Starting phenix.real_space_refine on Thu Jul 31 12:34:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eju_31163/07_2025/7eju_31163.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eju_31163/07_2025/7eju_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7eju_31163/07_2025/7eju_31163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eju_31163/07_2025/7eju_31163.map" model { file = "/net/cci-nas-00/data/ceres_data/7eju_31163/07_2025/7eju_31163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eju_31163/07_2025/7eju_31163.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.39, per 1000 atoms: 0.61 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: 3.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.87 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: 4.99 Time building geometry restraints manager: 4.13 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: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.880 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 38.060 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.070 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:3.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.050 0.005 TRP A1716 HIS 0.016 0.003 HIS A 964 PHE 0.040 0.004 PHE A1636 TYR 0.042 0.004 TYR A 557 ARG 0.013 0.002 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.18642 ( 462) hydrogen bonds : angle 7.00480 ( 1335) metal coordination : bond 0.16951 ( 6) SS BOND : bond 0.01464 ( 2) SS BOND : angle 1.66272 ( 4) covalent geometry : bond 0.00912 (13964) covalent geometry : angle 1.28711 (18820) *********************** 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 : 1.561 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: 0.3001 time to fit residues: 112.5297 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 : 1.476 ------------------------------------------------------------------------------- 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 142 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 86 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS A 276 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 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 = 0.4189 r_free = 0.4189 target = 0.189681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.158000 restraints weight = 15793.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.156045 restraints weight = 18085.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.158200 restraints weight = 16382.303| |-----------------------------------------------------------------------------| r_work (final): 0.3838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.017 1.939 13972 Z= 0.564 Angle : 0.713 9.213 18824 Z= 0.368 Chirality : 0.043 0.165 2137 Planarity : 0.005 0.053 2376 Dihedral : 6.746 39.957 1840 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.11 % Favored : 86.83 % Rotamer: Outliers : 2.69 % Allowed : 10.87 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.17 (0.17), residues: 1670 helix: -1.78 (0.17), residues: 749 sheet: -3.52 (0.43), residues: 106 loop : -3.71 (0.18), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1716 HIS 0.012 0.001 HIS A 424 PHE 0.025 0.002 PHE A 43 TYR 0.013 0.001 TYR A1096 ARG 0.004 0.000 ARG A 975 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 462) hydrogen bonds : angle 4.72462 ( 1335) metal coordination : bond 0.79147 ( 6) SS BOND : bond 0.00131 ( 2) SS BOND : angle 1.30223 ( 4) covalent geometry : bond 0.00307 (13964) covalent geometry : angle 0.71313 (18820) *********************** 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 251 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 209 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.9020 (mp) cc_final: 0.8579 (tt) REVERT: A 1033 GLN cc_start: 0.5975 (tp40) cc_final: 0.5118 (mt0) REVERT: A 1174 LYS cc_start: 0.7960 (mtmt) cc_final: 0.7610 (mtpp) REVERT: A 1751 LEU cc_start: 0.6568 (tp) cc_final: 0.6291 (mm) REVERT: B 33 LEU cc_start: 0.5642 (tm) cc_final: 0.5419 (tp) outliers start: 42 outliers final: 19 residues processed: 241 average time/residue: 0.2683 time to fit residues: 95.1912 Evaluate side-chains 199 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 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 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 59 optimal weight: 3.9990 chunk 131 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 108 optimal weight: 10.0000 chunk 18 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 137 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 736 ASN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.184323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.152084 restraints weight = 15882.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149825 restraints weight = 17155.