.179836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.146705 restraints weight = 16570.992| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 1.88 r_work: 0.3562 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3547 r_free = 0.3547 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.3547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11298 Z= 0.133 Angle : 0.641 9.485 15411 Z= 0.294 Chirality : 0.040 0.251 1803 Planarity : 0.004 0.039 1756 Dihedral : 18.675 176.632 3111 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.41 % Allowed : 26.46 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.24), residues: 1228 helix: 1.35 (0.18), residues: 829 sheet: -2.68 (0.82), residues: 34 loop : -0.71 (0.34), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1628 TYR 0.016 0.001 TYR A 417 PHE 0.014 0.001 PHE A1753 TRP 0.017 0.001 TRP A 157 HIS 0.003 0.001 HIS A1206 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.13 (11277) covalent geometry : angle 0.62638 / 0.29 (15353) SS BOND : bond 0.00310 / 0.21 ( 5) SS BOND : angle 1.12264 / 0.72 ( 10) hydrogen bonds : bond 0.05531 / 3.69 ( 641) hydrogen bonds : angle 4.32452 / 3.03 ( 1820) link_ALPHA1-3 : bond 0.01142 / 0.60 ( 1) link_ALPHA1-3 : angle 2.03798 / 1.10 ( 3) link_ALPHA1-6 : bond 0.01379 / 0.70 ( 2) link_ALPHA1-6 : angle 1.49408 / 0.85 ( 6) link_BETA1-3 : bond 0.00932 / 0.49 ( 1) link_BETA1-3 : angle 2.54594 / 1.34 ( 3) link_BETA1-4 : bond 0.00951 / 0.58 ( 5) link_BETA1-4 : angle 3.10015 / 2.22 ( 15) link_NAG-ASN : bond 0.00437 / 0.24 ( 7) link_NAG-ASN : angle 2.24053 / 1.69 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 0.349 Fit side-chains REVERT: A 228 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (mt) REVERT: A 740 TYR cc_start: 0.8120 (t80) cc_final: 0.7784 (t80) REVERT: A 1544 MET cc_start: 0.8037 (ttt) cc_final: 0.7731 (ttt) REVERT: A 1693 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8608 (mtp) outliers start: 26 outliers final: 14 residues processed: 142 average time/residue: 0.0722 time to fit residues: 16.1315 Evaluate side-chains 139 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 735 MET Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 795 MET Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1693 MET Chi-restraints excluded: chain A residue 1703 MET Chi-restraints excluded: chain A residue 1779 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 6.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 915 GLN ** A1724 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 = 0.4163 r_free = 0.4163 target = 0.177619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144005 restraints weight = 17153.884| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 1.83 r_work: 0.3536 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3526 r_free = 0.3526 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11298 Z= 0.135 Angle : 0.603 10.448 15411 Z= 0.278 Chirality : 0.039 0.228 1803 Planarity : 0.003 0.037 1756 Dihedral : 16.904 177.763 3108 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.88 % Allowed : 26.37 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.24), residues: 1228 helix: 1.54 (0.18), residues: 832 sheet: -2.58 (0.83), residues: 34 loop : -0.87 (0.35), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.015 0.001 TYR A 417 PHE 0.019 0.001 PHE A1753 TRP 0.018 0.001 TRP A 157 HIS 0.003 0.001 HIS A1206 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (11277) covalent geometry : angle 0.58447 / 0.27 (15353) SS BOND : bond 0.00321 / 0.20 ( 5) SS BOND : angle 0.92260 / 0.56 ( 10) hydrogen bonds : bond 0.04653 / 3.06 ( 641) hydrogen bonds : angle 4.04198 / 2.82 ( 1820) link_ALPHA1-3 : bond 0.00980 / 0.52 ( 1) link_ALPHA1-3 : angle 1.45081 / 0.79 ( 3) link_ALPHA1-6 : bond 0.01298 / 