Starting phenix.real_space_refine on Fri Jul 3 14:34:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.cif" model { file = "/net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i5y_35198/07_2026/8i5y_35198.cif" } resolution = 2.6 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= 0.010 sd= 0.103 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: 7 Type Number sf(0) Gaussians P 21 5.49 5 S 97 5.16 5 Na 1 4.78 5 C 9003 2.51 5 N 2050 2.21 5 O 2444 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 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: 13617 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 10259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1273, 10259 Classifications: {'peptide': 1273} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1230} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 971 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 119, 971 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 112} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 805 Unusual residues: {' NA': 1, '1PW': 1, '9Z9': 1, 'LPE': 12, 'NAG': 2, 'PCW': 5, 'TB4': 1, 'Y01': 4} Classifications: {'peptide': 1, 'undetermined': 27} Link IDs: {None: 27} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'P5S:plan-2': 1, '1PW:plan-1': 1, 'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 76 Unusual residues: {'LPE': 2, 'NAG': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 2.58, per 1000 atoms: 0.19 Number of scatterers: 13617 At special positions: 0 Unit cell: (130.982, 142.89, 130.982, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 97 16.00 P 21 15.00 Na 1 11.00 F 1 9.00 O 2444 8.00 N 2050 7.00 C 9003 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.04 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.03 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.03 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A2001 " - " ASN A 283 " " NAG A2006 " - " ASN A1375 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 110 " " NAG B 303 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " " NAG F 1 " - " ASN B 135 " Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 584.7 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2970 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 65.5% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 16 through 34 Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.876A pdb=" N VAL A 71 " --> pdb=" O PRO A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 4.044A pdb=" N ASP A 84 " --> pdb=" O PRO A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 113 through 124 Processing helix chain 'A' and resid 125 through 143 removed outlier: 3.583A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 175 removed outlier: 4.054A pdb=" N VAL A 155 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 204 removed outlier: 3.722A pdb=" N TRP A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N TYR A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 218 Processing helix chain 'A' and resid 219 through 222 Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 230 through 244 removed outlier: 3.552A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 removed outlier: 3.508A pdb=" N MET A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 285 through 291 removed outlier: 3.866A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 346 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.809A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.872A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 418 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.571A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 798 Processing helix chain 'A' and resid 799 through 804 Processing helix chain 'A' and resid 806 through 825 Processing helix chain 'A' and resid 833 through 848 removed outlier: 3.505A pdb=" N PHE A 837 " --> pdb=" O LEU A 834 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 863 removed outlier: 3.690A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 895 removed outlier: 5.768A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.288A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS A 893 " --> pdb=" O GLY A 889 " (cutoff:3.500A) Processing helix chain 'A' and resid 896 through 899 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.628A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 973 removed outlier: 3.587A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.592A pdb=" N ASN A1000 " --> pdb=" O LYS A 996 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1191 Processing helix chain 'A' and resid 1191 through 1208 Processing helix chain 'A' and resid 1219 through 1249 Processing helix chain 'A' and resid 1249 through 1255 Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1283 through 1291 Processing helix chain 'A' and resid 1292 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1344 Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1366 through 1377 Processing helix chain 'A' and resid 1391 through 1404 Processing helix chain 'A' and resid 1407 through 1417 removed outlier: 3.870A pdb=" N ILE A1411 " --> pdb=" O GLY A1407 " (cutoff:3.500A) Processing helix chain 'A' and resid 1430 through 1432 No H-bonds generated for 'chain 'A' and resid 1430 through 1432' Processing helix chain 'A' and resid 1433 through 1467 removed outlier: 3.746A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE A1447 " --> pdb=" O PHE A1443 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N THR A1448 " --> pdb=" O GLY A1444 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU A1467 " --> pdb=" O GLN A1463 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1490 removed outlier: 3.679A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER A1490 " --> pdb=" O LYS A1486 " (cutoff:3.500A) Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1514 through 1535 removed outlier: 3.742A pdb=" N ASP A1518 " --> pdb=" O ASN A1514 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLU A1535 " --> pdb=" O THR A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1540 through 1570 Processing helix chain 'A' and resid 1571 through 1575 removed outlier: 3.522A pdb=" N PHE A1574 " --> pdb=" O HIS A1571 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR A1575 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1571 through 1575' Processing helix chain 'A' and resid 1576 through 1603 Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1617 through 1622 removed outlier: 3.692A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.200A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1666 Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 4.238A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1705 Processing helix chain 'A' and resid 1706 through 1709 removed outlier: 3.595A pdb=" N ASN A1709 " --> pdb=" O PRO A1706 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1706 through 1709' Processing helix chain 'A' and resid 1732 through 1767 Processing helix chain 'B' and resid 83 through 87 removed outlier: 3.569A pdb=" N PHE B 86 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 115 Processing helix chain 'B' and resid 153 through 192 Processing helix chain 'C' and resid 118 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 75 through 76 removed outlier: 3.876A pdb=" N PHE A 88 " --> pdb=" O PHE A 100 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 273 through 277 Processing sheet with id=AA3, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA4, first strand: chain 'B' and resid 29 through 31 removed outlier: 4.672A pdb=" N ASN B 50 " --> pdb=" O PHE B 128 " (cutoff:3.500A) removed outlier: 9.423A pdb=" N THR B 53 " --> pdb=" O GLU B 74 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N GLU B 74 " --> pdb=" O THR B 53 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.613A pdb=" N TYR B 132 " --> pdb=" O PHE B 129 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA7, first strand: chain 'C' and resid 31 through 33 removed outlier: 3.987A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.307A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.307A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 46 through 48 819 hydrogen bonds defined for protein. 2322 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.07 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2032 1.31 - 1.44: 3712 1.44 - 1.57: 7960 1.57 - 1.70: 44 1.70 - 1.82: 157 Bond restraints: 13905 Sorted by residual: bond pdb=" C06 TB4 A2008 " pdb=" C07 TB4 A2008 " ideal model delta sigma weight residual 1.539 1.289 0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C08 TB4 A2008 " pdb=" N04 TB4 A2008 " ideal model delta sigma weight residual 1.457 1.262 0.195 2.00e-02 2.50e+03 9.46e+01 bond pdb=" C06 TB4 A2008 " pdb=" N04 TB4 A2008 " ideal model delta sigma weight residual 1.469 1.638 -0.169 2.00e-02 2.50e+03 7.11e+01 bond pdb=" OAX 1PW A2012 " pdb=" PBB 1PW A2012 " ideal model delta sigma weight residual 1.725 1.614 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" C11 TB4 A2008 " pdb=" N05 TB4 A2008 " ideal model delta sigma weight residual 1.346 1.450 -0.104 2.00e-02 2.50e+03 2.72e+01 ... (remaining 13900 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 18319 2.31 - 4.61: 358 4.61 - 6.92: 83 6.92 - 9.22: 20 9.22 - 11.53: 3 Bond angle restraints: 18783 Sorted by residual: angle pdb=" CB MET C 79 " pdb=" CG MET C 79 " pdb=" SD MET C 79 " ideal model delta sigma weight residual 112.70 124.23 -11.53 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CB MET A 130 " pdb=" CG MET A 130 " pdb=" SD MET A 130 " ideal model delta sigma weight residual 112.70 122.71 -10.01 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C3 NAG E 1 " pdb=" C4 NAG E 1 " pdb=" O4 NAG E 1 " ideal model delta sigma weight residual 107.29 116.88 -9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" C32 LPE A2015 " pdb=" C31 LPE A2015 " pdb=" O33 LPE A2015 " ideal model delta sigma weight residual 103.79 112.64 -8.85 3.00e+00 1.11e-01 8.70e+00 angle pdb=" C32 LPE A2023 " pdb=" C31 LPE A2023 " pdb=" O33 LPE A2023 " ideal model delta sigma weight residual 103.79 112.28 -8.49 3.00e+00 1.11e-01 8.00e+00 ... (remaining 18778 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.67: 7797 31.67 - 63.35: 421 63.35 - 95.02: 30 95.02 - 126.70: 10 126.70 - 158.37: 3 Dihedral angle restraints: 8261 sinusoidal: 3668 harmonic: 4593 Sorted by residual: dihedral pdb=" CB CYS A 895 " pdb=" SG CYS A 895 " pdb=" SG CYS C 55 " pdb=" CB CYS C 55 " ideal model delta sinusoidal sigma weight residual 93.00 135.29 -42.29 1 1.00e+01 1.00e-02 2.50e+01 dihedral pdb=" N PCW A2017 " pdb=" C4 PCW A2017 " pdb=" C5 PCW A2017 " pdb=" O4P PCW A2017 " ideal model delta sinusoidal sigma weight residual -66.66 91.71 -158.37 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" C33 PCW A2027 " pdb=" C31 PCW A2027 " pdb=" C32 PCW A2027 " pdb=" O2 PCW A2027 " ideal model delta sinusoidal sigma weight residual 191.83 54.85 136.98 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 8258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1862 0.064 - 0.128: 242 0.128 - 0.192: 16 0.192 - 0.256: 5 0.256 - 0.320: 1 Chirality restraints: 2126 Sorted by residual: chirality pdb=" C1 NAG A2001 " pdb=" ND2 ASN A 283 " pdb=" C2 NAG A2001 " pdb=" O5 NAG A2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.57e+00 chirality pdb=" C1 NAG B 301 " pdb=" ND2 ASN B 93 " pdb=" C2 NAG B 301 " pdb=" O5 NAG B 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" C2 PCW A2026 " pdb=" C1 PCW A2026 " pdb=" C3 PCW A2026 " pdb=" O2 PCW A2026 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 2123 not shown) Planarity restraints: 2213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A1375 " -0.419 2.00e-02 2.50e+03 4.58e-01 2.63e+03 pdb=" CG ASN A1375 " 0.177 2.00e-02 2.50e+03 pdb=" OD1 ASN A1375 " 0.138 2.00e-02 2.50e+03 pdb=" ND2 ASN A1375 " 0.692 2.00e-02 2.50e+03 pdb=" C1 NAG A2006 " -0.588 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 2 " -0.350 2.00e-02 2.50e+03 3.02e-01 1.14e+03 pdb=" C7 NAG D 2 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG D 2 " -0.117 2.00e-02 2.50e+03 pdb=" N2 NAG D 2 " 0.538 2.00e-02 2.50e+03 pdb=" O7 NAG D 2 " -0.155 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A2006 " -0.326 2.00e-02 2.50e+03 2.82e-01 9.95e+02 pdb=" C7 NAG A2006 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG A2006 " -0.143 2.00e-02 2.50e+03 pdb=" N2 NAG A2006 " 0.504 2.00e-02 2.50e+03 pdb=" O7 NAG A2006 " -0.110 2.00e-02 2.50e+03 ... (remaining 2210 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 64 2.56 - 3.14: 10424 3.14 - 3.73: 20704 3.73 - 4.31: 30009 4.31 - 4.90: 49862 Nonbonded interactions: 111063 Sorted by model distance: nonbonded pdb=" OD1 ASN A1375 " pdb=" O5 NAG A2006 " model vdw 1.969 3.040 nonbonded pdb=" O PHE A 391 " pdb=" ND2 ASN A 395 " model vdw 2.179 3.120 nonbonded pdb=" N GLU B 66 " pdb=" OE1 GLU B 66 " model vdw 2.200 3.120 nonbonded pdb=" OD2 ASP A 77 " pdb=" OG1 THR A 87 " model vdw 2.207 3.040 nonbonded pdb=" N GLU B 84 " pdb=" OE1 GLU B 84 " model vdw 2.208 3.120 ... (remaining 111058 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.680 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.358 13927 Z= 0.385 Angle : 0.854 35.167 18838 Z= 0.367 Chirality : 0.044 0.320 2126 Planarity : 0.013 0.302 2205 Dihedral : 18.169 158.373 5258 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.71 % Allowed : 19.17 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.22), residues: 1549 helix: 1.73 (0.17), residues: 917 sheet: -0.39 (0.44), residues: 140 loop : -0.33 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 174 TYR 0.018 0.002 TYR C 128 PHE 0.023 0.002 PHE A1583 TRP 0.022 0.002 TRP C 67 HIS 0.008 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00724 / 0.35 (13905) covalent geometry : angle 0.80312 / 0.35 (18783) SS BOND : bond 0.00236 / 0.16 ( 11) SS BOND : angle 1.12625 / 0.81 ( 22) hydrogen bonds : bond 0.13696 / 8.77 ( 805) hydrogen bonds : angle 5.67555 / 4.05 ( 2322) link_BETA1-4 : bond 0.00828 / 0.51 ( 3) link_BETA1-4 : angle 3.29929 / 1.76 ( 9) link_NAG-ASN : bond 0.12659 / 10.63 ( 8) link_NAG-ASN : angle 7.91489 / 7.55 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 165 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 903 CYS cc_start: 0.8269 (m) cc_final: 0.7779 (t) outliers start: 10 outliers final: 6 residues processed: 173 average time/residue: 0.4660 time to fit residues: 89.4300 Evaluate side-chains 159 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 153 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1459 ASN A1762 ASN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.204316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.126836 restraints weight = 14227.427| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.03 r_work: 0.3355 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 1 (4 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.0683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 13927 Z= 0.145 Angle : 0.579 11.432 18838 Z= 0.291 Chirality : 0.042 0.315 2126 Planarity : 0.004 0.047 2205 Dihedral : 15.504 162.992 2273 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.49 % Allowed : 15.75 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.21), residues: 1549 helix: 1.92 (0.17), residues: 912 sheet: -0.54 (0.41), residues: 140 loop : -0.14 (0.29), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.020 0.002 TYR A 367 PHE 0.017 0.002 PHE A1440 TRP 0.008 0.001 TRP A1700 HIS 0.007 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13905) covalent geometry : angle 0.56053 / 0.29 (18783) SS BOND : bond 0.00367 / 0.24 ( 11) SS BOND : angle 1.11217 / 0.75 ( 22) hydrogen bonds : bond 0.04958 / 3.29 ( 805) hydrogen bonds : angle 4.58733 / 3.32 ( 2322) link_BETA1-4 : bond 0.00639 / 0.39 ( 3) link_BETA1-4 : angle 3.65963 / 2.06 ( 9) link_NAG-ASN : bond 0.00764 / 0.55 ( 8) link_NAG-ASN : angle 3.36716 / 2.61 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 152 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7115 (tpp) cc_final: 0.6681 (mmp) REVERT: A 791 MET cc_start: 0.6528 (OUTLIER) cc_final: 0.6316 (ttt) REVERT: A 1573 TYR cc_start: 0.8161 (t80) cc_final: 0.7902 (t80) REVERT: A 1762 ASN cc_start: 0.7388 (OUTLIER) cc_final: 0.7136 (t0) outliers start: 49 outliers final: 19 residues processed: 181 average time/residue: 0.4655 time to fit residues: 94.0501 Evaluate side-chains 165 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain A residue 1762 ASN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 49 optimal weight: 7.9990 chunk 44 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 40 optimal weight: 7.9990 chunk 119 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 78 optimal weight: 9.9990 chunk 117 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN A1459 ASN A1541 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.203608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.131445 restraints weight = 14308.882| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.15 r_work: 0.3358 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 13927 Z= 0.161 Angle : 0.575 8.748 18838 Z= 0.290 Chirality : 0.042 0.306 2126 Planarity : 0.004 0.045 2205 Dihedral : 15.049 161.525 2269 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.92 % Allowed : 15.32 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.21), residues: 1549 helix: 1.94 (0.17), residues: 911 sheet: -0.46 (0.40), residues: 140 loop : -0.16 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 174 TYR 0.019 0.002 TYR A 367 PHE 0.018 0.002 PHE A1440 TRP 0.010 0.001 TRP A1700 HIS 0.006 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.16 (13905) covalent geometry : angle 0.55699 / 0.29 (18783) SS BOND : bond 0.00369 / 0.24 ( 11) SS BOND : angle 1.12708 / 0.78 ( 22) hydrogen bonds : bond 0.04990 / 3.31 ( 805) hydrogen bonds : angle 4.48312 / 3.25 ( 2322) link_BETA1-4 : bond 0.00733 / 0.45 ( 3) link_BETA1-4 : angle 3.58018 / 1.89 ( 9) link_NAG-ASN : bond 0.00683 / 0.47 ( 8) link_NAG-ASN : angle 3.24223 / 2.49 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 156 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7130 (tpp) cc_final: 0.6695 (OUTLIER) REVERT: A 791 MET cc_start: 0.6649 (OUTLIER) cc_final: 0.6375 (ttt) REVERT: A 812 ASP cc_start: 0.7603 (t0) cc_final: 0.7394 (t0) REVERT: A 1537 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8437 (tm-30) REVERT: A 1573 TYR cc_start: 0.8184 (t80) cc_final: 0.7877 (t80) REVERT: A 1616 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8271 (ptm-80) REVERT: A 1761 GLU cc_start: 0.7476 (mm-30) cc_final: 0.7181 (mm-30) outliers start: 55 outliers final: 29 residues processed: 194 average time/residue: 0.4756 time to fit residues: 102.6298 Evaluate side-chains 180 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 149 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1268 VAL Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 128 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 130 optimal weight: 0.1980 chunk 111 optimal weight: 0.6980 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 809 ASN A1459 ASN A1541 GLN C 62 GLN C 126 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.211619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.141608 restraints weight = 14439.264| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.83 r_work: 0.3511 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3421 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3421 r_free = 0.3421 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3421 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13927 Z= 0.121 Angle : 