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.152324 restraints weight = 15289.972| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.2058 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= 0.203 Angle : 0.757 9.745 18824 Z= 0.386 Chirality : 0.046 0.161 2137 Planarity : 0.005 0.049 2376 Dihedral : 6.587 50.253 1838 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.09 % Favored : 84.85 % Rotamer: Outliers : 3.45 % Allowed : 13.68 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.18), residues: 1670 helix: -1.32 (0.18), residues: 758 sheet: -3.25 (0.45), residues: 102 loop : -3.69 (0.18), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A1716 HIS 0.012 0.001 HIS A 471 PHE 0.024 0.002 PHE A1377 TYR 0.015 0.002 TYR A 544 ARG 0.005 0.001 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.04890 ( 462) hydrogen bonds : angle 4.61848 ( 1335) metal coordination : bond 0.02211 ( 6) SS BOND : bond 0.00215 ( 2) SS BOND : angle 2.12663 ( 4) covalent geometry : bond 0.00486 (13964) covalent geometry : angle 0.75650 (18820) *********************** 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 242 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 188 time to evaluate : 1.484 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7599 (tp) REVERT: A 182 GLN cc_start: 0.7132 (OUTLIER) cc_final: 0.5192 (tm130) REVERT: A 272 LEU cc_start: 0.9053 (mp) cc_final: 0.8570 (tt) REVERT: A 1174 LYS cc_start: 0.8002 (mtmt) cc_final: 0.7663 (mtpp) REVERT: A 1751 LEU cc_start: 0.6587 (tp) cc_final: 0.6301 (mm) outliers start: 54 outliers final: 29 residues processed: 230 average time/residue: 0.2392 time to fit residues: 82.7394 Evaluate side-chains 206 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 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 1454 THR 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 47 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 108 optimal weight: 10.0000 chunk 131 optimal weight: 0.2980 chunk 84 optimal weight: 2.9990 chunk 137 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 chunk 35 optimal weight: 20.0000 chunk 160 optimal weight: 4.9990 overall best weight: 1.2588 ------------------------------------------------------------------------------- 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** ** 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 = 0.4208 r_free = 0.4208 target = 0.191769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.159840 restraints weight = 15655.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.158722 restraints weight = 17334.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.160791 restraints weight = 14818.946| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13972 Z= 0.114 Angle : 0.645 9.482 18824 Z= 0.327 Chirality : 0.041 0.151 2137 Planarity : 0.004 0.046 2376 Dihedral : 5.995 47.914 1838 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 3.96 % Allowed : 13.75 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.19), residues: 1670 helix: -0.70 (0.19), residues: 763 sheet: -3.94 (0.46), residues: 77 loop : -3.43 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1716 HIS 0.004 0.001 HIS A 471 PHE 0.023 0.001 PHE A 43 TYR 0.011 0.001 TYR A 147 ARG 0.003 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.03537 ( 462) hydrogen bonds : angle 4.06546 ( 1335) metal coordination : bond 0.00829 ( 6) SS BOND : bond 0.00167 ( 2) SS BOND : angle 1.34643 ( 4) covalent geometry : bond 0.00252 (13964) covalent geometry : angle 0.64458 (18820) *********************** 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 259 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 197 time to evaluate : 1.488 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7461 (tp) REVERT: A 182 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6395 (tp40) REVERT: A 184 TYR cc_start: 0.6410 (m-80) cc_final: 0.6159 (m-80) REVERT: A 272 LEU cc_start: 0.9009 (mp) cc_final: 0.8544 (tt) REVERT: A 602 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6688 (m90) REVERT: A 614 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.9038 (tt) REVERT: A 707 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8398 (ttmm) REVERT: A 1174 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7589 (mtpp) REVERT: A 1520 ARG cc_start: 0.7435 (ttm110) cc_final: 0.7170 (ttm170) REVERT: A 1755 MET cc_start: 0.8287 (ttt) cc_final: 0.8013 (ttm) outliers start: 62 outliers final: 32 residues processed: 245 average time/residue: 0.2549 time to fit residues: 92.1735 Evaluate side-chains 212 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 182 GLN Chi-restraints excluded: chain A residue 333 CYS 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 614 LEU Chi-restraints excluded: chain A residue 617 LEU 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 Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 2 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 chunk 139 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 133 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- 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 A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4176 r_free = 0.4176 target = 0.188499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.156537 restraints weight = 15698.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.156999 restraints weight = 16358.