Starting phenix.real_space_refine on Fri Jul 3 09:26:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xmo_38484/07_2026/8xmo_38484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xmo_38484/07_2026/8xmo_38484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xmo_38484/07_2026/8xmo_38484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xmo_38484/07_2026/8xmo_38484.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xmo_38484/07_2026/8xmo_38484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xmo_38484/07_2026/8xmo_38484.map" } resolution = 3.39 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= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 99 5.16 5 C 8773 2.51 5 N 2063 2.21 5 O 2376 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 178 residue(s): 0.02s 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: 13323 Number of models: 1 Model: "" Number of chains: 7 Chain: "C" Number of atoms: 980 Number of conformers: 2 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 Conformer: "B" 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 bond proxies already assigned to first conformer: 981 Chain: "A" Number of atoms: 10387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1286, 10387 Classifications: {'peptide': 1286} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 1243} 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: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 428 Unusual residues: {'LPE': 7, 'NAG': 2, 'PCW': 5} Classifications: {'undetermined': 14} Link IDs: {None: 13} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PCW:plan-4': 3} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.10, per 1000 atoms: 0.23 Number of scatterers: 13323 At special positions: 0 Unit cell: (120.769, 133.944, 137.238, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 99 16.00 P 12 15.00 O 2376 8.00 N 2063 7.00 C 8773 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 55 " - pdb=" SG CYS A 895 " distance=2.02 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 324 " distance=2.02 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.01 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.02 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=1.96 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-ASN " NAG A2001 " - " ASN A1375 " " NAG A2002 " - " ASN A 283 " " NAG B 301 " - " ASN B 93 " " NAG B 302 " - " ASN B 135 " " NAG B 303 " - " ASN B 110 " " NAG B 304 " - " ASN B 114 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 638.8 milliseconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3004 Finding SS restraints... Secondary structure from input PDB file: 67 helices and 9 sheets defined 65.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.630A pdb=" N LEU A 20 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ARG A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 31 " --> pdb=" O ILE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 64 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.852A 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 125 Processing helix chain 'A' and resid 125 through 144 removed outlier: 3.551A pdb=" N SER A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 175 removed outlier: 4.252A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN A 154 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA A 173 " --> pdb=" O VAL A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 206 removed outlier: 4.149A pdb=" N LEU A 191 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 192 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 219 removed outlier: 4.102A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 219' Processing helix chain 'A' and resid 220 through 222 No H-bonds generated for 'chain 'A' and resid 220 through 222' Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.566A pdb=" N ILE A 234 " --> pdb=" O GLY A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 268 Processing helix chain 'A' and resid 285 through 292 removed outlier: 3.621A pdb=" N ASN A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N THR A 292 " --> pdb=" O SER A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.728A pdb=" N TYR A 302 " --> pdb=" O ASP A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 341 Processing helix chain 'A' and resid 346 through 359 Processing helix chain 'A' and resid 362 through 374 removed outlier: 4.255A pdb=" N LEU A 366 " --> pdb=" O TYR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 378 through 389 removed outlier: 4.116A pdb=" N PHE A 382 " --> pdb=" O TYR A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 431 Processing helix chain 'A' and resid 729 through 741 Processing helix chain 'A' and resid 742 through 762 removed outlier: 3.667A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 5.317A 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 832 through 848 removed outlier: 3.667A pdb=" N ARG A 835 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 864 removed outlier: 3.621A pdb=" N SER A 862 " --> pdb=" O ILE A 858 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 889 Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 912 through 926 Processing helix chain 'A' and resid 929 through 940 Processing helix chain 'A' and resid 940 through 972 removed outlier: 3.595A pdb=" N CYS A 944 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N SER A 972 " --> pdb=" O LEU A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1014 removed outlier: 3.679A pdb=" N VAL A 992 " --> pdb=" O LEU A 988 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N THR A 993 " --> pdb=" O GLN A 989 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLY A 998 " --> pdb=" O ARG A 994 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A1001 " --> pdb=" O LYS A 997 