Starting phenix.real_space_refine on Wed Mar 4 12:01:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eju_31163/03_2026/7eju_31163.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eju_31163/03_2026/7eju_31163.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7eju_31163/03_2026/7eju_31163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eju_31163/03_2026/7eju_31163.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7eju_31163/03_2026/7eju_31163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eju_31163/03_2026/7eju_31163.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 1 5.21 5 S 104 5.16 5 C 8761 2.51 5 N 2322 2.21 5 O 2523 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13713 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 13287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1648, 13287 Classifications: {'peptide': 1648} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 53, 'TRANS': 1593} Chain breaks: 13 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 423 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 423 Classifications: {'peptide': 52} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 48} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2250 SG CYS A 284 49.406 69.499 28.181 1.00 17.67 S ATOM 2274 SG CYS A 287 52.033 68.116 26.224 1.00 23.83 S ATOM 13360 SG CYS B 39 23.315 79.239 60.513 1.00 31.24 S ATOM 13381 SG CYS B 42 25.002 80.311 57.535 1.00 28.92 S ATOM 13540 SG CYS B 61 22.099 78.744 56.008 1.00 48.21 S Time building chain proxies: 2.47, per 1000 atoms: 0.18 Number of scatterers: 13713 At special positions: 0 Unit cell: (124.15, 112.45, 117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 104 16.00 Mg 1 11.99 O 2523 8.00 N 2322 7.00 C 8761 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1651 " - pdb=" SG CYS A1663 " distance=2.04 Simple disulfide: pdb=" SG CYS A1690 " - pdb=" SG CYS A1775 " distance=2.05 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 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 559.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2301 " pdb="ZN ZN A2301 " - pdb=" ND1 HIS A 471 " pdb="ZN ZN A2301 " - pdb=" SG CYS A 287 " pdb="ZN ZN A2301 " - pdb=" SG CYS A 284 " pdb=" ZN B 101 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 42 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 61 " pdb="ZN ZN B 101 " - pdb=" SG CYS B 39 " 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3248 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 10 sheets defined 46.7% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 26 through 31 removed outlier: 4.001A pdb=" N SER A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 58 removed outlier: 3.790A pdb=" N LEU A 40 " --> pdb=" O SER A 36 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 42 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 45 " --> pdb=" O GLU A 41 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A 58 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 77 removed outlier: 4.378A pdb=" N HIS A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 128 removed outlier: 3.939A pdb=" N SER A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASN A 125 " --> pdb=" O SER A 121 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU A 126 " --> pdb=" O LYS A 122 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 127 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N SER A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.985A pdb=" N LEU A 163 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ILE A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ASP A 166 " --> pdb=" O TRP A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 192 Processing helix chain 'A' and resid 203 through 207 removed outlier: 4.325A pdb=" N CYS A 206 " --> pdb=" O ASN A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 220 removed outlier: 3.950A pdb=" N GLU A 216 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ARG A 217 " --> pdb=" O GLY A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 250 removed outlier: 3.807A pdb=" N ILE A 235 " --> pdb=" O ARG A 231 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU A 237 " --> pdb=" O SER A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 284 through 289 removed outlier: 4.033A pdb=" N ALA A 288 " --> pdb=" O CYS A 284 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ASN A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 284 through 289' Processing helix chain 'A' and resid 291 through 299 removed outlier: 3.575A pdb=" N VAL A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 339 removed outlier: 3.950A pdb=" N GLN A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 367 removed outlier: 3.663A pdb=" N PHE A 364 " --> pdb=" O LEU A 360 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LYS A 365 " --> pdb=" O CYS A 361 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N TYR A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 403 Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.849A pdb=" N THR A 408 " --> pdb=" O LYS A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 422 removed outlier: 3.643A pdb=" N ARG A 418 " --> pdb=" O GLN A 414 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR A 419 " --> pdb=" O MET A 415 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.503A pdb=" N LEU A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ILE A 445 " --> pdb=" O ASP A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 477 Processing helix chain 'A' and resid 478 through 499 removed outlier: 3.575A pdb=" N LEU A 489 " --> pdb=" O LEU A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 577 Processing helix chain 'A' and resid 585 through 598 removed outlier: 4.038A pdb=" N LEU A 598 " --> pdb=" O MET A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 622 removed outlier: 3.605A pdb=" N LEU A 620 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 632 removed outlier: 3.543A pdb=" N GLN A 628 " --> pdb=" O SER A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 643 removed outlier: 3.949A pdb=" N PHE A 637 " --> pdb=" O GLY A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 678 removed outlier: 3.934A pdb=" N LEU A 665 " --> pdb=" O GLY A 661 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLN A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ILE A 677 " --> pdb=" O LEU A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 700 removed outlier: 3.683A pdb=" N ARG A 691 " --> pdb=" O TYR A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 704 removed outlier: 3.517A pdb=" N LEU A 704 " --> pdb=" O LEU A 701 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 701 through 704' Processing helix chain 'A' and resid 711 through 719 removed outlier: 3.802A pdb=" N ASP A 715 " --> pdb=" O ASP A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 731 Processing helix chain 'A' and resid 744 through 759 removed outlier: 3.934A pdb=" N GLU A 748 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 788 removed outlier: 3.681A pdb=" N ARG A 788 " --> pdb=" O SER A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 854 removed outlier: 4.228A pdb=" N GLU A 849 " --> pdb=" O SER A 845 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N PHE A 851 " --> pdb=" O MET A 847 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N LYS A 852 " --> pdb=" O ALA A 848 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 873 Processing helix chain 'A' and resid 887 through 894 Processing helix chain 'A' and resid 897 through 918 removed outlier: 3.809A pdb=" N ASP A 910 " --> pdb=" O GLY A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 974 removed outlier: 3.608A pdb=" N VAL A 973 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE A 974 " --> pdb=" O PRO A 971 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 970 through 974' Processing helix chain 'A' and resid 983 through 988 removed outlier: 4.079A pdb=" N TYR A 987 " --> pdb=" O CYS A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1019 Processing helix chain 'A' and resid 1022 through 1034 removed outlier: 3.656A pdb=" N CYS A1026 " --> pdb=" O GLU A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1155 removed outlier: 3.700A pdb=" N MET A1155 " --> pdb=" O VAL A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1163 through 1180 removed outlier: 3.700A pdb=" N MET A1175 " --> pdb=" O CYS A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1190 through 1195 removed outlier: 3.758A pdb=" N MET A1195 " --> pdb=" O TRP A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1196 through 1205 removed outlier: 3.557A pdb=" N PHE A1200 " --> pdb=" O SER A1196 " (cutoff:3.500A) Processing helix chain 'A' and resid 1220 through 1232 removed outlier: 3.772A pdb=" N TRP A1229 " --> pdb=" O ASN A1225 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1245 removed outlier: 3.611A pdb=" N ALA A1244 " --> pdb=" O ASN A1240 " (cutoff:3.500A) Processing helix chain 'A' and resid 1266 through 1274 removed outlier: 3.716A pdb=" N GLN A1271 " --> pdb=" O GLU A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1317 removed outlier: 3.757A pdb=" N GLU A1306 " --> pdb=" O GLY A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1350 through 1365 removed outlier: 3.596A pdb=" N ASN A1365 " --> pdb=" O SER A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1404 removed outlier: 3.691A pdb=" N PHE A1398 " --> pdb=" O LEU A1394 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N HIS A1404 " --> pdb=" O SER A1400 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1425 Processing helix chain 'A' and resid 1431 through 1447 removed outlier: 3.720A pdb=" N VAL A1435 " --> pdb=" O SER A1431 " (cutoff:3.500A) Processing helix chain 'A' and resid 1471 through 1484 removed outlier: 3.595A pdb=" N PHE A1484 " --> pdb=" O ILE A1480 " (cutoff:3.500A) Processing helix chain 'A' and resid 1493 through 1506 removed outlier: 3.559A pdb=" N LYS A1505 " --> pdb=" O PHE A1501 " (cutoff:3.500A) Processing helix chain 'A' and resid 1514 through 1519 Processing helix chain 'A' and resid 1522 through 1534 removed outlier: 3.975A pdb=" N ALA A1533 " --> pdb=" O PHE A1529 " (cutoff:3.500A) Processing helix chain 'A' and resid 1536 through 1541 removed outlier: 3.923A pdb=" N ARG A1541 " --> pdb=" O GLU A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1579 through 1589 removed outlier: 4.188A pdb=" N THR A1583 " --> pdb=" O THR A1579 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A1589 " --> pdb=" O GLN A1585 " (cutoff:3.500A) Processing helix chain 'A' and resid 1613 through 1623 Processing helix chain 'A' and resid 1638 through 1644 removed outlier: 3.838A pdb=" N ILE A1642 " --> pdb=" O TYR A1638 " (cutoff:3.500A) Processing helix chain 'A' and resid 1652 through 1656 removed outlier: 3.565A pdb=" N ARG A1656 " --> pdb=" O ILE A1653 " (cutoff:3.500A) Processing helix chain 'A' and resid 1663 through 1667 removed outlier: 3.548A pdb=" N SER A1666 " --> pdb=" O CYS A1663 " (cutoff:3.500A) Processing helix chain 'A' and resid 1677 through 1690 removed outlier: 3.623A pdb=" N ALA A1689 " --> pdb=" O VAL A1685 " (cutoff:3.500A) Processing helix chain 'A' and resid 1694 through 1698 removed outlier: 3.933A pdb=" N PHE A1697 " --> pdb=" O GLU A1694 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER A1698 " --> pdb=" O TRP A1695 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1694 through 1698' Processing helix chain 'A' and resid 1736 through 1741 removed outlier: 3.574A