0.63 ( 2) link_ALPHA1-6 : angle 1.88309 / 1.00 ( 6) link_BETA1-3 : bond 0.01578 / 0.83 ( 1) link_BETA1-3 : angle 3.93258 / 2.07 ( 3) link_BETA1-4 : bond 0.00664 / 0.34 ( 5) link_BETA1-4 : angle 3.01233 / 2.07 ( 15) link_NAG-ASN : bond 0.00261 / 0.16 ( 7) link_NAG-ASN : angle 2.57929 / 1.84 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 0.264 Fit side-chains revert: symmetry clash REVERT: A 1544 MET cc_start: 0.8063 (ttt) cc_final: 0.7803 (ttt) REVERT: A 1703 MET cc_start: 0.7806 (OUTLIER) cc_final: 0.7601 (tpt) outliers start: 31 outliers final: 16 residues processed: 144 average time/residue: 0.0750 time to fit residues: 16.6577 Evaluate side-chains 135 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1691 ASP Chi-restraints excluded: chain A residue 1703 MET Chi-restraints excluded: chain A residue 1779 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 3 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.0000 chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.179359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.146862 restraints weight = 19045.398| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.14 r_work: 0.3538 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11298 Z= 0.113 Angle : 0.567 10.280 15411 Z= 0.261 Chirality : 0.038 0.260 1803 Planarity : 0.003 0.037 1756 Dihedral : 16.066 176.759 3108 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 2.32 % Allowed : 27.30 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.25), residues: 1228 helix: 1.59 (0.18), residues: 843 sheet: -2.59 (0.82), residues: 34 loop : -0.93 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1628 TYR 0.016 0.001 TYR A 417 PHE 0.015 0.001 PHE A1753 TRP 0.014 0.001 TRP A 157 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (11277) covalent geometry : angle 0.54969 / 0.26 (15353) SS BOND : bond 0.00261 / 0.16 ( 5) SS BOND : angle 0.79571 / 0.48 ( 10) hydrogen bonds : bond 0.04002 / 2.63 ( 641) hydrogen bonds : angle 3.88913 / 2.70 ( 1820) link_ALPHA1-3 : bond 0.00978 / 0.51 ( 1) link_ALPHA1-3 : angle 1.52233 / 0.84 ( 3) link_ALPHA1-6 : bond 0.01059 / 0.52 ( 2) link_ALPHA1-6 : angle 1.60194 / 0.91 ( 6) link_BETA1-3 : bond 0.01517 / 0.80 ( 1) link_BETA1-3 : angle 4.12260 / 2.19 ( 3) link_BETA1-4 : bond 0.00651 / 0.36 ( 5) link_BETA1-4 : angle 2.92575 / 2.07 ( 15) link_NAG-ASN : bond 0.00280 / 0.19 ( 7) link_NAG-ASN : angle 2.31094 / 1.68 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 119 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 1235 LYS cc_start: 0.7264 (mtmt) cc_final: 0.6964 (mmtp) REVERT: A 1298 MET cc_start: 0.7264 (mtp) cc_final: 0.7036 (mtp) REVERT: A 1544 MET cc_start: 0.8111 (ttt) cc_final: 0.7848 (ttt) outliers start: 25 outliers final: 13 residues processed: 134 average time/residue: 0.0781 time to fit residues: 15.9218 Evaluate side-chains 130 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 117 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1691 ASP Chi-restraints excluded: chain A residue 1703 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 4 optimal weight: 9.9990 chunk 93 optimal weight: 0.0980 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 51 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.146380 restraints weight = 19398.597| |-----------------------------------------------------------------------------| r_work (start): 0.3822 rms_B_bonded: 2.24 r_work: 0.3522 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.1756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11298 Z= 0.122 Angle : 0.572 10.953 15411 Z= 0.264 Chirality : 0.038 0.249 1803 Planarity : 0.003 0.036 1756 Dihedral : 15.720 177.245 3108 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.32 % Allowed : 27.30 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1228 