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.158449 restraints weight = 11994.813| |-----------------------------------------------------------------------------| r_work (final): 0.3834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13972 Z= 0.146 Angle : 0.684 10.624 18824 Z= 0.343 Chirality : 0.044 0.266 2137 Planarity : 0.004 0.041 2376 Dihedral : 5.954 50.848 1838 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.99 % Favored : 86.95 % Rotamer: Outliers : 4.22 % Allowed : 14.90 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.20), residues: 1670 helix: -0.58 (0.19), residues: 766 sheet: -2.73 (0.50), residues: 100 loop : -3.46 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1716 HIS 0.005 0.001 HIS A1404 PHE 0.022 0.002 PHE A 43 TYR 0.012 0.001 TYR A 544 ARG 0.004 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 462) hydrogen bonds : angle 4.13498 ( 1335) metal coordination : bond 0.01005 ( 6) SS BOND : bond 0.00138 ( 2) SS BOND : angle 2.68016 ( 4) covalent geometry : bond 0.00345 (13964) covalent geometry : angle 0.68253 (18820) *********************** 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 247 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 181 time to evaluate : 1.485 Fit side-chains REVERT: A 38 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7452 (tp) REVERT: A 182 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.5392 (tt0) REVERT: A 184 TYR cc_start: 0.6511 (m-80) cc_final: 0.6199 (m-80) REVERT: A 272 LEU cc_start: 0.9076 (mp) cc_final: 0.8556 (tt) REVERT: A 707 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8462 (ttmm) REVERT: A 918 MET cc_start: 0.8287 (tpp) cc_final: 0.7968 (tpp) REVERT: A 1033 GLN cc_start: 0.5654 (tp40) cc_final: 0.5126 (mt0) REVERT: A 1174 LYS cc_start: 0.7935 (mtmt) cc_final: 0.7601 (mtpp) REVERT: A 1267 GLU cc_start: 0.7269 (tp30) cc_final: 0.6866 (tp30) REVERT: A 1520 ARG cc_start: 0.7513 (ttm110) cc_final: 0.7064 (ttm170) REVERT: A 1755 MET cc_start: 0.8325 (ttt) cc_final: 0.8058 (ttm) outliers start: 66 outliers final: 42 residues processed: 235 average time/residue: 0.2601 time to fit residues: 90.9499 Evaluate side-chains 220 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 175 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 38 LEU 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 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 510 ILE Chi-restraints excluded: chain A residue 617 LEU 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 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 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 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 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 Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 84 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 137 optimal weight: 8.9990 chunk 82 optimal weight: 0.0870 chunk 54 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 130 optimal weight: 0.8980 chunk 80 optimal weight: 8.9990 chunk 120 optimal weight: 20.0000 chunk 56 optimal weight: 7.9990 overall best weight: 2.1562 ------------------------------------------------------------------------------- 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 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1019 GLN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4164 r_free = 0.4164 target = 0.187421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154773 restraints weight = 15834.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.154006 restraints weight = 16914.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.156044 restraints weight = 14720.241| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13972 Z= 0.137 Angle : 0.670 10.694 18824 Z= 0.338 Chirality : 0.043 0.266 2137 Planarity : 0.004 0.042 2376 Dihedral : 5.899 53.099 1838 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.75 % Favored : 87.19 % Rotamer: Outliers : 4.35 % Allowed : 15.03 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.20), residues: 1670 helix: -0.48 (0.19), residues: 772 sheet: -2.59 (0.51), residues: 99 loop : -3.42 (0.20), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1716 HIS 0.006 0.001 HIS A1232 PHE 0.022 0.001 PHE A 43 TYR 0.016 0.001 TYR A1311 ARG 0.004 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 462) hydrogen bonds : angle 4.07080 ( 1335) metal coordination : bond 0.00903 ( 6) SS BOND : bond 0.00234 ( 2) SS BOND : angle 1.91016 ( 4) covalent geometry : bond 0.00320 (13964) covalent geometry : angle 0.66938 (18820) *********************** 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 246 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 178 time to evaluate : 1.454 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7409 (tp) REVERT: A 182 GLN cc_start: 0.6827 (OUTLIER) cc_final: 0.5208 (tt0) REVERT: A 184 TYR cc_start: 0.6548 (m-80) cc_final: 0.6260 (m-80) REVERT: A 272 LEU cc_start: 0.9068 (mp) cc_final: 0.8532 (tt) REVERT: A 707 LYS cc_start: 0.8781 (OUTLIER) cc_final: 0.8433 (ttmm) REVERT: A 854 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7669 (ttpt) REVERT: A 918 MET cc_start: 0.8293 (tpp) cc_final: 0.7957 (tpp) REVERT: A 1033 GLN cc_start: 0.5646 (tp40) cc_final: 0.5160 (mt0) REVERT: A 1174 LYS cc_start: 0.7967 (mtmt) cc_final: 0.7614 (mtpp) REVERT: A 1520 ARG cc_start: 0.7585 (ttm110) cc_final: 0.6928 (ttm170) outliers start: 68 outliers final: 48 residues processed: 235 average time/residue: 0.2654 time to fit residues: 92.7507 Evaluate side-chains 226 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 38 LEU 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 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 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 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 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 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 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 1234 VAL 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 1466 ASP 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 A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 23 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 139 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 148 optimal weight: 0.0060 chunk 135 optimal weight: 6.9990 chunk 141 optimal weight: 0.1980 chunk 163 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 overall best weight: 3.2402 ------------------------------------------------------------------------------- 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** ** 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 = 0.4146 r_free = 0.4146 target = 0.185477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.152671 restraints weight = 15835.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.149676 restraints weight = 17130.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.150665 restraints weight = 16431.611| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13972 Z= 0.176 Angle : 0.712 11.462 18824 Z= 0.358 Chirality : 0.045 0.294 2137 Planarity : 0.004 0.042 2376 Dihedral : 6.012 56.454 1838 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.19 % Favored : 85.75 % Rotamer: Outliers : 4.41 % Allowed : 15.92 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.20), residues: 1670 helix: -0.59 (0.18), residues: 776 sheet: -2.61 (0.51), residues: 100 loop : -3.47 (0.19), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1716 HIS 0.006 0.001 HIS A1404 PHE 0.021 0.002 PHE A 43 TYR 0.014 0.001 TYR A 544 ARG 0.005 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 462) hydrogen bonds : angle 4.22486 ( 1335) metal coordination : bond 0.01137 ( 6) SS BOND : bond 0.00352 ( 2) SS BOND : angle 1.74748 ( 4) covalent geometry : bond 0.00423 (13964) covalent geometry : angle 0.71114 (18820) *********************** 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 248 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 179 time to evaluate : 1.697 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6496 (tpp) cc_final: 0.6185 (tpt) REVERT: A 38 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7546 (tp) REVERT: A 182 GLN cc_start: 0.6647 (OUTLIER) cc_final: 0.5016 (tt0) REVERT: A 184 TYR cc_start: 0.6645 (m-80) cc_final: 0.6259 (m-80) REVERT: A 272 LEU cc_start: 0.9084 (mp) cc_final: 0.8530 (tt) REVERT: A 707 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8447 (ttmm) REVERT: A 854 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7628 (ttpt) REVERT: A 918 MET cc_start: 0.8353 (tpp) cc_final: 0.7969 (tpp) REVERT: A 1033 GLN cc_start: 0.5622 (tp40) cc_final: 0.5100 (mt0) REVERT: A 1174 LYS cc_start: 0.7972 (mtmt) cc_final: 0.7638 (mtpp) outliers start: 69 outliers final: 53 residues processed: 237 average time/residue: 0.2645 time to fit residues: 92.8153 Evaluate side-chains 230 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 173 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 38 LEU 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 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 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 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 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 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 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 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 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 Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 135 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 5 optimal weight: 0.0770 chunk 120 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 147 optimal weight: 6.9990 chunk 6 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 155 optimal weight: 8.9990 overall best weight: 3.1944 ------------------------------------------------------------------------------- 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 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4146 r_free = 0.4146 target = 0.185317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152869 restraints weight = 15844.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.150992 restraints weight = 16157.