pdb=" N ARG A1740 " --> pdb=" O LEU A1736 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG A1741 " --> pdb=" O HIS A1737 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1736 through 1741' Processing helix chain 'A' and resid 1744 through 1748 removed outlier: 4.359A pdb=" N PHE A1747 " --> pdb=" O PRO A1744 " (cutoff:3.500A) Processing helix chain 'A' and resid 1771 through 1776 Processing helix chain 'A' and resid 1776 through 1782 Processing helix chain 'A' and resid 1787 through 1792 removed outlier: 3.550A pdb=" N LEU A1792 " --> pdb=" O ILE A1788 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 69 removed outlier: 3.664A pdb=" N GLN B 63 " --> pdb=" O LEU B 59 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N SER B 69 " --> pdb=" O MET B 65 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 61 through 62 removed outlier: 3.561A pdb=" N GLY A 90 " --> pdb=" O LEU A 101 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU A 101 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU A 98 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL A 140 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N LEU A 100 " --> pdb=" O VAL A 140 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ASP A 142 " --> pdb=" O LEU A 100 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU A 102 " --> pdb=" O ASP A 142 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N ARG A 144 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N PHE A 104 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 258 through 260 Processing sheet with id=AA3, first strand: chain 'A' and resid 384 through 386 removed outlier: 3.616A pdb=" N CYS A 527 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 541 through 543 removed outlier: 3.511A pdb=" N LEU A 541 " --> pdb=" O TYR A 557 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 552 " --> pdb=" O CYS A 572 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N CYS A 572 " --> pdb=" O ARG A 552 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AA6, first strand: chain 'A' and resid 1116 through 1120 Processing sheet with id=AA7, first strand: chain 'A' and resid 1182 through 1187 removed outlier: 3.736A pdb=" N GLN A1330 " --> pdb=" O TYR A1186 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1378 through 1379 Processing sheet with id=AA9, first strand: chain 'A' and resid 1547 through 1548 Processing sheet with id=AB1, first strand: chain 'A' and resid 1716 through 1717 462 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4030 1.34 - 1.46: 3079 1.46 - 1.58: 6705 1.58 - 1.71: 0 1.71 - 1.83: 150 Bond restraints: 13964 Sorted by residual: bond pdb=" C LYS B 77 " pdb=" N PRO B 78 " ideal model delta sigma weight residual 1.334 1.394 -0.060 2.34e-02 1.83e+03 6.63e+00 bond pdb=" N PHE A 969 " pdb=" CA PHE A 969 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.23e-02 6.61e+03 6.48e+00 bond pdb=" CB VAL A1354 " pdb=" CG1 VAL A1354 " ideal model delta sigma weight residual 1.521 1.437 0.084 3.30e-02 9.18e+02 6.43e+00 bond pdb=" CG LEU A 496 " pdb=" CD2 LEU A 496 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.53e+00 bond pdb=" CG1 ILE A1677 " pdb=" CD1 ILE A1677 " ideal model delta sigma weight residual 1.513 1.432 0.081 3.90e-02 6.57e+02 4.36e+00 ... (remaining 13959 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.05: 18138 3.05 - 6.10: 569 6.10 - 9.15: 87 9.15 - 12.20: 22 12.20 - 15.26: 4 Bond angle restraints: 18820 Sorted by residual: angle pdb=" C ASP A 968 " pdb=" N PHE A 969 " pdb=" CA PHE A 969 " ideal model delta sigma weight residual 120.82 130.70 -9.88 1.50e+00 4.44e-01 4.34e+01 angle pdb=" C THR A1376 " pdb=" N PHE A1377 " pdb=" CA PHE A1377 " ideal model delta sigma weight residual 121.54 132.31 -10.77 1.91e+00 2.74e-01 3.18e+01 angle pdb=" C LEU A1287 " pdb=" N ASP A1288 " pdb=" CA ASP A1288 " ideal model delta sigma weight residual 121.54 131.80 -10.26 1.91e+00 2.74e-01 2.89e+01 angle pdb=" C LEU A 427 " pdb=" N TRP A 428 " pdb=" CA TRP A 428 " ideal model delta sigma weight residual 121.54 131.14 -9.60 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C ASN A 389 " pdb=" N ASP A 390 " pdb=" CA ASP A 390 " ideal model delta sigma weight residual 121.54 130.79 -9.25 1.91e+00 2.74e-01 2.34e+01 ... (remaining 18815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 7812 16.33 - 32.66: 583 32.66 - 48.98: 113 48.98 - 65.31: 9 65.31 - 81.64: 7 Dihedral angle restraints: 8524 sinusoidal: 3536 harmonic: 4988 Sorted by residual: dihedral pdb=" CA ARG A 19 " pdb=" C ARG A 19 " pdb=" N GLN A 20 " pdb=" CA GLN A 20 " ideal model delta harmonic sigma weight residual 180.00 -127.90 -52.10 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA GLY B 35 " pdb=" C GLY B 35 " pdb=" N ARG B 36 " pdb=" CA ARG B 36 " ideal model delta harmonic sigma weight residual -180.00 -133.16 -46.84 0 5.00e+00 4.00e-02 8.78e+01 dihedral pdb=" CA TRP B 76 " pdb=" C TRP B 76 " pdb=" N LYS B 77 " pdb=" CA LYS B 77 " ideal model delta harmonic sigma weight residual 180.00 143.90 36.10 0 5.00e+00 4.00e-02 5.21e+01 ... (remaining 8521 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1656 0.077 - 0.154: 425 0.154 - 0.230: 45 0.230 - 0.307: 8 0.307 - 0.384: 3 Chirality restraints: 2137 Sorted by residual: chirality pdb=" CB ILE A1677 " pdb=" CA ILE A1677 " pdb=" CG1 ILE A1677 " pdb=" CG2 ILE A1677 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.68e+00 chirality pdb=" CB ILE A 771 " pdb=" CA ILE A 771 " pdb=" CG1 ILE A 771 " pdb=" CG2 ILE A 771 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CB ILE A 957 " pdb=" CA ILE A 957 " pdb=" CG1 ILE A 957 " pdb=" CG2 ILE A 957 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 2134 not shown) Planarity restraints: 2376 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A1289 " -0.020 2.00e-02 2.50e+03 3.99e-02 1.59e+01 pdb=" C MET A1289 " 0.069 2.00e-02 2.50e+03 pdb=" O MET A1289 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY A1290 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A1716 " 0.028 2.00e-02 2.50e+03 1.90e-02 9.03e+00 pdb=" CG TRP A1716 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A1716 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP A1716 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A1716 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A1716 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A1716 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1716 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1716 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A1716 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 949 " -0.045 5.00e-02 4.00e+02 6.86e-02 7.53e+00 pdb=" N PRO A 950 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO A 950 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 950 " -0.039 5.00e-02 4.00e+02 ... (remaining 2373 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3182 2.79 - 3.31: 12398 3.31 - 3.84: 20831 3.84 - 4.37: 24381 4.37 - 4.90: 41825 Nonbonded interactions: 102617 Sorted by model distance: nonbonded pdb=" O PHE A1359 " pdb=" OG SER A1362 " model vdw 2.257 3.040 nonbonded pdb=" O LYS A 958 " pdb=" OG SER A 962 " model vdw 2.260 3.040 nonbonded pdb=" O ILE A 677 " pdb=" NH1 ARG A 691 " model vdw 2.279 3.120 nonbonded pdb=" OH TYR A 866 " pdb=" OE2 GLU A 888 " model vdw 2.292 3.040 nonbonded pdb=" OG SER A 121 " pdb=" OH TYR A 834 " model vdw 2.296 3.040 ... (remaining 102612 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.350 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 12.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 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 : 0.010 0.216 13972 Z= 0.396 Angle : 1.287 15.256 18824 Z= 0.668 Chirality : 0.067 0.384 2137 Planarity : 0.008 0.069 2376 Dihedral : 11.944 81.640 5270 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 17.01 % Favored : 82.81 % Rotamer: Outliers : 1.15 % Allowed : 7.35 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 1.82 % Twisted General : 0.37 % 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: -5.48 (0.15), residues: 1670 helix: -3.24 (0.13), residues: 730 sheet: -3.84 (0.40), residues: 102 loop : -4.05 (0.16), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 691 TYR 0.042 0.004 TYR A 557 PHE 0.040 0.004 PHE A1636 TRP 0.050 0.005 TRP A1716 HIS 0.016 0.003 HIS A 964 Details of bonding type rmsd covalent geometry : bond 0.00912 (13964) covalent geometry : angle 1.28711 (18820) SS BOND : bond 0.01464 ( 2) SS BOND : angle 1.66272 ( 4) hydrogen bonds : bond 0.18642 ( 462) hydrogen bonds : angle 7.00480 ( 1335) metal coordination : bond 0.16951 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 218 LEU cc_start: 0.8836 (tm) cc_final: 0.8576 (tt) REVERT: A 657 ASP cc_start: 0.8096 (p0) cc_final: 0.7886 (p0) REVERT: A 739 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8025 (tp) REVERT: A 1100 SER cc_start: 0.8127 (t) cc_final: 0.7894 (p) REVERT: A 1174 LYS cc_start: 0.7894 (mtmt) cc_final: 0.7622 (mtpp) REVERT: A 1751 LEU cc_start: 0.6625 (tp) cc_final: 0.6309 (mm) outliers start: 18 outliers final: 4 residues processed: 264 average time/residue: 0.1258 time to fit residues: 47.2059 Evaluate side-chains 175 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 170 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 347 ASN A 424 HIS A 471 HIS A 602 HIS A 647 HIS A 787 ASN ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1033 GLN A1110 ASN A1127 ASN A1232 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 HIS A1307 GLN A1330 GLN A1585 GLN A1784 ASN A1790 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.191414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.158876 restraints weight = 15732.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.158655 restraints weight = 16032.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.160287 restraints weight = 15011.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.160847 restraints weight = 10672.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161093 restraints weight = 9606.256| |-----------------------------------------------------------------------------| r_work (final): 0.3873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 1.921 13972 Z= 0.556 Angle : 0.703 9.286 18824 Z= 0.363 Chirality : 0.043 0.164 2137 Planarity : 0.005 0.054 2376 Dihedral : 6.714 39.113 1840 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.99 % Favored : 86.95 % Rotamer: Outliers : 2.81 % Allowed : 10.55 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.14 (0.17), residues: 1670 helix: -1.77 (0.17), residues: 749 sheet: -3.47 (0.43), residues: 105 loop : -3.70 (0.18), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 975 TYR 0.013 0.001 TYR A1096 PHE 0.025 0.001 PHE A 43 TRP 0.024 0.002 TRP A1716 HIS 0.012 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00265 (13964) covalent geometry : angle 0.70316 (18820) SS BOND : bond 0.00182 ( 2) SS BOND : angle 1.31748 ( 4) hydrogen bonds : bond 0.04272 ( 462) hydrogen bonds : angle 4.70685 ( 1335) metal coordination : bond 0.78418 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 210 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.9039 (mp) cc_final: 0.8606 (tt) REVERT: A 1033 GLN cc_start: 0.5920 (tp40) cc_final: 0.5038 (mt0) REVERT: A 1174 LYS cc_start: 0.7951 (mtmt) cc_final: 0.7572 (mtpp) REVERT: A 1520 ARG cc_start: 0.7499 (ttm110) cc_final: 0.7290 (ttm110) REVERT: A 1624 MET cc_start: 0.7768 (mmt) cc_final: 0.7532 (mmt) REVERT: A 1751 LEU cc_start: 0.6594 (tp) cc_final: 0.6289 (mm) REVERT: B 33 LEU cc_start: 0.5612 (tm) cc_final: 0.5405 (tp) outliers start: 44 outliers final: 19 residues processed: 242 average time/residue: 0.1008 time to fit residues: 36.6046 Evaluate side-chains 198 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 153 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 110 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 122 optimal weight: 0.0970 chunk 39 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 HIS ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1330 GLN A1357 HIS A1733 ASN A1734 HIS A1784 ASN ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1804 GLN B 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152475 restraints weight = 15976.