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU A1006 " --> pdb=" O VAL A1002 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ARG A1007 " --> pdb=" O LYS A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1176 through 1190 removed outlier: 3.646A pdb=" N GLU A1190 " --> pdb=" O TYR A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1211 Processing helix chain 'A' and resid 1213 through 1218 removed outlier: 4.232A pdb=" N GLU A1217 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing helix chain 'A' and resid 1219 through 1255 removed outlier: 3.765A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N TYR A1250 " --> pdb=" O ILE A1246 " (cutoff:3.500A) removed outlier: 8.973A pdb=" N LYS A1251 " --> pdb=" O ALA A1247 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A1252 " --> pdb=" O TYR A1248 " (cutoff:3.500A) Processing helix chain 'A' and resid 1256 through 1279 Processing helix chain 'A' and resid 1280 through 1282 No H-bonds generated for 'chain 'A' and resid 1280 through 1282' Processing helix chain 'A' and resid 1283 through 1291 removed outlier: 3.669A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) Processing helix chain 'A' and resid 1292 through 1301 Proline residue: A1297 - end of helix Processing helix chain 'A' and resid 1304 through 1317 Processing helix chain 'A' and resid 1317 through 1344 removed outlier: 3.540A pdb=" N ILE A1321 " --> pdb=" O ALA A1317 " (cutoff:3.500A) 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 1416 removed outlier: 4.027A 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 1445 removed outlier: 3.723A pdb=" N PHE A1437 " --> pdb=" O MET A1433 " (cutoff:3.500A) Processing helix chain 'A' and resid 1445 through 1468 Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1489 through 1491 No H-bonds generated for 'chain 'A' and resid 1489 through 1491' Processing helix chain 'A' and resid 1502 through 1513 Processing helix chain 'A' and resid 1516 through 1534 Processing helix chain 'A' and resid 1540 through 1569 removed outlier: 3.684A pdb=" N GLU A1545 " --> pdb=" O GLN A1541 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER A1568 " --> pdb=" O LEU A1564 " (cutoff:3.500A) Processing helix chain 'A' and resid 1572 through 1575 removed outlier: 3.678A pdb=" N THR A1575 " --> pdb=" O TYR A1572 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1572 through 1575' Processing helix chain 'A' and resid 1576 through 1602 removed outlier: 3.661A pdb=" N ILE A1580 " --> pdb=" O VAL A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1605 through 1614 Processing helix chain 'A' and resid 1617 through 1622 removed outlier: 3.740A pdb=" N ARG A1622 " --> pdb=" O GLY A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1622 through 1627 removed outlier: 4.349A pdb=" N GLY A1626 " --> pdb=" O ARG A1622 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA A1627 " --> pdb=" O LEU A1623 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1622 through 1627' Processing helix chain 'A' and resid 1629 through 1666 removed outlier: 3.975A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1683 through 1696 removed outlier: 3.981A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1709 removed outlier: 3.874A pdb=" N LEU A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) Proline residue: A1706 - end of helix removed outlier: 4.143A pdb=" N ASN A1709 " --> pdb=" O ALA A1705 " (cutoff:3.500A) Processing helix chain 'A' and resid 1732 through 1767 Processing helix chain 'B' and resid 153 through 192 Processing sheet with id=AA1, first strand: chain 'C' and resid 31 through 33 removed outlier: 4.403A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR C 51 " --> pdb=" O THR C 33 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 37 through 41 removed outlier: 6.125A pdb=" N LEU C 38 " --> pdb=" O GLN C 145 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU C 147 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C 40 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE C 88 " --> pdb=" O GLN C 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.818A pdb=" N MET C 113 " --> pdb=" O GLU C 100 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU C 100 " --> pdb=" O MET C 113 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA5, first strand: chain 'A' and resid 274 through 277 removed outlier: 3.563A pdb=" N VAL A 331 " --> pdb=" O LYS A 274 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1357 through 1358 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 31 removed outlier: 6.641A pdb=" N ALA B 30 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR B 55 " --> pdb=" O ARG B 72 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ARG B 72 " --> pdb=" O THR B 55 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N TRP B 57 " --> pdb=" O ILE B 70 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 36 through 38 Processing sheet with id=AA9, first strand: chain 'B' and resid 126 through 128 removed outlier: 3.935A pdb=" N LEU B 127 " --> pdb=" O HIS B 134 " (cutoff:3.500A) 784 hydrogen bonds defined for protein. 