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.153472 restraints weight = 14583.944| |-----------------------------------------------------------------------------| r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13972 Z= 0.175 Angle : 0.710 11.891 18824 Z= 0.357 Chirality : 0.045 0.341 2137 Planarity : 0.004 0.044 2376 Dihedral : 6.039 59.335 1838 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.47 % Favored : 86.47 % Rotamer: Outliers : 4.60 % Allowed : 16.75 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.00 (0.19), residues: 1670 helix: -0.64 (0.18), residues: 783 sheet: -2.59 (0.51), residues: 100 loop : -3.45 (0.19), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1716 HIS 0.007 0.001 HIS A1404 PHE 0.021 0.002 PHE A 43 TYR 0.013 0.001 TYR A 544 ARG 0.005 0.000 ARG A 691 Details of bonding type rmsd hydrogen bonds : bond 0.04230 ( 462) hydrogen bonds : angle 4.21802 ( 1335) metal coordination : bond 0.01107 ( 6) SS BOND : bond 0.00492 ( 2) SS BOND : angle 1.24725 ( 4) covalent geometry : bond 0.00419 (13964) covalent geometry : angle 0.70965 (18820) *********************** 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 249 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 177 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7449 (tp) REVERT: A 182 GLN cc_start: 0.6883 (OUTLIER) cc_final: 0.5202 (tt0) REVERT: A 184 TYR cc_start: 0.6552 (m-80) cc_final: 0.6243 (m-80) REVERT: A 272 LEU cc_start: 0.9073 (mp) cc_final: 0.8539 (tt) REVERT: A 707 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8374 (ttmm) REVERT: A 854 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7711 (ttpt) REVERT: A 918 MET cc_start: 0.8331 (tpp) cc_final: 0.7952 (tpp) REVERT: A 1174 LYS cc_start: 0.7943 (mtmt) cc_final: 0.7646 (mtpp) outliers start: 72 outliers final: 56 residues processed: 236 average time/residue: 0.2437 time to fit residues: 85.3312 Evaluate side-chains 231 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 171 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 38 LEU 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 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 709 THR 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 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 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 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 1454 THR 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 1490 THR 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 Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 135 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 116 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 67 optimal weight: 0.0000 chunk 91 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN A1033 GLN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4198 r_free = 0.4198 target = 0.190873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.159327 restraints weight = 15652.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.158457 restraints weight = 16751.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.160568 restraints weight = 15280.489| |-----------------------------------------------------------------------------| r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3057 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= 0.114 Angle : 0.652 10.434 18824 Z= 0.328 Chirality : 0.042 0.314 2137 Planarity : 0.004 0.043 2376 Dihedral : 5.687 58.316 1838 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer: Outliers : 3.77 % Allowed : 17.77 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.61 (0.20), residues: 1670 helix: -0.27 (0.19), residues: 776 sheet: -2.45 (0.52), residues: 99 loop : -3.26 (0.20), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1716 HIS 0.005 0.001 HIS A 646 PHE 0.022 0.001 PHE A 43 TYR 0.011 0.001 TYR A1120 ARG 0.006 0.000 ARG A 908 Details of bonding type rmsd hydrogen bonds : bond 0.03368 ( 462) hydrogen bonds : angle 3.90154 ( 1335) metal coordination : bond 0.00639 ( 6) SS BOND : bond 0.00278 ( 2) SS BOND : angle 1.01182 ( 4) covalent geometry : bond 0.00253 (13964) covalent geometry : angle 0.65221 (18820) *********************** 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 248 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 189 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7377 (tp) REVERT: A 182 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.5170 (tt0) REVERT: A 184 TYR cc_start: 0.6481 (m-80) cc_final: 0.6228 (m-80) REVERT: A 272 LEU cc_start: 0.9051 (mp) cc_final: 0.8538 (tt) REVERT: A 707 LYS cc_start: 0.8752 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: A 854 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7663 (ttpt) REVERT: A 918 MET cc_start: 0.8229 (tpp) cc_final: 0.7900 (tpp) REVERT: A 1174 LYS cc_start: 0.7954 (mtmt) cc_final: 0.7624 (mtpp) outliers start: 59 outliers final: 45 residues processed: 237 average time/residue: 0.3584 time to fit residues: 128.6912 Evaluate side-chains 227 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 178 time to evaluate : 1.