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.150467 restraints weight = 16146.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.152201 restraints weight = 16286.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.152739 restraints weight = 10743.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.153060 restraints weight = 9718.301| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13972 Z= 0.211 Angle : 0.764 9.907 18824 Z= 0.390 Chirality : 0.046 0.166 2137 Planarity : 0.005 0.049 2376 Dihedral : 6.589 52.039 1838 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.21 % Favored : 84.73 % Rotamer: Outliers : 3.26 % Allowed : 13.62 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.79 (0.18), residues: 1670 helix: -1.33 (0.18), residues: 758 sheet: -3.26 (0.45), residues: 102 loop : -3.70 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 691 TYR 0.016 0.002 TYR A 544 PHE 0.024 0.002 PHE A1377 TRP 0.028 0.002 TRP A1716 HIS 0.010 0.002 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00507 (13964) covalent geometry : angle 0.76372 (18820) SS BOND : bond 0.00363 ( 2) SS BOND : angle 2.21934 ( 4) hydrogen bonds : bond 0.04954 ( 462) hydrogen bonds : angle 4.63969 ( 1335) metal coordination : bond 0.02375 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 187 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.5129 (tm130) REVERT: A 272 LEU cc_start: 0.9102 (mp) cc_final: 0.8606 (tt) REVERT: A 1174 LYS cc_start: 0.7997 (mtmt) cc_final: 0.7635 (mtpp) REVERT: A 1751 LEU cc_start: 0.6618 (tp) cc_final: 0.6320 (mm) outliers start: 51 outliers final: 29 residues processed: 227 average time/residue: 0.1069 time to fit residues: 36.4118 Evaluate side-chains 203 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1490 THR Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 17 optimal weight: 0.0000 chunk 111 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 1 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 0.0670 chunk 102 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 70 optimal weight: 0.0970 overall best weight: 0.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1033 GLN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.192793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.161450 restraints weight = 15670.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.160450 restraints weight = 17670.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.162902 restraints weight = 15157.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.162613 restraints weight = 10997.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.163427 restraints weight = 9697.986| |-----------------------------------------------------------------------------| r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13972 Z= 0.108 Angle : 0.641 9.089 18824 Z= 0.324 Chirality : 0.041 0.152 2137 Planarity : 0.004 0.045 2376 Dihedral : 5.923 46.723 1838 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 3.77 % Allowed : 14.00 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.19), residues: 1670 helix: -0.68 (0.19), residues: 763 sheet: -3.94 (0.48), residues: 73 loop : -3.42 (0.19), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1520 TYR 0.011 0.001 TYR A1120 PHE 0.023 0.001 PHE A 43 TRP 0.017 0.001 TRP A1716 HIS 0.005 0.001 HIS A 471 Details of bonding type rmsd covalent geometry : bond 0.00228 (13964) covalent geometry : angle 0.64103 (18820) SS BOND : bond 0.00110 ( 2) SS BOND : angle 1.25151 ( 4) hydrogen bonds : bond 0.03370 ( 462) hydrogen bonds : angle 4.03299 ( 1335) metal coordination : bond 0.00703 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 195 time to evaluate : 0.521 Fit side-chains REVERT: A 184 TYR cc_start: 0.6378 (m-80) cc_final: 0.6071 (m-80) REVERT: A 262 GLN cc_start: 0.6285 (mp10) cc_final: 0.5718 (mp10) REVERT: A 272 LEU cc_start: 0.9026 (mp) cc_final: 0.8559 (tt) REVERT: A 602 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6660 (m90) REVERT: A 707 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8451 (ttmm) REVERT: A 1174 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7548 (mtpp) outliers start: 59 outliers final: 31 residues processed: 241 average time/residue: 0.1125 time to fit residues: 40.0092 Evaluate side-chains 207 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 174 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 602 HIS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1551 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 140 optimal weight: 1.9990 chunk 64 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 20.0000 chunk 144 optimal weight: 20.0000 chunk 69 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 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 = 0.4138 r_free = 0.4138 target = 0.184539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152000 restraints weight = 15806.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.151031 restraints weight = 18909.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153206 restraints weight = 15065.