helix: 1.58 (0.18), residues: 848 sheet: -2.57 (0.83), residues: 34 loop : -1.01 (0.35), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1628 TYR 0.015 0.001 TYR A 417 PHE 0.017 0.001 PHE A1753 TRP 0.013 0.001 TRP A 157 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (11277) covalent geometry : angle 0.55339 / 0.26 (15353) SS BOND : bond 0.00257 / 0.15 ( 5) SS BOND : angle 0.84213 / 0.49 ( 10) hydrogen bonds : bond 0.03948 / 2.60 ( 641) hydrogen bonds : angle 3.84832 / 2.67 ( 1820) link_ALPHA1-3 : bond 0.00954 / 0.50 ( 1) link_ALPHA1-3 : angle 1.35143 / 0.75 ( 3) link_ALPHA1-6 : bond 0.01147 / 0.56 ( 2) link_ALPHA1-6 : angle 1.57751 / 0.90 ( 6) link_BETA1-3 : bond 0.01685 / 0.89 ( 1) link_BETA1-3 : angle 4.41289 / 2.33 ( 3) link_BETA1-4 : bond 0.00691 / 0.37 ( 5) link_BETA1-4 : angle 2.97061 / 2.15 ( 15) link_NAG-ASN : bond 0.00256 / 0.17 ( 7) link_NAG-ASN : angle 2.38497 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 1235 LYS cc_start: 0.7299 (mtmt) cc_final: 0.6992 (mmtp) REVERT: A 1298 MET cc_start: 0.7262 (mtp) cc_final: 0.7024 (mtp) REVERT: A 1544 MET cc_start: 0.8157 (ttt) cc_final: 0.7920 (ttt) outliers start: 25 outliers final: 16 residues processed: 136 average time/residue: 0.0762 time to fit residues: 15.6710 Evaluate side-chains 135 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 119 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 790 VAL Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1691 ASP Chi-restraints excluded: chain A residue 1703 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 10 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 0.0070 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.178638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.144607 restraints weight = 16724.056| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.73 r_work: 0.3566 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3407 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3407 r_free = 0.3407 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3407 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11298 Z= 0.126 Angle : 0.585 10.901 15411 Z= 0.272 Chirality : 0.038 0.257 1803 Planarity : 0.003 0.035 1756 Dihedral : 15.389 177.351 3108 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 2.51 % Allowed : 27.11 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1228 helix: 1.59 (0.18), residues: 849 sheet: -2.61 (0.84), residues: 34 loop : -1.05 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1625 TYR 0.016 0.001 TYR A 417 PHE 0.017 0.001 PHE A1753 TRP 0.019 0.001 TRP A 157 HIS 0.003 0.001 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 (11277) covalent geometry : angle 0.56733 / 0.27 (15353) SS BOND : bond 0.00261 / 0.15 ( 5) SS BOND : angle 0.85597 / 0.50 ( 10) hydrogen bonds : bond 0.03896 / 2.56 ( 641) hydrogen bonds : angle 3.82986 / 2.66 ( 1820) link_ALPHA1-3 : bond 0.00898 / 0.47 ( 1) link_ALPHA1-3 : angle 1.24763 / 0.69 ( 3) link_ALPHA1-6 : bond 0.01111 / 0.54 ( 2) link_ALPHA1-6 : angle 1.52266 / 0.88 ( 6) link_BETA1-3 : bond 0.01747 / 0.92 ( 1) link_BETA1-3 : angle 4.49293 / 2.37 ( 3) link_BETA1-4 : bond 0.00698 / 0.38 ( 5) link_BETA1-4 : angle 3.00811 / 2.22 ( 15) link_NAG-ASN : bond 0.00270 / 0.18 ( 7) link_NAG-ASN : angle 2.37600 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 1235 LYS cc_start: 0.7254 (mtmt) cc_final: 0.6952 (mmtp) REVERT: A 1298 MET cc_start: 0.7226 (mtp) cc_final: 0.7002 (mtp) outliers start: 27 outliers final: 19 residues processed: 140 average time/residue: 0.0777 time to fit residues: 16.4705 Evaluate side-chains 141 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1237 ILE Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1691 ASP Chi-restraints excluded: chain A residue 1703 