0.519 8.420 18838 Z= 0.265 Chirality : 0.040 0.305 2126 Planarity : 0.004 0.044 2205 Dihedral : 14.430 162.078 2269 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 4.13 % Allowed : 14.90 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.91 (0.21), residues: 1549 helix: 2.22 (0.17), residues: 900 sheet: -0.35 (0.40), residues: 140 loop : 0.08 (0.29), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 174 TYR 0.017 0.001 TYR A 367 PHE 0.015 0.001 PHE A1440 TRP 0.011 0.001 TRP A1700 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (13905) covalent geometry : angle 0.50252 / 0.26 (18783) SS BOND : bond 0.00406 / 0.25 ( 11) SS BOND : angle 0.94244 / 0.66 ( 22) hydrogen bonds : bond 0.04389 / 2.92 ( 805) hydrogen bonds : angle 4.29305 / 3.13 ( 2322) link_BETA1-4 : bond 0.00770 / 0.48 ( 3) link_BETA1-4 : angle 3.27245 / 1.70 ( 9) link_NAG-ASN : bond 0.00600 / 0.39 ( 8) link_NAG-ASN : angle 3.03531 / 2.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 154 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7180 (tpp) cc_final: 0.6739 (OUTLIER) REVERT: A 791 MET cc_start: 0.6613 (OUTLIER) cc_final: 0.6318 (ttt) REVERT: A 1176 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.4704 (mmtt) REVERT: A 1613 ARG cc_start: 0.8801 (OUTLIER) cc_final: 0.8557 (ttp80) REVERT: A 1616 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8157 (ptm-80) REVERT: A 1761 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7226 (mm-30) outliers start: 58 outliers final: 26 residues processed: 191 average time/residue: 0.4779 time to fit residues: 101.4510 Evaluate side-chains 176 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 307 GLU Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 85 optimal weight: 1.9990 chunk 144 optimal weight: 30.0000 chunk 67 optimal weight: 40.0000 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 79 optimal weight: 0.7980 chunk 8 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 134 optimal weight: 6.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN A 240 GLN A1459 ASN A1541 GLN C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.211134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.138638 restraints weight = 14384.243| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.76 r_work: 0.3510 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 13927 Z= 0.130 Angle : 0.536 8.491 18838 Z= 0.269 Chirality : 0.041 0.310 2126 Planarity : 0.004 0.043 2205 Dihedral : 14.185 162.951 2269 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.99 % Allowed : 15.18 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.21), residues: 1549 helix: 2.24 (0.17), residues: 901 sheet: -0.22 (0.40), residues: 140 loop : 0.09 (0.29), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 174 TYR 0.018 0.001 TYR A 367 PHE 0.018 0.001 PHE A 733 TRP 0.011 0.001 TRP A1700 HIS 0.003 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (13905) covalent geometry : angle 0.51938 / 0.27 (18783) SS BOND : bond 0.00331 / 0.21 ( 11) SS BOND : angle 0.97145 / 0.69 ( 22) hydrogen bonds : bond 0.04426 / 2.95 ( 805) hydrogen bonds : angle 4.24123 / 3.09 ( 2322) link_BETA1-4 : bond 0.00738 / 0.46 ( 3) link_BETA1-4 : angle 3.27844 / 1.71 ( 9) link_NAG-ASN : bond 0.00600 / 0.39 ( 8) link_NAG-ASN : angle 3.07201 / 2.32 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 159 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7131 (tpp) cc_final: 0.6706 (mmp) REVERT: A 791 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.6290 (ttt) REVERT: A 812 ASP cc_start: 0.7602 (t0) cc_final: 0.7388 (t0) REVERT: A 816 VAL cc_start: 0.7609 (t) cc_final: 0.7408 (t) REVERT: A 1537 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8375 (tm-30) REVERT: A 1570 ARG cc_start: 0.8071 (mpp-170) cc_final: 0.7817 (mpp-170) REVERT: A 1616 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8120 (ptm-80) REVERT: A 1761 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7157 (mm-30) outliers start: 56 outliers final: 31 residues processed: 195 average time/residue: 0.4864 time to fit residues: 105.3239 Evaluate side-chains 187 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 834 LEU Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1331 PHE Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1448 THR Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 136 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 2 optimal weight: 30.0000 chunk 140 optimal weight: 7.9990 chunk 38 optimal weight: 10.0000 chunk 64 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 123 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 143 optimal weight: 7.9990 chunk 81 optimal weight: 0.7980 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 809 ASN A1459 ASN A1494 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.208520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.135501 restraints weight = 14348.969| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 