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.153343 restraints weight = 10089.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.154326 restraints weight = 9986.394| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13972 Z= 0.184 Angle : 0.729 11.377 18824 Z= 0.367 Chirality : 0.045 0.250 2137 Planarity : 0.004 0.042 2376 Dihedral : 6.106 50.091 1838 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.83 % Favored : 86.11 % Rotamer: Outliers : 4.16 % Allowed : 15.03 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.19), residues: 1670 helix: -0.73 (0.18), residues: 768 sheet: -2.76 (0.49), residues: 100 loop : -3.52 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 691 TYR 0.018 0.002 TYR A 687 PHE 0.021 0.002 PHE A 43 TRP 0.024 0.002 TRP A1716 HIS 0.007 0.001 HIS A1404 Details of bonding type rmsd covalent geometry : bond 0.00445 (13964) covalent geometry : angle 0.72792 (18820) SS BOND : bond 0.00124 ( 2) SS BOND : angle 2.76519 ( 4) hydrogen bonds : bond 0.04433 ( 462) hydrogen bonds : angle 4.32518 ( 1335) metal coordination : bond 0.01236 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 178 time to evaluate : 0.457 Fit side-chains REVERT: A 182 GLN cc_start: 0.7039 (OUTLIER) cc_final: 0.5425 (tt0) REVERT: A 184 TYR cc_start: 0.6542 (m-80) cc_final: 0.6281 (m-80) REVERT: A 262 GLN cc_start: 0.6431 (mp10) cc_final: 0.5857 (mp10) REVERT: A 272 LEU cc_start: 0.9084 (mp) cc_final: 0.8591 (tt) REVERT: A 707 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8472 (ttmm) REVERT: A 918 MET cc_start: 0.8330 (tpp) cc_final: 0.7986 (tpp) REVERT: A 1174 LYS cc_start: 0.7961 (mtmt) cc_final: 0.7622 (mtpp) REVERT: A 1454 THR cc_start: 0.8074 (m) cc_final: 0.7870 (m) outliers start: 65 outliers final: 40 residues processed: 233 average time/residue: 0.1130 time to fit residues: 39.0473 Evaluate side-chains 214 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 129 optimal weight: 0.0770 chunk 90 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1019 GLN A1033 GLN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.190147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.156880 restraints weight = 15590.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.157849 restraints weight = 14453.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.159331 restraints weight = 12716.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.159776 restraints weight = 9957.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.160092 restraints weight = 9283.986| |-----------------------------------------------------------------------------| r_work (final): 0.3864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13972 Z= 0.115 Angle : 0.646 10.213 18824 Z= 0.325 Chirality : 0.042 0.256 2137 Planarity : 0.004 0.041 2376 Dihedral : 5.756 53.409 1838 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.74 % Favored : 88.26 % Rotamer: Outliers : 3.96 % Allowed : 14.90 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.20), residues: 1670 helix: -0.35 (0.19), residues: 767 sheet: -2.63 (0.49), residues: 101 loop : -3.34 (0.20), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 691 TYR 0.016 0.001 TYR A 687 PHE 0.022 0.001 PHE A 43 TRP 0.016 0.001 TRP A1716 HIS 0.005 0.001 HIS A1357 Details of bonding type rmsd covalent geometry : bond 0.00257 (13964) covalent geometry : angle 0.64528 (18820) SS BOND : bond 0.00220 ( 2) SS BOND : angle 1.80292 ( 4) hydrogen bonds : bond 0.03413 ( 462) hydrogen bonds : angle 3.96904 ( 1335) metal coordination : bond 0.00695 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 187 time to evaluate : 0.544 Fit side-chains REVERT: A 182 GLN cc_start: 0.6926 (OUTLIER) cc_final: 0.5307 (tt0) REVERT: A 184 TYR cc_start: 0.6497 (m-80) cc_final: 0.6244 (m-80) REVERT: A 262 GLN cc_start: 0.6290 (mp10) cc_final: 0.5776 (mp10) REVERT: A 272 LEU cc_start: 0.9060 (mp) cc_final: 0.8559 (tt) REVERT: A 707 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8458 (ttmm) REVERT: A 854 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7663 (ttpt) REVERT: A 918 MET cc_start: 0.8254 (tpp) cc_final: 0.7948 (tpp) REVERT: A 1174 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7599 (mtpp) outliers start: 62 outliers final: 36 residues processed: 238 average time/residue: 0.1047 time to fit residues: 37.0899 Evaluate side-chains 213 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 174 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 35 optimal weight: 6.9990 chunk 97 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 89 optimal weight: 0.0970 chunk 152 optimal weight: 9.9990 chunk 131 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 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 = 0.4177 r_free = 0.4177 target = 0.188794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156953 restraints weight = 15756.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156680 restraints weight = 16781.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.158467 restraints weight = 14457.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158694 restraints weight = 10669.