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.177058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.144582 restraints weight = 19052.614| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 2.26 r_work: 0.3500 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11298 Z= 0.145 Angle : 0.610 10.987 15411 Z= 0.282 Chirality : 0.039 0.244 1803 Planarity : 0.003 0.034 1756 Dihedral : 15.081 177.310 3108 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.14 % Allowed : 27.76 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.25), residues: 1228 helix: 1.57 (0.18), residues: 843 sheet: -2.51 (0.86), residues: 34 loop : -1.03 (0.35), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1625 TYR 0.018 0.001 TYR A 417 PHE 0.019 0.001 PHE A 106 TRP 0.018 0.001 TRP A 157 HIS 0.003 0.001 HIS A 883 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11277) covalent geometry : angle 0.59072 / 0.28 (15353) SS BOND : bond 0.00313 / 0.18 ( 5) SS BOND : angle 0.98030 / 0.57 ( 10) hydrogen bonds : bond 0.04004 / 2.63 ( 641) hydrogen bonds : angle 3.85798 / 2.68 ( 1820) link_ALPHA1-3 : bond 0.00858 / 0.45 ( 1) link_ALPHA1-3 : angle 1.16116 / 0.64 ( 3) link_ALPHA1-6 : bond 0.01042 / 0.51 ( 2) link_ALPHA1-6 : angle 1.50013 / 0.87 ( 6) link_BETA1-3 : bond 0.01821 / 0.96 ( 1) link_BETA1-3 : angle 4.74670 / 2.50 ( 3) link_BETA1-4 : bond 0.00749 / 0.40 ( 5) link_BETA1-4 : angle 3.19300 / 2.40 ( 15) link_NAG-ASN : bond 0.00315 / 0.20 ( 7) link_NAG-ASN : angle 2.43209 / 1.72 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.258 Fit side-chains REVERT: A 1235 LYS cc_start: 0.7235 (mtmt) cc_final: 0.7031 (mmtp) REVERT: A 1298 MET cc_start: 0.7226 (mtp) cc_final: 0.6985 (mtp) outliers start: 23 outliers final: 17 residues processed: 139 average time/residue: 0.0808 time to fit residues: 17.0681 Evaluate side-chains 137 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1282 ASP Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1691 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 20.0000 chunk 81 optimal weight: 0.0170 chunk 110 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 102 optimal weight: 0.9990 chunk 25 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.7222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.184745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.140237 restraints weight = 24888.343| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.21 r_work: 0.3540 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3380 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11298 Z= 0.117 Angle : 0.583 11.028 15411 Z= 0.270 Chirality : 0.038 0.224 1803 Planarity : 0.003 0.034 1756 Dihedral : 14.689 176.566 3108 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.14 % Allowed : 27.21 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.25), residues: 1228 helix: 1.63 (0.18), residues: 847 sheet: -2.51 (0.87), residues: 34 loop : -1.05 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1628 TYR 0.020 0.001 TYR A 417 PHE 0.016 0.001 PHE A1753 TRP 0.017 0.001 TRP A 157 HIS 0.002 0.001 HIS A1206 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (11277) covalent geometry : angle 0.56315 / 0.26 (15353) SS BOND : bond 0.00244 / 0.14 ( 5) SS BOND : angle 0.82715 / 0.48 ( 10) hydrogen bonds : bond 0.03767 / 2.48 ( 641) hydrogen bonds : angle 3.78296 / 2.63 ( 1820) link_ALPHA1-3 : bond 0.00906 / 0.48 ( 1) link_ALPHA1-3 : angle 1.23810 / 0.68 ( 3) link_ALPHA1-6 : bond 0.01033 / 0.50 ( 2) link_ALPHA1-6 : angle 1.39758 / 0.81 ( 6) link_BETA1-3 : bond 0.01951 / 1.03 ( 1) link_BETA1-3 : angle 4.77420 / 2.52 ( 3) link_BETA1-4 : bond 0.00766 / 0.41 ( 5) link_BETA1-4 : angle 3.22984 / 2.49 ( 15) link_NAG-ASN : bond 0.00290 / 0.20 ( 7) link_NAG-ASN : angle 2.39300 / 1.73 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.292 