1.74 r_work: 0.3466 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3370 r_free = 0.3370 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.112 13927 Z= 0.227 Angle : 0.650 10.288 18838 Z= 0.325 Chirality : 0.046 0.319 2126 Planarity : 0.004 0.045 2205 Dihedral : 14.524 167.125 2269 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.56 % Allowed : 16.11 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.21), residues: 1549 helix: 1.86 (0.17), residues: 920 sheet: -0.28 (0.39), residues: 139 loop : -0.30 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 185 TYR 0.020 0.002 TYR A 367 PHE 0.021 0.002 PHE A1679 TRP 0.011 0.002 TRP A 928 HIS 0.005 0.001 HIS A 273 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (13905) covalent geometry : angle 0.63258 / 0.32 (18783) SS BOND : bond 0.00510 / 0.33 ( 11) SS BOND : angle 1.36966 / 0.95 ( 22) hydrogen bonds : bond 0.05383 / 3.57 ( 805) hydrogen bonds : angle 4.41176 / 3.20 ( 2322) link_BETA1-4 : bond 0.00792 / 0.49 ( 3) link_BETA1-4 : angle 3.66039 / 1.90 ( 9) link_NAG-ASN : bond 0.00636 / 0.40 ( 8) link_NAG-ASN : angle 3.45185 / 2.59 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 156 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7111 (tpp) cc_final: 0.6731 (mmp) REVERT: A 296 GLU cc_start: 0.7934 (tt0) cc_final: 0.7664 (tt0) REVERT: A 791 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.6469 (ttt) REVERT: A 809 ASN cc_start: 0.7388 (m-40) cc_final: 0.7121 (m-40) REVERT: A 1176 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.4818 (mmtt) REVERT: A 1567 ILE cc_start: 0.7873 (OUTLIER) cc_final: 0.7376 (mp) REVERT: A 1570 ARG cc_start: 0.8147 (mpp-170) cc_final: 0.7906 (mpp-170) REVERT: A 1616 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8227 (ptm-80) REVERT: A 1761 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7155 (mm-30) outliers start: 50 outliers final: 27 residues processed: 187 average time/residue: 0.4716 time to fit residues: 98.0982 Evaluate side-chains 182 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 151 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1567 ILE Chi-restraints excluded: chain A residue 1595 LEU Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 111 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 126 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A1459 ASN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.213330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141790 restraints weight = 14444.762| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 1.73 r_work: 0.3553 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 13927 Z= 0.113 Angle : 0.518 9.954 18838 Z= 0.262 Chirality : 0.040 0.308 2126 Planarity : 0.004 0.044 2205 Dihedral : 13.711 165.332 2269 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.99 % Allowed : 17.11 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.21), residues: 1549 helix: 2.11 (0.17), residues: 922 sheet: -0.15 (0.40), residues: 140 loop : -0.21 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.016 0.001 TYR A 367 PHE 0.017 0.001 PHE A 733 TRP 0.013 0.001 TRP A1700 HIS 0.002 0.001 HIS C 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (13905) covalent geometry : angle 0.50165 / 0.26 (18783) SS BOND : bond 0.00359 / 0.27 ( 11) SS BOND : angle 0.93139 / 0.67 ( 22) hydrogen bonds : bond 0.04199 / 2.79 ( 805) hydrogen bonds : angle 4.16432 / 3.04 ( 2322) link_BETA1-4 : bond 0.00807 / 0.50 ( 3) link_BETA1-4 : angle 3.26687 / 1.70 ( 9) link_NAG-ASN : bond 0.00622 / 0.40 ( 8) link_NAG-ASN : angle 2.97649 / 2.24 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7269 (tpp) cc_final: 0.6899 (mmp) REVERT: A 791 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.6306 (ttt) REVERT: A 903 CYS cc_start: 0.8409 (m) cc_final: 0.7889 (t) REVERT: A 1176 LYS cc_start: 0.7100 (OUTLIER) cc_final: 0.4858 (mmtt) REVERT: A 1613 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.8592 (ttp80) REVERT: A 1616 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.8202 (ptm-80) REVERT: A 1761 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7151 (mm-30) outliers start: 42 outliers final: 19 residues processed: 179 average time/residue: 0.4879 time to fit residues: 96.7383 Evaluate side-chains 174 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1327 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 61 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 2 optimal weight: 8.9990 chunk 91 optimal weight: 0.0770 overall best weight: 2.1744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 189 ASN A 240 GLN A 809 ASN A1459 ASN C 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.211633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.140294 restraints weight = 14349.434| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.69 r_work: 0.3521 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3421 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 