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159002 restraints weight = 10593.124| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13972 Z= 0.138 Angle : 0.674 10.649 18824 Z= 0.339 Chirality : 0.043 0.288 2137 Planarity : 0.004 0.042 2376 Dihedral : 5.763 55.827 1838 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.29 % Favored : 86.71 % Rotamer: Outliers : 4.09 % Allowed : 15.41 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.20), residues: 1670 helix: -0.37 (0.19), residues: 771 sheet: -2.53 (0.50), residues: 100 loop : -3.35 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 691 TYR 0.020 0.001 TYR A 687 PHE 0.026 0.001 PHE A1492 TRP 0.019 0.001 TRP A1716 HIS 0.005 0.001 HIS A1404 Details of bonding type rmsd covalent geometry : bond 0.00322 (13964) covalent geometry : angle 0.67357 (18820) SS BOND : bond 0.00294 ( 2) SS BOND : angle 1.56679 ( 4) hydrogen bonds : bond 0.03748 ( 462) hydrogen bonds : angle 4.02207 ( 1335) metal coordination : bond 0.00923 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 177 time to evaluate : 0.566 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6320 (tpp) cc_final: 0.6087 (tpt) REVERT: A 93 LEU cc_start: 0.7552 (tp) cc_final: 0.7318 (tt) REVERT: A 182 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.5289 (tt0) REVERT: A 184 TYR cc_start: 0.6526 (m-80) cc_final: 0.6265 (m-80) REVERT: A 262 GLN cc_start: 0.6324 (mp10) cc_final: 0.5843 (mp10) REVERT: A 272 LEU cc_start: 0.9067 (mp) cc_final: 0.8556 (tt) REVERT: A 707 LYS cc_start: 0.8783 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: A 854 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7671 (ttpt) REVERT: A 918 MET cc_start: 0.8242 (tpp) cc_final: 0.7919 (tpp) REVERT: A 1033 GLN cc_start: 0.5646 (tp40) cc_final: 0.5110 (mt0) REVERT: A 1174 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7617 (mtpp) REVERT: A 1234 VAL cc_start: 0.8988 (OUTLIER) cc_final: 0.8774 (m) outliers start: 64 outliers final: 47 residues processed: 230 average time/residue: 0.1064 time to fit residues: 36.3928 Evaluate side-chains 225 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 174 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 56 GLU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1121 LYS Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 150 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 521 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 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 = 0.4096 r_free = 0.4096 target = 0.180294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147825 restraints weight = 15900.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.146687 restraints weight = 19554.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148831 restraints weight = 16627.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.148962 restraints weight = 11219.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149124 restraints weight = 11541.369| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 13972 Z= 0.274 Angle : 0.826 13.040 18824 Z= 0.418 Chirality : 0.050 0.390 2137 Planarity : 0.005 0.048 2376 Dihedral : 6.463 58.246 1838 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.23 % Favored : 83.71 % Rotamer: Outliers : 4.09 % Allowed : 16.24 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.34 (0.19), residues: 1670 helix: -0.92 (0.18), residues: 771 sheet: -2.59 (0.51), residues: 96 loop : -3.62 (0.18), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 908 TYR 0.028 0.002 TYR A 687 PHE 0.024 0.003 PHE A 851 TRP 0.033 0.002 TRP A1716 HIS 0.010 0.001 HIS A1404 Details of bonding type rmsd covalent geometry : bond 0.00669 (13964) covalent geometry : angle 0.82616 (18820) SS BOND : bond 0.00656 ( 2) SS BOND : angle 1.54844 ( 4) hydrogen bonds : bond 0.05456 ( 462) hydrogen bonds : angle 4.65551 ( 1335) metal coordination : bond 0.01647 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.504 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.6930 (OUTLIER) cc_final: 0.5236 (tt0) REVERT: A 184 TYR cc_start: 0.6591 (m-80) cc_final: 0.6274 (m-80) REVERT: A 262 GLN cc_start: 0.6515 (mp10) cc_final: 0.5998 (mp10) REVERT: A 272 LEU cc_start: 0.9117 (mp) cc_final: 0.8566 (tt) REVERT: A 707 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8396 (ttmm) REVERT: A 854 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7734 (ttpt) REVERT: A 1174 LYS cc_start: 0.7971 (mtmt) cc_final: 0.7651 (mtpp) REVERT: A 1724 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5570 (ppt170) outliers start: 64 outliers final: 48 residues processed: 230 average time/residue: 0.1078 time to fit residues: 36.7366 Evaluate side-chains 219 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 182 GLN Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1107 ILE Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1466 ASP Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1724 ARG Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1794 VAL Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 73 optimal weight: 0.4980 chunk 133 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 83 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 135 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1033 GLN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.190083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.159130 restraints weight = 15745.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156885 restraints weight = 15387.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.158480 restraints weight = 13730.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.159063 restraints weight = 10622.