Starting phenix.real_space_refine on Mon Dec 30 16:00:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7eju_31163/12_2024/7eju_31163.cif Found real_map, /net/cci-nas-00/data/ceres_data/7eju_31163/12_2024/7eju_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_31163/12_2024/7eju_31163.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7eju_31163/12_2024/7eju_31163.map" model { file = "/net/cci-nas-00/data/ceres_data/7eju_31163/12_2024/7eju_31163.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7eju_31163/12_2024/7eju_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-5532/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: 7.62, per 1000 atoms: 0.56 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: 3.16 Conformation dependent library (CDL) restraints added in 1.7 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: 1.92 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: 4.91 Time building geometry restraints manager: 3.64 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: 0.910 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: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.300 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.320 ------------------------------------------------------------------------------- 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 : 0.009 0.084 13964 Z= 0.588 Angle : 1.287 15.256 18820 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 *********************** 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 : 1.830 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: 0.3108 time to fit residues: 116.4372 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 : 1.698 ------------------------------------------------------------------------------- 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: 0.0020 chunk 86 optimal weight: 0.3980 chunk 68 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 overall best weight: 1.0390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 76 HIS A 347 ASN A 424 HIS A 471 HIS A 602 HIS A 647 HIS A 787 ASN ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1033 GLN A1110 ASN A1127 ASN A1232 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1295 HIS A1307 GLN A1585 GLN A1784 ASN A1790 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13964 Z= 0.174 Angle : 0.691 9.414 18820 Z= 0.356 Chirality : 0.042 0.161 2137 Planarity : 0.005 0.056 2376 Dihedral : 6.596 40.041 1840 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.69 % Favored : 87.25 % Rotamer: Outliers : 2.75 % Allowed : 10.61 % Favored : 86.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: -4.11 (0.18), residues: 1670 helix: -1.74 (0.17), residues: 751 sheet: -3.44 (0.42), residues: 110 loop : -3.68 (0.18), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1716 HIS 0.012 0.001 HIS A 424 PHE 0.026 0.001 PHE A 43 TYR 0.013 0.001 TYR A1096 ARG 0.005 0.000 ARG A 975 *********************** 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 257 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 214 time to evaluate : 1.595 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8980 (mp) cc_final: 0.8596 (tt) REVERT: A 864 MET cc_start: 0.7184 (tmm) cc_final: 0.6848 (tmm) REVERT: A 1033 GLN cc_start: 0.5950 (tp40) cc_final: 0.5153 (mt0) REVERT: A 1174 LYS cc_start: 0.7931 (mtmt) cc_final: 0.7588 (mtpp) REVERT: A 1751 LEU cc_start: 0.6529 (tp) cc_final: 0.6256 (mm) REVERT: B 33 LEU cc_start: 0.5723 (tm) cc_final: 0.5429 (tt) outliers start: 43 outliers final: 18 residues processed: 246 average time/residue: 0.2536 time to fit residues: 92.6405 Evaluate side-chains 193 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 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 85 optimal weight: 0.9980 chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 chunk 152 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 123 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 HIS A 276 HIS ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1733 ASN A1784 ASN ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13964 Z= 0.263 Angle : 0.725 9.570 18820 Z= 0.369 Chirality : 0.044 0.158 2137 Planarity : 0.005 0.049 2376 Dihedral : 6.367 48.845 1838 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.07 % Favored : 85.87 % Rotamer: Outliers : 3.32 % Allowed : 14.00 % Favored : 82.67 % 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: -3.64 (0.19), residues: 1670 helix: -1.20 (0.18), residues: 758 sheet: -3.13 (0.46), residues: 100 loop : -3.64 (0.19), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1716 HIS 0.015 0.002 HIS A 471 PHE 0.023 0.002 PHE A 43 TYR 0.013 0.002 TYR A 544 ARG 0.004 0.001 ARG A 691 *********************** 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 241 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 1.537 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7448 (tp) REVERT: A 182 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6639 (tp40) REVERT: A 262 GLN cc_start: 0.6435 (mp10) cc_final: 0.5715 (mp10) REVERT: A 272 LEU cc_start: 0.9023 (mp) cc_final: 0.8569 (tt) REVERT: A 602 HIS cc_start: 0.6991 (OUTLIER) cc_final: 0.6725 (m90) REVERT: A 1021 GLU cc_start: 0.6499 (tm-30) cc_final: 0.6110 (tm-30) REVERT: A 1033 GLN cc_start: 0.5804 (tp40) cc_final: 0.5154 (mt0) REVERT: A 1174 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7632 (mtpp) REVERT: A 1751 LEU cc_start: 0.6547 (tp) cc_final: 0.6283 (mm) outliers start: 52 outliers final: 31 residues processed: 229 average time/residue: 0.2625 time to fit residues: 89.5826 Evaluate side-chains 209 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 401 LEU 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 602 HIS Chi-restraints excluded: chain A residue 617 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 785 LEU 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 1459 ILE 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 B residue 59 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 17 optimal weight: 0.0470 chunk 73 optimal weight: 10.0000 chunk 103 optimal weight: 0.0980 chunk 154 optimal weight: 4.9990 chunk 163 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 146 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 overall best weight: 2.