Fit side-chains REVERT: A 1235 LYS cc_start: 0.7388 (mtmt) cc_final: 0.6961 (mmtp) REVERT: A 1298 MET cc_start: 0.7018 (mtp) cc_final: 0.6768 (mtp) outliers start: 23 outliers final: 18 residues processed: 135 average time/residue: 0.0855 time to fit residues: 17.7364 Evaluate side-chains 134 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 772 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1691 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.183750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138534 restraints weight = 24020.665| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.25 r_work: 0.3526 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11298 Z= 0.136 Angle : 0.608 11.214 15411 Z= 0.282 Chirality : 0.039 0.227 1803 Planarity : 0.003 0.034 1756 Dihedral : 14.445 176.836 3108 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.97 % Favored : 94.95 % Rotamer: Outliers : 2.14 % Allowed : 27.39 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.24), residues: 1228 helix: 1.54 (0.18), residues: 853 sheet: -2.49 (0.87), residues: 34 loop : -1.09 (0.35), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1628 TYR 0.019 0.001 TYR A 417 PHE 0.018 0.001 PHE A1753 TRP 0.017 0.001 TRP A 157 HIS 0.003 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (11277) covalent geometry : angle 0.58734 / 0.28 (15353) SS BOND : bond 0.00293 / 0.16 ( 5) SS BOND : angle 0.92801 / 0.53 ( 10) hydrogen bonds : bond 0.03877 / 2.55 ( 641) hydrogen bonds : angle 3.80651 / 2.65 ( 1820) link_ALPHA1-3 : bond 0.00783 / 0.41 ( 1) link_ALPHA1-3 : angle 1.14254 / 0.63 ( 3) link_ALPHA1-6 : bond 0.01007 / 0.49 ( 2) link_ALPHA1-6 : angle 1.44536 / 0.84 ( 6) link_BETA1-3 : bond 0.01966 / 1.03 ( 1) link_BETA1-3 : angle 5.02057 / 2.65 ( 3) link_BETA1-4 : bond 0.00830 / 0.44 ( 5) link_BETA1-4 : angle 3.40808 / 2.66 ( 15) link_NAG-ASN : bond 0.00290 / 0.18 ( 7) link_NAG-ASN : angle 2.40235 / 1.71 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: A 1235 LYS cc_start: 0.7300 (mtmt) cc_final: 0.6925 (mmtp) REVERT: A 1298 MET cc_start: 0.7077 (mtp) cc_final: 0.6830 (mtp) outliers start: 23 outliers final: 20 residues processed: 140 average time/residue: 0.0771 time to fit residues: 16.7815 Evaluate side-chains 143 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 123 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 253 ASP Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 321 THR Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1213 ILE Chi-restraints excluded: chain A residue 1251 VAL Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1463 THR Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1503 LEU Chi-restraints excluded: chain A residue 1542 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1674 SER Chi-restraints excluded: chain A residue 1691 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 0.0050 chunk 7 optimal weight: 4.9990 chunk 59 optimal weight: 0.5980 chunk 2 optimal weight: 20.0000 chunk 111 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 8 optimal weight: 0.0570 chunk 53 optimal weight: 0.0870 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 overall best weight: 0.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.150480 restraints weight = 23279.121| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.38 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3864 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3864 r_free = 0.3864 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3864 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11298 Z= 0.104 Angle : 0.575 11.308 15411 Z= 0.266 Chirality : 0.037 0.212 1803 Planarity : 0.003 0.035 1756 Dihedral : 13.826 175.074 3108 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.48 % Favored : 95.44 % Rotamer: Outliers : 1.39 % Allowed : 27.95 % Favored : 70.