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.159548 restraints weight = 9251.590| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13972 Z= 0.117 Angle : 0.667 10.399 18824 Z= 0.335 Chirality : 0.043 0.324 2137 Planarity : 0.004 0.047 2376 Dihedral : 5.825 55.622 1838 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 3.77 % Allowed : 16.88 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.20), residues: 1670 helix: -0.32 (0.19), residues: 771 sheet: -3.64 (0.51), residues: 79 loop : -3.24 (0.19), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 375 TYR 0.023 0.001 TYR A 687 PHE 0.023 0.001 PHE A1492 TRP 0.017 0.001 TRP A1716 HIS 0.005 0.001 HIS A 646 Details of bonding type rmsd covalent geometry : bond 0.00256 (13964) covalent geometry : angle 0.66646 (18820) SS BOND : bond 0.00205 ( 2) SS BOND : angle 1.12599 ( 4) hydrogen bonds : bond 0.03475 ( 462) hydrogen bonds : angle 3.99216 ( 1335) metal coordination : bond 0.00661 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 185 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.7691 (tp) cc_final: 0.7474 (tt) REVERT: A 184 TYR cc_start: 0.6489 (m-80) cc_final: 0.6135 (m-80) REVERT: A 262 GLN cc_start: 0.6360 (mp10) cc_final: 0.5883 (mp10) REVERT: A 272 LEU cc_start: 0.9055 (mp) cc_final: 0.8514 (tt) REVERT: A 707 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8425 (ttmm) REVERT: A 854 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7629 (ttpt) REVERT: A 1174 LYS cc_start: 0.7919 (mtmt) cc_final: 0.7598 (mtpp) REVERT: A 1724 ARG cc_start: 0.5489 (OUTLIER) cc_final: 0.5240 (ppt170) outliers start: 59 outliers final: 45 residues processed: 233 average time/residue: 0.1049 time to fit residues: 36.5100 Evaluate side-chains 227 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 179 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1357 HIS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1724 ARG Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1785 LEU Chi-restraints excluded: chain A residue 1794 VAL Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 105 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 88 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 92 optimal weight: 0.0170 chunk 113 optimal weight: 7.9990 chunk 36 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 chunk 3 optimal weight: 20.0000 chunk 41 optimal weight: 0.3980 overall best weight: 1.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 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 = 0.4179 r_free = 0.4179 target = 0.188733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.157066 restraints weight = 15669.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.155537 restraints weight = 19165.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158723 restraints weight = 16097.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158285 restraints weight = 10370.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.158587 restraints weight = 9946.133| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13972 Z= 0.134 Angle : 0.692 10.805 18824 Z= 0.345 Chirality : 0.043 0.381 2137 Planarity : 0.004 0.045 2376 Dihedral : 5.643 48.694 1836 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 3.58 % Allowed : 17.01 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.69 (0.20), residues: 1670 helix: -0.31 (0.19), residues: 784 sheet: -2.41 (0.52), residues: 101 loop : -3.39 (0.19), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 375 TYR 0.028 0.001 TYR A1311 PHE 0.023 0.001 PHE A1492 TRP 0.019 0.001 TRP A1716 HIS 0.008 0.001 HIS A1357 Details of bonding type rmsd covalent geometry : bond 0.00310 (13964) covalent geometry : angle 0.69185 (18820) SS BOND : bond 0.00350 ( 2) SS BOND : angle 1.16545 ( 4) hydrogen bonds : bond 0.03695 ( 462) hydrogen bonds : angle 3.99624 ( 1335) metal coordination : bond 0.00889 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 181 time to evaluate : 0.525 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.7630 (tp) cc_final: 0.7394 (tt) REVERT: A 184 TYR cc_start: 0.6384 (m-80) cc_final: 0.6047 (m-80) REVERT: A 262 GLN cc_start: 0.6370 (mp10) cc_final: 0.5908 (mp10) REVERT: A 272 LEU cc_start: 0.9057 (mp) cc_final: 0.8518 (tt) REVERT: A 707 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8429 (ttmm) REVERT: A 854 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7674 (ttpt) REVERT: A 1174 LYS cc_start: 0.7900 (mtmt) cc_final: 0.7593 (mtpp) REVERT: A 1724 ARG cc_start: 0.5612 (OUTLIER) cc_final: 0.5346 (ppt170) outliers start: 56 outliers final: 46 residues processed: 228 average time/residue: 0.1083 time to fit residues: 36.9193 Evaluate side-chains 224 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 709 THR Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1724 ARG Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1794 VAL Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 123 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.186483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.154029 restraints weight = 15903.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.153076 restraints weight = 15870.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.154921 restraints weight = 14362.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.155435 restraints weight = 9676.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.155614 restraints weight = 9169.273| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13972 Z= 0.162 Angle : 0.718 11.645 18824 Z= 0.359 Chirality : 0.044 0.305 2137 Planarity : 0.004 0.044 2376 Dihedral : 5.713 49.764 1836 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.83 % Favored : 86.11 % Rotamer: Outliers : 3.45 % Allowed : 17.52 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.77 (0.20), residues: 1670 helix: -0.38 (0.19), residues: 782 sheet: -2.45 (0.52), residues: 102 loop : -3.40 (0.19), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 375 TYR 0.024 0.001 TYR A 687 PHE 0.022 0.002 PHE A 43 TRP 0.022 0.001 TRP A1716 HIS 0.006 0.001 HIS A1404 Details of bonding type rmsd covalent geometry : bond 0.00384 (13964) covalent geometry : angle 0.71832 (18820) SS BOND : bond 0.00404 ( 2) SS BOND : angle 1.25462 ( 4) hydrogen bonds : bond 0.04074 ( 462) hydrogen bonds : angle 4.11597 ( 1335) metal coordination : bond 0.01064 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2237.30 seconds wall clock time: 39 minutes 31.58 seconds (2371.58 seconds total)