2223 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: 2.21 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: 1.17 - 1.30: 2038 1.30 - 1.43: 3726 1.43 - 1.56: 7664 1.56 - 1.69: 25 1.69 - 1.82: 160 Bond restraints: 13613 Sorted by residual: bond pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 1.524 1.424 0.100 1.23e-02 6.61e+03 6.64e+01 bond pdb=" CA TYR A 305 " pdb=" C TYR A 305 " ideal model delta sigma weight residual 1.522 1.429 0.093 1.20e-02 6.94e+03 5.99e+01 bond pdb=" CA ARG A1367 " pdb=" C ARG A1367 " ideal model delta sigma weight residual 1.523 1.424 0.100 1.30e-02 5.92e+03 5.89e+01 bond pdb=" CA LEU A 793 " pdb=" C LEU A 793 " ideal model delta sigma weight residual 1.524 1.427 0.097 1.27e-02 6.20e+03 5.84e+01 bond pdb=" CA ASP A 912 " pdb=" C ASP A 912 " ideal model delta sigma weight residual 1.524 1.432 0.092 1.23e-02 6.61e+03 5.59e+01 ... (remaining 13608 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 17157 2.95 - 5.90: 970 5.90 - 8.85: 196 8.85 - 11.80: 43 11.80 - 14.75: 9 Bond angle restraints: 18375 Sorted by residual: angle pdb=" N LEU A 793 " pdb=" CA LEU A 793 " pdb=" C LEU A 793 " ideal model delta sigma weight residual 111.07 99.79 11.28 1.07e+00 8.73e-01 1.11e+02 angle pdb=" N PHE A 176 " pdb=" CA PHE A 176 " pdb=" C PHE A 176 " ideal model delta sigma weight residual 114.12 99.68 14.44 1.39e+00 5.18e-01 1.08e+02 angle pdb=" N SER B 47 " pdb=" CA SER B 47 " pdb=" C SER B 47 " ideal model delta sigma weight residual 111.28 121.87 -10.59 1.09e+00 8.42e-01 9.45e+01 angle pdb=" N CYS B 21 " pdb=" CA CYS B 21 " pdb=" C CYS B 21 " ideal model delta sigma weight residual 110.23 124.00 -13.77 1.45e+00 4.76e-01 9.02e+01 angle pdb=" C LYS A1711 " pdb=" N PRO A1712 " pdb=" CA PRO A1712 " ideal model delta sigma weight residual 119.66 112.80 6.86 7.30e-01 1.88e+00 8.83e+01 ... (remaining 18370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 7978 35.95 - 71.90: 340 71.90 - 107.86: 25 107.86 - 143.81: 3 143.81 - 179.76: 1 Dihedral angle restraints: 8347 sinusoidal: 3701 harmonic: 4646 Sorted by residual: dihedral pdb=" CB CYS A1715 " pdb=" SG CYS A1715 " pdb=" SG CYS A1730 " pdb=" CB CYS A1730 " ideal model delta sinusoidal sigma weight residual 93.00 10.41 82.59 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual 93.00 166.05 -73.05 1 1.00e+01 1.00e-02 6.80e+01 dihedral pdb=" CB CYS C 72 " pdb=" SG CYS C 72 " pdb=" SG CYS C 75 " pdb=" CB CYS C 75 " ideal model delta sinusoidal sigma weight residual 93.00 161.59 -68.59 1 1.00e+01 1.00e-02 6.10e+01 ... (remaining 8344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1811 0.116 - 0.232: 205 0.232 - 0.348: 49 0.348 - 0.465: 19 0.465 - 0.581: 2 Chirality restraints: 2086 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.90e+01 chirality pdb=" CA ASP A1677 " pdb=" N ASP A1677 " pdb=" C ASP A1677 " pdb=" CB ASP A1677 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.43e+00 chirality pdb=" CA GLU A 294 " pdb=" N GLU A 294 " pdb=" C GLU A 294 " pdb=" CB GLU A 294 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.92e+00 ... (remaining 2083 not shown) Planarity restraints: 2222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " 0.307 2.00e-02 2.50e+03 2.69e-01 9.04e+02 pdb=" C7 NAG E 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " 0.126 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " -0.483 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " 0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 302 " 0.166 2.00e-02 2.50e+03 1.37e-01 2.34e+02 pdb=" C7 NAG B 302 " -0.046 2.00e-02 2.50e+03 pdb=" C8 NAG B 302 " 0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B 302 " -0.220 2.00e-02 2.50e+03 pdb=" O7 NAG B 302 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 301 " -0.156 2.00e-02 2.50e+03 1.27e-01 2.03e+02 pdb=" C7 NAG B 301 " 0.044 2.00e-02 2.50e+03 pdb=" C8 NAG B 301 " -0.116 2.00e-02 2.50e+03 pdb=" N2 NAG B 301 " 0.201 2.00e-02 2.50e+03 pdb=" O7 NAG B 301 " 0.028 2.00e-02 2.50e+03 ... (remaining 2219 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 260 2.61 - 3.18: 13029 3.18 - 3.76: 20491 3.76 - 4.33: 28309 4.33 - 4.90: 45749 Nonbonded interactions: 107838 Sorted by model distance: nonbonded pdb=" N GLN A1494 " pdb=" OE1 GLN A1494 " model vdw 2.039 3.120 nonbonded pdb=" O SER A1430 " pdb=" OG SER A1430 " model vdw 2.151 3.040 nonbonded pdb=" OD1 ASP C 45 " pdb=" NE ARG C 115 " model vdw 2.202 3.120 nonbonded pdb=" OG1 THR C 68 " pdb=" ND2 ASN C 126 " model vdw 2.214 3.120 nonbonded pdb=" N GLU A 771 " pdb=" OE1 GLU A 771 " model vdw 2.216 3.120 ... (remaining 107833 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.14 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.250 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.015 0.130 13634 Z= 0.952 Angle : 1.632 25.138 18427 Z= 0.967 Chirality : 0.092 0.581 2086 Planarity : 0.010 0.269 2214 Dihedral : 18.615 179.759 5310 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 20.48 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.01 % Rotamer: Outliers : 2.81 % Allowed : 5.35 % Favored : 91.84 % Cbeta Deviations : 0.87 % 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: -0.94 (0.20), residues: 1565 helix: -0.13 (0.16), residues: 889 sheet: -0.39 (0.43), residues: 150 loop : -1.34 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG A1308 TYR 0.040 0.004 TYR B 132 PHE 0.043 0.004 PHE B 54 TRP 0.088 0.004 TRP A 908 HIS 0.012 0.002 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.01543 / 0.95 (13613) covalent geometry : angle 1.59358 / 0.96 (18375) SS BOND : bond 0.02316 / 1.40 ( 11) SS BOND : angle 7.63733 / 5.71 ( 22) hydrogen bonds : bond 0.18126 / 12.27 ( 784) hydrogen bonds : angle 7.81555 / 5.35 ( 2223) link_BETA1-4 : bond 0.00642 / 0.31 ( 2) link_BETA1-4 : angle 2.15706 / 1.14 ( 6) link_NAG-ASN : bond 0.01151 / 0.46 ( 8) link_NAG-ASN : angle 6.79058 / 3.93 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.7671 (mmm-85) cc_final: 0.7391 (mmm-85) REVERT: A 379 MET cc_start: 0.7914 (ttp) cc_final: 0.7616 (ttt) REVERT: A 794 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7144 (tppp) REVERT: A 854 MET cc_start: 0.6997 (tpp) cc_final: 0.6356 (tpp) REVERT: A 1182 ARG cc_start: 0.6711 (ttt-90) cc_final: 0.6469 (ttt-90) REVERT: A 1359 PHE cc_start: 0.8720 (OUTLIER) cc_final: 0.8463 (m-10) REVERT: A 1537 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7042 (tt0) REVERT: B 166 LEU cc_start: 0.9578 (mp) cc_final: 0.9339 (mp) REVERT: B 183 LYS cc_start: 0.8829 (mttt) cc_final: 0.8447 (mttm) outliers start: 40 outliers final: 15 residues processed: 262 average time/residue: 0.1191 time to fit residues: 45.5014 Evaluate side-chains 197 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 951 VAL Chi-restraints excluded: chain A residue 1278 LEU Chi-restraints excluded: chain A residue 1359 PHE Chi-restraints excluded: chain A residue 1454 CYS 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 B residue 43 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 189 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 70 GLN A 125 HIS A 270 ASN A 273 HIS ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 412 ASN A 774 ASN A 809 ASN A1004 GLN A1180 ASN A1483 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.144109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.098452 restraints weight = 45824.614| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 3.34 r_work: 0.3183 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13634 Z= 0.164 Angle : 0.738 10.321 18427 Z= 0.380 Chirality : 0.045 0.396 2086 Planarity : 0.005 0.050 2214 Dihedral : 14.975 162.623 2302 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.96 % Allowed : 13.79 % Favored : 83.25 % 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: -0.38 (0.21), residues: 1565 helix: 0.48 (0.16), residues: 924 sheet: -0.60 (0.43), residues: 140 loop : -1.40 (0.27), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 922 TYR 0.022 0.002 TYR A 803 PHE 0.031 0.002 PHE A1233 TRP 0.036 0.002 TRP A 908 HIS 0.008 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (13613) covalent geometry : angle 0.72563 / 0.38 (18375) SS BOND : bond 0.00316 / 0.19 ( 11) SS BOND : angle 1.58727 / 0.86 ( 22) hydrogen bonds : bond 0.05509 / 3.62 ( 784) hydrogen bonds : angle 5.46092 / 3.82 ( 2223) link_BETA1-4 : bond 0.00197 / 0.09 ( 2) link_BETA1-4 : angle 2.93273 / 1.50 ( 6) link_NAG-ASN : bond 0.00508 / 0.31 ( 8) link_NAG-ASN : angle 3.22168 / 1.83 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 216 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.6425 (OUTLIER) cc_final: 0.5454 (mmm) REVERT: A 130 MET cc_start: 0.8507 (tmm) cc_final: 0.7649 (tpp) REVERT: A 296 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6439 (mm-30) REVERT: A 365 ASN cc_start: 0.8660 (OUTLIER) cc_final: 0.8416 (m-40) REVERT: A 379 MET cc_start: 0.8559 (ttp) cc_final: 0.8135 (ttt) REVERT: A 841 ARG cc_start: 0.7285 (ttm110) cc_final: 0.7017 (mtt90) REVERT: A 945 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9151 (mt) REVERT: A 949 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8121 (mpt) REVERT: A 1672 GLU cc_start: 0.7867 (mm-30) cc_final: 0.7639 (tt0) REVERT: B 162 MET cc_start: 0.8314 (mmm) cc_final: 0.7947 (mmt) REVERT: B 177 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8421 (mt-10) REVERT: B 178 MET cc_start: 0.8444 (ppp) cc_final: 0.8116 (ppp) REVERT: B 180 TYR cc_start: 0.9136 (t80) cc_final: 0.8821 (t80) REVERT: B 183 LYS cc_start: 0.8597 (mttt) cc_final: 0.8288 (mtmt) REVERT: B 184 LYS cc_start: 0.9044 (mtmm) cc_final: 0.8693 (mtmt) outliers start: 42 outliers final: 17 residues processed: 239 average time/residue: 0.1078 time to fit residues: 38.8998 Evaluate side-chains 212 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 365 ASN Chi-restraints excluded: chain A residue 806 VAL Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1232 ILE Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1454 CYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 95 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 70 GLN A 154 ASN A 365 ASN ** A 395 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.141241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097007 restraints weight = 31622.183| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 3.03 r_work: 0.3139 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13634 Z= 0.233 Angle : 0.723 9.181 18427 Z= 0.370 Chirality : 0.046 0.424 2086 Planarity : 0.004 0.039 2214 Dihedral : 13.829 159.606 2277 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.96 % Allowed : 18.09 % Favored : 78.96 % 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: -0.20 (0.21), residues: 1565 helix: 0.61 (0.17), residues: 905 sheet: -0.76 (0.43), residues: 140 loop : -1.13 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 84 TYR 0.022 0.002 TYR B 132 PHE 0.019 0.002 PHE A1740 TRP 0.034 0.002 TRP A 908 HIS 0.008 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.23 (13613) covalent geometry : angle 0.71261 / 0.37 (18375) SS BOND : bond 0.00535 / 0.34 ( 11) SS BOND : angle 1.52223 / 0.84 ( 22) hydrogen bonds : bond 0.05200 / 3.40 ( 784) hydrogen bonds : angle 5.24058 / 3.67 ( 2223) link_BETA1-4 : bond 0.00368 / 0.19 ( 2) link_BETA1-4 : angle 2.20026 / 1.12 ( 6) link_NAG-ASN : bond 0.00375 / 0.21 ( 8) link_NAG-ASN : angle 3.02530 / 1.74 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 200 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.6592 (OUTLIER) cc_final: 0.5713 (mmm) REVERT: A 296 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6592 (mm-30) REVERT: A 379 MET cc_start: 0.8691 (ttp) cc_final: 0.8464 (ttt) REVERT: A 854 MET cc_start: 0.7533 (tpp) cc_final: 0.6869 (tpp) REVERT: A 945 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9139 (tt) REVERT: B 162 MET cc_start: 0.8340 (mmm) cc_final: 0.8026 (mmt) REVERT: B 177 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8407 (mt-10) REVERT: B 183 LYS cc_start: 0.8558 (mttt) cc_final: 0.8271 (mmtp) REVERT: B 184 LYS cc_start: 0.8997 (mtmm) cc_final: 0.8787 (mmtm) outliers start: 42 outliers final: 22 residues processed: 222 average time/residue: 0.1039 time to fit residues: 35.3855 Evaluate side-chains 215 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 123 LEU Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 