13927 Z= 0.194 Angle : 0.617 9.736 18838 Z= 0.309 Chirality : 0.044 0.318 2126 Planarity : 0.004 0.045 2205 Dihedral : 14.015 174.494 2267 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.14 % Allowed : 17.39 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.21), residues: 1549 helix: 1.94 (0.17), residues: 921 sheet: -0.12 (0.40), residues: 139 loop : -0.24 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 174 TYR 0.020 0.002 TYR A1743 PHE 0.022 0.002 PHE A1440 TRP 0.010 0.002 TRP A1700 HIS 0.003 0.001 HIS A 915 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.19 (13905) covalent geometry : angle 0.59910 / 0.31 (18783) SS BOND : bond 0.00484 / 0.30 ( 11) SS BOND : angle 1.28948 / 0.90 ( 22) hydrogen bonds : bond 0.05107 / 3.39 ( 805) hydrogen bonds : angle 4.31657 / 3.13 ( 2322) link_BETA1-4 : bond 0.00876 / 0.54 ( 3) link_BETA1-4 : angle 3.58395 / 1.89 ( 9) link_NAG-ASN : bond 0.00611 / 0.39 ( 8) link_NAG-ASN : angle 3.34717 / 2.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7199 (tpp) cc_final: 0.6829 (mmp) REVERT: A 408 GLN cc_start: 0.6691 (pt0) cc_final: 0.6484 (pt0) REVERT: A 791 MET cc_start: 0.6673 (OUTLIER) cc_final: 0.6387 (ttt) REVERT: A 903 CYS cc_start: 0.8400 (m) cc_final: 0.7909 (t) REVERT: A 1176 LYS cc_start: 0.7140 (OUTLIER) cc_final: 0.4893 (mmtt) REVERT: A 1570 ARG cc_start: 0.8282 (mpp-170) cc_final: 0.8077 (mpp-170) REVERT: A 1616 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8202 (ptm-80) REVERT: A 1761 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7208 (mm-30) outliers start: 44 outliers final: 25 residues processed: 180 average time/residue: 0.5285 time to fit residues: 105.3551 Evaluate side-chains 181 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 782 VAL Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 856 ILE Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1561 GLU Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 18 optimal weight: 20.0000 chunk 151 optimal weight: 0.3980 chunk 48 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 128 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 105 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A1459 ASN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.213254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.142548 restraints weight = 14536.800| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.77 r_work: 0.3545 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13927 Z= 0.127 Angle : 0.542 11.660 18838 Z= 0.274 Chirality : 0.041 0.312 2126 Planarity : 0.004 0.043 2205 Dihedral : 13.611 176.098 2267 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.42 % Allowed : 18.25 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.75 (0.21), residues: 1549 helix: 2.09 (0.17), residues: 921 sheet: -0.08 (0.40), residues: 140 loop : -0.21 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.017 0.001 TYR A 367 PHE 0.017 0.001 PHE C 63 TRP 0.013 0.001 TRP A1700 HIS 0.003 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (13905) covalent geometry : angle 0.52514 / 0.27 (18783) SS BOND : bond 0.00314 / 0.21 ( 11) SS BOND : angle 0.94983 / 0.69 ( 22) hydrogen bonds : bond 0.04412 / 2.93 ( 805) hydrogen bonds : angle 4.17861 / 3.04 ( 2322) link_BETA1-4 : bond 0.00825 / 0.51 ( 3) link_BETA1-4 : angle 3.36134 / 1.77 ( 9) link_NAG-ASN : bond 0.00608 / 0.39 ( 8) link_NAG-ASN : angle 3.06968 / 2.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7200 (tpp) cc_final: 0.6862 (mmp) REVERT: A 408 GLN cc_start: 0.6552 (pt0) cc_final: 0.6271 (pt0) REVERT: A 761 MET cc_start: 0.8163 (mtm) cc_final: 0.7947 (mtp) REVERT: A 791 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.6273 (ttt) REVERT: A 1176 LYS cc_start: 0.7095 (OUTLIER) cc_final: 0.4861 (mmtt) REVERT: A 1570 ARG cc_start: 0.8221 (mpp-170) cc_final: 0.7986 (mpp-170) REVERT: A 1613 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8627 (ttp80) REVERT: A 1616 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8103 (ptm-80) REVERT: A 1620 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7475 (mp) REVERT: A 1641 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7528 (mp) REVERT: A 1761 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7093 (mm-30) outliers start: 34 outliers final: 19 residues processed: 178 average time/residue: 0.4994 time to fit residues: 98.4118 Evaluate side-chains 177 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 791 MET Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1274 VAL Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain A residue 1641 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 96 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 149 optimal weight: 0.0970 chunk 82 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A1459 ASN C 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.213221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141657 restraints