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 HIS Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 39 LEU 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 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 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 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 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 1414 LEU Chi-restraints excluded: chain A residue 1454 THR 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 1730 LEU 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 53 optimal weight: 0.8980 chunk 142 optimal weight: 0.0060 chunk 72 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 136 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 GLN A 909 ASN A1230 HIS ** A1240 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 = 0.4207 r_free = 0.4207 target = 0.191788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.158923 restraints weight = 15521.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.158058 restraints weight = 17824.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.160238 restraints weight = 15028.738| |-----------------------------------------------------------------------------| r_work (final): 0.3870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13972 Z= 0.111 Angle : 0.659 11.956 18824 Z= 0.327 Chirality : 0.042 0.322 2137 Planarity : 0.004 0.043 2376 Dihedral : 5.358 45.391 1836 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 3.01 % Allowed : 18.67 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.20), residues: 1670 helix: -0.16 (0.19), residues: 788 sheet: -2.45 (0.52), residues: 101 loop : -3.19 (0.20), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1716 HIS 0.005 0.001 HIS A1230 PHE 0.037 0.001 PHE A1492 TYR 0.011 0.001 TYR A1120 ARG 0.007 0.000 ARG A 908 Details of bonding type rmsd hydrogen bonds : bond 0.03216 ( 462) hydrogen bonds : angle 3.80992 ( 1335) metal coordination : bond 0.00530 ( 6) SS BOND : bond 0.00307 ( 2) SS BOND : angle 0.91376 ( 4) covalent geometry : bond 0.00239 (13964) covalent geometry : angle 0.65879 (18820) ********************** 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 240 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 1.880 Fit side-chains revert: symmetry clash REVERT: A 184 TYR cc_start: 0.6424 (m-80) cc_final: 0.6076 (m-80) REVERT: A 272 LEU cc_start: 0.9050 (mp) cc_final: 0.8506 (tt) REVERT: A 707 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8408 (ttmm) REVERT: A 854 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: A 918 MET cc_start: 0.8109 (tpp) cc_final: 0.7816 (tpp) REVERT: A 1174 LYS cc_start: 0.7947 (mtmt) cc_final: 0.7606 (mtpp) outliers start: 47 outliers final: 40 residues processed: 231 average time/residue: 0.3490 time to fit residues: 123.0770 Evaluate side-chains 221 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 3.658 ------------------------------------------------------------------------------- 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 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 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 617 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 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 1322 VAL Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1454 THR 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 1730 LEU 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 102 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 164 optimal weight: 0.5980 chunk 85 optimal weight: 1.9990 chunk 168 optimal weight: 0.0270 chunk 53 optimal weight: 0.8980 chunk 9 optimal weight: 10.0000 chunk 92 optimal weight: 20.0000 chunk 149 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 chunk 78 optimal weight: 2.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.183789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147941 restraints weight = 15522.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.150701 restraints weight = 12519.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.152413 restraints weight = 9208.894| |-----------------------------------------------------------------------------| r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 13972 Z= 0.112 Angle : 0.660 10.407 18824 Z= 0.327 Chirality : 0.041 0.161 2137 Planarity : 0.004 0.043 2376 Dihedral : 5.277 45.010 1836 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.51 % Favored : 87.49 % Rotamer: Outliers : 2.88 % Allowed : 18.99 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.21), residues: 1670 helix: 0.02 (0.19), residues: 780 sheet: -2.47 (0.51), residues: 101 loop : -3.11 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1716 HIS 0.007 0.001 HIS A1232 PHE 0.022 0.001 PHE A 43 TYR 0.021 0.001 TYR A1301 ARG 0.004 0.000 ARG A 908 Details of bonding type rmsd hydrogen bonds : bond 0.03146 ( 462) hydrogen bonds : angle 3.78126 ( 1335) metal coordination : bond 0.00555 ( 6) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.93043 ( 4) covalent geometry : bond 0.00248 (13964) covalent geometry : angle 0.65954 (18820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6770.06 seconds wall clock time: 123 minutes 5.62 seconds (7385.62 seconds total)