758 THR Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1301 LEU Chi-restraints excluded: chain A residue 1454 CYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 37 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 88 optimal weight: 7.9990 chunk 89 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.144031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.100582 restraints weight = 38443.580| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.53 r_work: 0.3173 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13634 Z= 0.127 Angle : 0.608 8.728 18427 Z= 0.312 Chirality : 0.042 0.361 2086 Planarity : 0.004 0.039 2214 Dihedral : 12.576 153.416 2274 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.81 % Allowed : 19.00 % Favored : 78.18 % 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: 0.23 (0.21), residues: 1565 helix: 1.00 (0.17), residues: 905 sheet: -0.73 (0.42), residues: 140 loop : -1.01 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 84 TYR 0.032 0.001 TYR A 157 PHE 0.015 0.001 PHE A1233 TRP 0.016 0.001 TRP A 908 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (13613) covalent geometry : angle 0.59950 / 0.31 (18375) SS BOND : bond 0.00510 / 0.27 ( 11) SS BOND : angle 1.11111 / 0.57 ( 22) hydrogen bonds : bond 0.04351 / 2.84 ( 784) hydrogen bonds : angle 4.86078 / 3.39 ( 2223) link_BETA1-4 : bond 0.00285 / 0.14 ( 2) link_BETA1-4 : angle 1.93970 / 0.99 ( 6) link_NAG-ASN : bond 0.00399 / 0.21 ( 8) link_NAG-ASN : angle 2.62084 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 210 time to evaluate : 0.528 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5341 (tmm) cc_final: 0.5093 (mmm) REVERT: C 113 MET cc_start: 0.6753 (OUTLIER) cc_final: 0.5951 (mmm) REVERT: A 82 TYR cc_start: 0.8338 (m-10) cc_final: 0.8136 (m-10) REVERT: A 130 MET cc_start: 0.8576 (tmm) cc_final: 0.7660 (tpp) REVERT: A 153 LYS cc_start: 0.8040 (tppt) cc_final: 0.7822 (tppt) REVERT: A 157 TYR cc_start: 0.8106 (m-80) cc_final: 0.7893 (m-80) REVERT: A 296 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6556 (mm-30) REVERT: A 379 MET cc_start: 0.8631 (ttp) cc_final: 0.8387 (ttt) REVERT: A 426 MET cc_start: 0.5648 (mmm) cc_final: 0.4954 (ttp) REVERT: A 854 MET cc_start: 0.7496 (tpp) cc_final: 0.7279 (tpp) REVERT: B 72 ARG cc_start: 0.8449 (ttt90) cc_final: 0.8004 (ttt90) REVERT: B 101 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8690 (mt) REVERT: B 162 MET cc_start: 0.8394 (mmm) cc_final: 0.8118 (mmt) REVERT: B 177 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8452 (mt-10) REVERT: B 179 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9176 (tp) REVERT: B 183 LYS cc_start: 0.8622 (mttt) cc_final: 0.8239 (mmtp) outliers start: 40 outliers final: 19 residues processed: 234 average time/residue: 0.1071 time to fit residues: 38.1389 Evaluate side-chains 213 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1454 CYS Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 74 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 15 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 23 optimal weight: 0.0020 chunk 72 optimal weight: 0.6980 chunk 147 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 overall best weight: 1.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 270 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1762 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.143675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.099881 restraints weight = 49945.313| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 3.60 r_work: 0.3134 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13634 Z= 0.142 Angle : 0.614 12.373 18427 Z= 0.310 Chirality : 0.042 0.373 2086 Planarity : 0.004 0.037 2214 Dihedral : 12.050 152.692 2270 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.67 % Allowed : 20.69 % Favored : 76.64 % 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: 0.29 (0.21), residues: 1565 helix: 1.04 (0.17), residues: 907 sheet: -0.68 (0.42), residues: 141 loop : -0.99 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 84 TYR 0.017 0.002 TYR A1235 PHE 0.024 0.001 PHE A1554 TRP 0.014 0.001 TRP C 67 HIS 0.009 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (13613) covalent geometry : angle 0.60524 / 0.31 (18375) SS BOND : bond 0.00356 / 0.21 ( 11) SS BOND : angle 1.12713 / 0.60 ( 22) hydrogen bonds : bond 0.04300 / 2.79 ( 784) hydrogen bonds : angle 4.80282 / 3.37 ( 2223) link_BETA1-4 : bond 0.00270 / 0.14 ( 2) link_BETA1-4 : angle 2.07153 / 1.06 ( 6) link_NAG-ASN : bond 0.00365 / 0.19 ( 8) link_NAG-ASN : angle 2.61992 / 1.54 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 205 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: C 113 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.5866 (mmm) REVERT: C 125 TYR cc_start: 0.5842 (m-80) cc_final: 0.5529 (m-80) REVERT: C 135 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7227 (mmp80) REVERT: A 217 ARG cc_start: 0.8661 (mmt180) cc_final: 0.8458 (mpt180) REVERT: A 296 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6638 (mm-30) REVERT: A 854 MET cc_start: 0.7567 (tpp) cc_final: 0.6905 (tpp) REVERT: A 908 TRP cc_start: 0.7687 (m100) cc_final: 0.7301 (m100) REVERT: A 1543 MET cc_start: 0.8694 (tpp) cc_final: 0.8300 (tpp) REVERT: B 101 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8706 (mt) REVERT: B 162 MET cc_start: 0.8389 (mmm) cc_final: 0.8131 (mmt) REVERT: B 177 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8453 (mt-10) REVERT: B 179 ILE cc_start: 0.9468 (tp) cc_final: 0.9211 (tp) REVERT: B 180 TYR cc_start: 0.9321 (t80) cc_final: 0.8858 (t80) REVERT: B 183 LYS cc_start: 0.8545 (mttt) cc_final: 0.8159 (mmtp) REVERT: B 184 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8611 (mtmt) outliers start: 38 outliers final: 25 residues processed: 