weight = 14452.564| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 1.81 r_work: 0.3560 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3459 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3449 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3449 r_free = 0.3449 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3449 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13927 Z= 0.121 Angle : 0.535 12.243 18838 Z= 0.270 Chirality : 0.041 0.312 2126 Planarity : 0.004 0.042 2205 Dihedral : 13.292 177.791 2267 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.35 % Allowed : 18.25 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.21), residues: 1549 helix: 2.17 (0.17), residues: 922 sheet: -0.02 (0.41), residues: 144 loop : -0.17 (0.29), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.017 0.001 TYR A 367 PHE 0.016 0.001 PHE A1440 TRP 0.013 0.001 TRP A1700 HIS 0.003 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (13905) covalent geometry : angle 0.51953 / 0.27 (18783) SS BOND : bond 0.00303 / 0.20 ( 11) SS BOND : angle 0.91618 / 0.66 ( 22) hydrogen bonds : bond 0.04253 / 2.83 ( 805) hydrogen bonds : angle 4.12999 / 3.01 ( 2322) link_BETA1-4 : bond 0.00886 / 0.55 ( 3) link_BETA1-4 : angle 3.30983 / 1.76 ( 9) link_NAG-ASN : bond 0.00600 / 0.39 ( 8) link_NAG-ASN : angle 2.97969 / 2.23 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.7248 (tpp) cc_final: 0.6896 (mmp) REVERT: A 296 GLU cc_start: 0.7931 (tt0) cc_final: 0.7585 (tt0) REVERT: A 408 GLN cc_start: 0.6618 (pt0) cc_final: 0.6345 (pt0) REVERT: A 761 MET cc_start: 0.8182 (mtm) cc_final: 0.7957 (mtp) REVERT: A 809 ASN cc_start: 0.7237 (m-40) cc_final: 0.6641 (t0) REVERT: A 903 CYS cc_start: 0.8379 (m) cc_final: 0.7875 (t) REVERT: A 1176 LYS cc_start: 0.7154 (OUTLIER) cc_final: 0.4949 (mmtt) REVERT: A 1613 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8613 (ttp80) REVERT: A 1616 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8094 (ptm-80) REVERT: A 1620 ILE cc_start: 0.8096 (OUTLIER) cc_final: 0.7432 (mp) REVERT: A 1761 GLU cc_start: 0.7553 (mm-30) cc_final: 0.6974 (mm-30) outliers start: 33 outliers final: 20 residues processed: 180 average time/residue: 0.5101 time to fit residues: 101.7668 Evaluate side-chains 180 residues out of total 1405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 156 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 414 GLU Chi-restraints excluded: chain A residue 759 LEU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 943 MET Chi-restraints excluded: chain A residue 1176 LYS Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1375 ASN Chi-restraints excluded: chain A residue 1456 ILE Chi-restraints excluded: chain A residue 1613 ARG Chi-restraints excluded: chain A residue 1616 ARG Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1630 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 178 MET Chi-restraints excluded: chain C residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 114 optimal weight: 1.9990 chunk 133 optimal weight: 0.9990 chunk 78 optimal weight: 9.9990 chunk 31 optimal weight: 0.9980 chunk 84 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 30.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 GLN A 809 ASN A1459 ASN C 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.213522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147773 restraints weight = 14534.889| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 1.91 r_work: 0.3534 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3434 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3416 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3416 r_free = 0.3416 target_work(ls_wunit_k1) = 0.123 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.3416 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 13927 Z= 0.130 Angle : 0.544 12.173 18838 Z= 0.275 Chirality : 0.041 0.314 2126 Planarity : 0.004 0.040 2205 Dihedral : 13.215 172.880 2267 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.28 % Allowed : 18.53 % Favored : 79.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.84 (0.21), residues: 1549 helix: 2.16 (0.17), residues: 922 sheet: -0.02 (0.40), residues: 140 loop : -0.18 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 174 TYR 0.017 0.001 TYR A 367 PHE 0.016 0.001 PHE A1440 TRP 0.012 0.001 TRP A1700 HIS 0.004 0.001 HIS A 766 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (13905) covalent geometry : angle 0.52771 / 0.27 (18783) SS BOND : bond 0.00321 / 0.21 ( 11) SS BOND : angle 1.03191 / 0.74 ( 22) hydrogen bonds : bond 0.04331 / 2.87 ( 805) hydrogen bonds : angle 4.12503 / 3.01 ( 2322) link_BETA1-4 : bond 0.00843 / 0.52 ( 3) link_BETA1-4 : angle 3.30666 / 1.76 ( 9) link_NAG-ASN : bond 0.00601 / 0.39 ( 8) link_NAG-ASN : angle 3.01450 / 2.25 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6166.52 seconds wall clock time: 105 minutes 32.81 seconds (6332.81 seconds total)