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.25), residues: 1228 helix: 1.71 (0.18), residues: 852 sheet: -2.57 (0.86), residues: 34 loop : -0.95 (0.35), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1628 TYR 0.022 0.001 TYR A 417 PHE 0.012 0.001 PHE A1753 TRP 0.018 0.001 TRP A 157 HIS 0.006 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.10 (11277) covalent geometry : angle 0.55473 / 0.26 (15353) SS BOND : bond 0.00151 / 0.09 ( 5) SS BOND : angle 0.64078 / 0.37 ( 10) hydrogen bonds : bond 0.03482 / 2.28 ( 641) hydrogen bonds : angle 3.68629 / 2.56 ( 1820) link_ALPHA1-3 : bond 0.00721 / 0.38 ( 1) link_ALPHA1-3 : angle 1.21530 / 0.66 ( 3) link_ALPHA1-6 : bond 0.01067 / 0.53 ( 2) link_ALPHA1-6 : angle 1.31705 / 0.77 ( 6) link_BETA1-3 : bond 0.01897 / 1.00 ( 1) link_BETA1-3 : angle 4.89066 / 2.60 ( 3) link_BETA1-4 : bond 0.00887 / 0.46 ( 5) link_BETA1-4 : angle 3.32203 / 2.66 ( 15) link_NAG-ASN : bond 0.00344 / 0.24 ( 7) link_NAG-ASN : angle 2.34404 / 1.75 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2456 Ramachandran restraints generated. 1228 Oldfield, 0 Emsley, 1228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 126 time to evaluate : 0.475 Fit side-chains outliers start: 15 outliers final: 11 residues processed: 135 average time/residue: 0.0847 time to fit residues: 17.4604 Evaluate side-chains 133 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 122 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 204 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 885 MET Chi-restraints excluded: chain A residue 909 CYS Chi-restraints excluded: chain A residue 1358 PHE Chi-restraints excluded: chain A residue 1466 LEU Chi-restraints excluded: chain A residue 1567 LEU Chi-restraints excluded: chain A residue 1691 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 5 optimal weight: 0.0370 chunk 37 optimal weight: 0.7980 chunk 55 optimal weight: 0.5980 chunk 84 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1724 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.181319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.148552 restraints weight = 17922.138| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.91 r_work: 0.3590 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3570 r_free = 0.3570 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11298 Z= 0.105 Angle : 0.573 11.078 15411 Z= 0.266 Chirality : 0.037 0.214 1803 Planarity : 0.003 0.035 1756 Dihedral : 13.529 176.041 3108 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.40 % Favored : 95.52 % Rotamer: Outliers : 1.39 % Allowed : 28.13 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.25), residues: 1228 helix: 1.77 (0.18), residues: 845 sheet: -2.56 (0.85), residues: 34 loop : -0.86 (0.35), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1628 TYR 0.018 0.001 TYR A 417 PHE 0.017 0.001 PHE A 106 TRP 0.017 0.001 TRP A 157 HIS 0.004 0.001 HIS A 119 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (11277) covalent geometry : angle 0.55332 / 0.26 (15353) SS BOND : bond 0.00181 / 0.10 ( 5) SS BOND : angle 0.67100 / 0.38 ( 10) hydrogen bonds : bond 0.03441 / 2.26 ( 641) hydrogen bonds : angle 3.64866 / 2.54 ( 1820) link_ALPHA1-3 : bond 0.00697 / 0.37 ( 1) link_ALPHA1-3 : angle 1.22627 / 0.66 ( 3) link_ALPHA1-6 : bond 0.00980 / 0.48 ( 2) link_ALPHA1-6 : angle 1.37679 / 0.80 ( 6) link_BETA1-3 : bond 0.01886 / 0.99 ( 1) link_BETA1-3 : angle 4.88243 / 2.59 ( 3) link_BETA1-4 : bond 0.00882 / 0.46 ( 5) link_BETA1-4 : angle 3.30969 / 2.65 ( 15) link_NAG-ASN : bond 0.00313 / 0.22 ( 7) link_NAG-ASN : angle 2.29883 / 1.69 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.67 seconds wall clock time: 45 minutes 35.34 seconds (2735.34 seconds total)