226 average time/residue: 0.1080 time to fit residues: 37.1906 Evaluate side-chains 218 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 190 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1203 LEU Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 106 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 125 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 19 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 145 GLN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.144788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.102090 restraints weight = 45040.550| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 3.52 r_work: 0.3166 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 13634 Z= 0.117 Angle : 0.595 10.447 18427 Z= 0.299 Chirality : 0.041 0.347 2086 Planarity : 0.004 0.037 2214 Dihedral : 11.603 150.997 2269 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.39 % Allowed : 21.60 % Favored : 76.00 % 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: 0.42 (0.21), residues: 1565 helix: 1.16 (0.17), residues: 906 sheet: -0.68 (0.41), residues: 141 loop : -0.93 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 84 TYR 0.024 0.001 TYR A 157 PHE 0.016 0.001 PHE A1603 TRP 0.013 0.001 TRP C 67 HIS 0.007 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (13613) covalent geometry : angle 0.58703 / 0.30 (18375) SS BOND : bond 0.00208 / 0.11 ( 11) SS BOND : angle 1.03730 / 0.54 ( 22) hydrogen bonds : bond 0.04044 / 2.63 ( 784) hydrogen bonds : angle 4.68679 / 3.29 ( 2223) link_BETA1-4 : bond 0.00249 / 0.12 ( 2) link_BETA1-4 : angle 1.99443 / 1.01 ( 6) link_NAG-ASN : bond 0.00380 / 0.19 ( 8) link_NAG-ASN : angle 2.44890 / 1.43 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 199 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.5515 (tmm) cc_final: 0.5287 (mmm) REVERT: C 113 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.5861 (mmm) REVERT: C 135 ARG cc_start: 0.8050 (mmp80) cc_final: 0.7686 (mmp80) REVERT: A 130 MET cc_start: 0.8562 (tmm) cc_final: 0.7688 (tpp) REVERT: A 214 ARG cc_start: 0.7374 (mmm-85) cc_final: 0.6657 (mmm-85) REVERT: A 296 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6648 (mm-30) REVERT: A 426 MET cc_start: 0.5168 (mmm) cc_final: 0.4533 (ttp) REVERT: A 854 MET cc_start: 0.7452 (tpp) cc_final: 0.6657 (tpp) REVERT: A 1743 TYR cc_start: 0.8943 (t80) cc_final: 0.8723 (t80) REVERT: B 72 ARG cc_start: 0.8480 (ttt90) cc_final: 0.8008 (ttt90) REVERT: B 162 MET cc_start: 0.8492 (mmm) cc_final: 0.8285 (mmt) REVERT: B 177 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8358 (mt-10) REVERT: B 179 ILE cc_start: 0.9478 (OUTLIER) cc_final: 0.9221 (tp) REVERT: B 180 TYR cc_start: 0.9323 (t80) cc_final: 0.8842 (t80) REVERT: B 183 LYS cc_start: 0.8545 (mttt) cc_final: 0.8161 (mmtp) REVERT: B 184 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8606 (mtmt) outliers start: 34 outliers final: 24 residues processed: 218 average time/residue: 0.1057 time to fit residues: 35.2753 Evaluate side-chains 212 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 185 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1267 ASP Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 179 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 126 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 130 optimal weight: 0.4980 chunk 42 optimal weight: 4.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.142588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099634 restraints weight = 50870.677| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.65 r_work: 0.3112 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3115 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3115 r_free = 0.3115 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.3115 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13634 Z= 0.179 Angle : 0.631 9.801 18427 Z= 0.319 Chirality : 0.043 0.403 2086 Planarity : 0.004 0.037 2214 Dihedral : 11.622 150.791 2269 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.89 % Allowed : 21.82 % Favored : 75.30 % 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: 0.30 (0.21), residues: 1565 helix: 1.05 (0.17), residues: 906 sheet: -0.75 (0.41), residues: 141 loop : -0.95 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 84 TYR 0.036 0.002 TYR A 157 PHE 0.020 0.002 PHE A1554 TRP 0.024 0.001 TRP A 908 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (13613) covalent geometry : angle 0.62224 / 0.32 (18375) SS BOND : bond 0.00346 / 0.22 ( 11) SS BOND : angle 1.27375 / 0.70 ( 22) hydrogen bonds : bond 0.04279 / 2.78 ( 784) hydrogen bonds : angle 4.75263 / 3.33 ( 2223) link_BETA1-4 : bond 0.00279 / 0.14 ( 2) link_BETA1-4 : angle 1.84778 / 0.94 ( 6) link_NAG-ASN : bond 0.00344 / 0.18 ( 8) link_NAG-ASN : angle 2.60550 / 1.51 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 79 MET cc_start: 0.5561 (tmm) cc_final: 0.5309 (mmm) REVERT: C 113 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.5890 (mmm) REVERT: C 125 TYR cc_start: 0.5901 (m-80) cc_final: 0.5523 (m-80) REVERT: C 135 ARG cc_start: 0.8001 (mmp80) cc_final: 0.7683 (mmp80) REVERT: A 130 MET cc_start: 0.8476 (tmm) cc_final: 0.7648 (tpp) REVERT: A 426 MET cc_start: 0.5143 (mmm) cc_final: 0.4402 (ttp) REVERT: A 854 MET cc_start: 0.7538 (tpp) cc_final: 0.6903 (tpp) REVERT: A 1369 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: B 45 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.8174 (ttp-170) REVERT: B 162 MET cc_start: 0.8420 (mmm) cc_final: 0.8218 (mmt) REVERT: B 177 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8346 (mt-10) REVERT: B 180 TYR cc_start: 0.9325 (t80) cc_final: 0.8786 (t80) REVERT: B 183 LYS cc_start: 0.8551 (mttt) cc_final: 0.8233 (mmtp) REVERT: B 184 LYS cc_start: 0.9172 (mmtm) cc_final: 0.8601 (mtmt) outliers start: 41 outliers final: 29 residues processed: 212 average time/residue: 0.1104 time to fit residues: 35.7380 Evaluate side-chains 213 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 154 optimal weight: 5.9990 chunk 15 optimal weight: 0.0170 chunk 26 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 59 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1461 ASN ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.141700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.099111 restraints weight = 54088.773| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.46 r_work: 0.3099 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13634 Z= 0.208 Angle : 0.659 11.500 18427 Z= 0.332 Chirality : 0.044 0.443 2086 Planarity : 0.004 0.037 2214 Dihedral : 11.752 149.865 2269 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.24 % Allowed : 21.53 % Favored : 75.23 % 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: 0.19 (0.21), residues: 1565 helix: 0.94 (0.17), residues: 909 sheet: -0.75 (0.42), residues: 140 loop : -0.98 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 84 TYR 0.018 0.002 TYR A 367 PHE 0.019 0.002 PHE A 128 TRP 0.030 0.002 TRP A 908 HIS 0.006 0.001 HIS A 765 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (13613) covalent geometry : angle 0.64995 / 0.33 (18375) SS BOND : bond 0.00391 / 0.25 ( 11) SS BOND : angle 1.37927 / 0.76 ( 22) hydrogen bonds : bond 0.04393 / 2.84 ( 784) hydrogen bonds : angle 4.81795 / 3.38 ( 2223) link_BETA1-4 : bond 0.00288 / 0.15 ( 2) link_BETA1-4 : angle 1.70145 / 0.86 ( 6) link_NAG-ASN : bond 0.00360 / 0.18 ( 8) link_NAG-ASN : angle 2.74925 / 1.59 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 184 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5542 (tmm) cc_final: 0.5302 (mmm) REVERT: C 113 MET cc_start: 0.6665 (OUTLIER) cc_final: 0.6323 (mmm) REVERT: C 125 TYR cc_start: 0.5702 (m-80) cc_final: 0.5187 (m-80) REVERT: C 135 ARG cc_start: 0.7975 (mmp80) cc_final: 0.7723 (mmp80) REVERT: A 130 MET cc_start: 0.8462 (tmm) cc_final: 0.7609 (tpp) REVERT: A 133 MET cc_start: 0.6963 (mtp) cc_final: 0.6693 (mtm) REVERT: A 217 ARG cc_start: 0.8438 (mpt180) cc_final: 0.8143 (mmt180) REVERT: A 296 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6717 (mm-30) REVERT: A 426 MET cc_start: 0.5205 (mmm) cc_final: 0.4491 (ttp) REVERT: A 854 MET cc_start: 0.7673 (tpp) cc_final: 0.7082 (tpp) REVERT: A 1369 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 45 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8176 (ttp-170) REVERT: B 177 GLU cc_start: 0.8976 (mm-30) cc_final: 0.8343 (mt-10) REVERT: B 180 TYR cc_start: 0.9258 (t80) cc_final: 0.8681 (t80) REVERT: B 183 LYS cc_start: 0.8575 (mttt) cc_final: 0.8244 (mmtp) REVERT: B 184 LYS cc_start: 0.9184 (mmtm) cc_final: 0.8630 (mtmt) outliers start: 46 outliers final: 31 residues processed: 213 average time/residue: 0.1037 time to fit residues: 34.0500 Evaluate side-chains 213 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 178 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1369 GLU Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 10 optimal weight: 0.7980 chunk 6 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 chunk 119 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 30.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.143098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.099914 restraints weight = 54478.269| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 3.59 r_work: 0.3115 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (6 function evaluations) r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13634 Z= 0.145 Angle : 0.621 11.750 18427 Z= 0.313 Chirality : 0.042 0.399 2086 Planarity : 0.004 0.037 2214 Dihedral : 11.519 148.434 2269 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.89 % Allowed : 22.17 % Favored : 74.95 % 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: 0.34 (0.21), residues: 1565 helix: 1.08 (0.17), residues: 909 sheet: -0.72 (0.41), residues: 141 loop : -0.96 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 84 TYR 0.038 0.002 TYR A 157 PHE 0.024 0.001 PHE A1554 TRP 0.016 0.001 TRP C 67 HIS 0.012 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (13613) covalent geometry : angle 0.61287 / 0.31 (18375) SS BOND : bond 0.00273 / 0.17 ( 11) SS BOND : angle 1.27320 / 0.69 ( 22) hydrogen bonds : bond 0.04155 / 2.69 ( 784) hydrogen bonds : angle 4.69996 / 3.31 ( 2223) link_BETA1-4 : bond 0.00200 / 0.10 ( 2) link_BETA1-4 : angle 1.57329 / 0.80 ( 6) link_NAG-ASN : bond 0.00355 / 0.18 ( 8) link_NAG-ASN : angle 2.58908 / 1.50 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5549 (tmm) cc_final: 0.5309 (mmm) REVERT: C 85 MET cc_start: 0.8177 (OUTLIER) cc_final: 0.7923 (mmp) REVERT: C 113 MET cc_start: 0.6661 (OUTLIER) cc_final: 0.6315 (mmm) REVERT: C 125 TYR cc_start: 0.5559 (m-80) cc_final: 0.5154 (m-80) REVERT: C 135 ARG cc_start: 0.7956 (mmp80) cc_final: 0.7733 (mmp80) REVERT: A 133 MET cc_start: 0.6914 (mtp) cc_final: 0.6659 (mtm) REVERT: A 217 ARG cc_start: 0.8258 (mpt180) cc_final: 0.7985 (mmt180) REVERT: A 296 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.6654 (mm-30) REVERT: A 426 MET cc_start: 0.5117 (mmm) cc_final: 0.4380 (ttp) REVERT: A 854 MET cc_start: 0.7613 (tpp) cc_final: 0.6938 (tpp) REVERT: B 45 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8166 (ttp-170) REVERT: B 72 ARG cc_start: 0.8513 (ttt90) cc_final: 0.8038 (ttt90) REVERT: B 177 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8264 (mt-10) REVERT: B 180 TYR cc_start: 0.9257 (t80) cc_final: 0.8676 (t80) REVERT: B 183 LYS cc_start: 0.8579 (mttt) cc_final: 0.8253 (mmtp) REVERT: B 184 LYS cc_start: 0.9181 (mmtm) cc_final: 0.8620 (mtmt) outliers start: 41 outliers final: 29 residues processed: 211 average time/residue: 0.1017 time to fit residues: 32.9408 Evaluate side-chains 214 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 181 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 3 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 137 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.142936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099473 restraints weight = 52916.946| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 3.75 r_work: 0.3100 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13634 Z= 0.154 Angle : 0.638 10.691 18427 Z= 0.321 Chirality : 0.043 0.397 2086 Planarity : 0.004 0.037 2214 Dihedral : 11.454 148.430 2269 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.89 % Allowed : 22.59 % Favored : 74.52 % 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: 0.35 (0.21), residues: 1565 helix: 1.10 (0.17), residues: 909 sheet: -0.70 (0.41), residues: 141 loop : -0.95 (0.28), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 84 TYR 0.022 0.002 TYR A 157 PHE 0.032 0.001 PHE A1554 TRP 0.018 0.001 TRP C 67 HIS 0.006 0.001 HIS A 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (13613) covalent geometry : angle 0.63039 / 0.32 (18375) SS BOND : bond 0.00262 / 0.17 ( 11) SS BOND : angle 1.29823 / 0.70 ( 22) hydrogen bonds : bond 0.04145 / 2.68 ( 784) hydrogen bonds : angle 4.68551 / 3.30 ( 2223) link_BETA1-4 : bond 0.00211 / 0.11 ( 2) link_BETA1-4 : angle 1.55385 / 0.79 ( 6) link_NAG-ASN : bond 0.00340 / 0.17 ( 8) link_NAG-ASN : angle 2.54059 / 1.47 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 185 time to evaluate : 0.522 Fit side-chains revert: symmetry clash REVERT: C 79 MET cc_start: 0.5548 (tmm) cc_final: 0.5333 (mmm) REVERT: C 85 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8031 (mmp) REVERT: C 113 MET cc_start: 0.6687 (OUTLIER) cc_final: 0.6330 (mmm) REVERT: C 125 TYR cc_start: 0.5684 (m-80) cc_final: 0.5253 (m-80) REVERT: C 135 ARG cc_start: 0.7963 (mmp80) cc_final: 0.7752 (mmp80) REVERT: A 130 MET cc_start: 0.8638 (tmm) cc_final: 0.7727 (tpp) REVERT: A 217 ARG cc_start: 0.8305 (mpt180) cc_final: 0.7990 (mmt180) REVERT: A 296 GLU cc_start: 0.7734 (OUTLIER) cc_final: 0.6633 (mm-30) REVERT: A 426 MET cc_start: 0.4943 (mmm) cc_final: 0.4236 (ttp) REVERT: A 854 MET cc_start: 0.7502 (tpp) cc_final: 0.6835 (tpp) REVERT: B 45 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8229 (ttp-170) REVERT: B 72 ARG cc_start: 0.8498 (ttt90) cc_final: 0.8006 (ttt90) REVERT: B 177 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8262 (mt-10) REVERT: B 180 TYR cc_start: 0.9270 (t80) cc_final: 0.8679 (t80) REVERT: B 183 LYS cc_start: 0.8577 (mttt) cc_final: 0.8253 (mmtp) REVERT: B 184 LYS cc_start: 0.9181 (mmtm) cc_final: 0.8614 (mtmt) outliers start: 41 outliers final: 33 residues processed: 209 average time/residue: 0.1026 time to fit residues: 33.2284 Evaluate side-chains 220 residues out of total 1417 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 85 MET Chi-restraints excluded: chain C residue 113 MET Chi-restraints excluded: chain A residue 70 MET Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 176 PHE Chi-restraints excluded: chain A residue 235 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 858 ILE Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 949 MET Chi-restraints excluded: chain A residue 977 THR Chi-restraints excluded: chain A residue 1177 ILE Chi-restraints excluded: chain A residue 1222 ILE Chi-restraints excluded: chain A residue 1225 ILE Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1311 VAL Chi-restraints excluded: chain A residue 1467 LEU Chi-restraints excluded: chain A residue 1488 LEU Chi-restraints excluded: chain A residue 1520 SER Chi-restraints excluded: chain A residue 1526 CYS Chi-restraints excluded: chain A residue 1562 CYS Chi-restraints excluded: chain A residue 1604 VAL Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1632 THR Chi-restraints excluded: chain A residue 1678 MET Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 133 GLU Chi-restraints excluded: chain B residue 166 LEU Chi-restraints excluded: chain B residue 170 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 42 optimal weight: 2.9990 chunk 147 optimal weight: 0.9980 chunk 132 optimal weight: 0.8980 chunk 113 optimal weight: 6.9990 chunk 136 optimal weight: 0.9990 chunk 75 optimal weight: 0.2980 chunk 121 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1505 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.144629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.102531 restraints weight = 38100.058| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.50 r_work: 0.3180 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13634 Z= 0.121 Angle : 0.611 10.712 18427 Z= 0.308 Chirality : 0.042 0.351 2086 Planarity : 0.003 0.038 2214 Dihedral : 11.136 147.841 2269 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 2.46 % Allowed : 23.15 % Favored : 74.38 % 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: 0.49 (0.21), residues: 1565 helix: 1.21 (0.17), residues: 915 sheet: -0.64 (0.41), residues: 141 loop : -0.94 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 84 TYR 0.031 0.001 TYR A 157 PHE 0.034 0.001 PHE A1554 TRP 0.016 0.001 TRP C 67 HIS 0.006 0.001 HIS C 136 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (13613) covalent geometry : angle 0.60383 / 0.31 (18375) SS BOND : bond 0.00203 / 0.11 ( 11) SS BOND : angle 1.15825 / 0.61 ( 22) hydrogen bonds : bond 0.03937 / 2.55 ( 784) hydrogen bonds : angle 4.58461 / 3.23 ( 2223) link_BETA1-4 : bond 0.00173 / 0.08 ( 2) link_BETA1-4 : angle 1.49208 / 0.74 ( 6) link_NAG-ASN : bond 0.00357 / 0.18 ( 8) link_NAG-ASN : angle 2.32727 / 1.35 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3874.62 seconds wall clock time: 67 minutes 12.47 seconds (4032.47 seconds total)