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13964 Z= 0.197 Angle : 0.667 10.340 18820 Z= 0.339 Chirality : 0.042 0.150 2137 Planarity : 0.004 0.041 2376 Dihedral : 6.032 47.807 1838 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 4.22 % Allowed : 13.94 % Favored : 81.84 % 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: -3.21 (0.19), residues: 1670 helix: -0.77 (0.19), residues: 764 sheet: -2.83 (0.48), residues: 99 loop : -3.53 (0.19), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1716 HIS 0.005 0.001 HIS A1404 PHE 0.022 0.001 PHE A 43 TYR 0.012 0.001 TYR A 991 ARG 0.004 0.000 ARG A 691 *********************** 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 251 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 185 time to evaluate : 1.502 Fit side-chains REVERT: A 38 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7408 (tp) REVERT: A 182 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.6733 (tp40) REVERT: A 262 GLN cc_start: 0.6392 (mp10) cc_final: 0.5816 (mp10) REVERT: A 272 LEU cc_start: 0.9008 (mp) cc_final: 0.8558 (tt) REVERT: A 707 LYS cc_start: 0.8727 (OUTLIER) cc_final: 0.8353 (ttmm) REVERT: A 1033 GLN cc_start: 0.5629 (tp40) cc_final: 0.5250 (mt0) REVERT: A 1174 LYS cc_start: 0.7904 (mtmt) cc_final: 0.7632 (mtpp) REVERT: A 1755 MET cc_start: 0.8142 (ttt) cc_final: 0.7890 (ttm) outliers start: 66 outliers final: 34 residues processed: 237 average time/residue: 0.2557 time to fit residues: 91.1832 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 : 1.533 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 713 LEU 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 1100 SER Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 8.9990 chunk 92 optimal weight: 0.0170 chunk 2 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.0970 chunk 139 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 437 HIS ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13964 Z= 0.171 Angle : 0.651 10.167 18820 Z= 0.327 Chirality : 0.042 0.185 2137 Planarity : 0.004 0.040 2376 Dihedral : 5.804 49.509 1838 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 4.09 % Allowed : 14.71 % Favored : 81.20 % 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: -2.91 (0.20), residues: 1670 helix: -0.48 (0.19), residues: 766 sheet: -2.63 (0.50), residues: 99 loop : -3.43 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1716 HIS 0.004 0.001 HIS A 646 PHE 0.030 0.001 PHE A1492 TYR 0.011 0.001 TYR A 991 ARG 0.003 0.000 ARG A 691 *********************** 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 253 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 189 time to evaluate : 1.645 Fit side-chains REVERT: A 38 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7314 (tp) REVERT: A 182 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.5515 (tt0) REVERT: A 262 GLN cc_start: 0.6364 (mp10) cc_final: 0.5820 (mp10) REVERT: A 272 LEU cc_start: 0.9007 (mp) cc_final: 0.8538 (tt) REVERT: A 707 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8335 (ttmm) REVERT: A 1033 GLN cc_start: 0.5528 (tp40) cc_final: 0.5143 (mt0) REVERT: A 1174 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7627 (mtpp) REVERT: A 1407 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7954 (tttt) outliers start: 64 outliers final: 37 residues processed: 240 average time/residue: 0.2606 time to fit residues: 93.8132 Evaluate side-chains 217 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 1.676 ------------------------------------------------------------------------------- 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 94 THR 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 363 LEU Chi-restraints excluded: chain A residue 440 MET Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 713 LEU 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 1100 SER Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1407 LYS 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 1769 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.0770 chunk 147 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 163 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 157 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- 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** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13964 Z= 0.243 Angle : 0.688 11.088 18820 Z= 0.348 Chirality : 0.044 0.249 2137 Planarity : 0.004 0.039 2376 Dihedral : 5.897 52.724 1838 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.41 % Favored : 86.53 % Rotamer: Outliers : 4.48 % Allowed : 14.90 % Favored : 80.63 % 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: -2.96 (0.20), residues: 1670 helix: -0.56 (0.19), residues: 771 sheet: -2.69 (0.49), residues: 100 loop : -3.43 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A1716 HIS 0.006 0.001 HIS A1404 PHE 0.021 0.002 PHE A 43 TYR 0.014 0.001 TYR A1311 ARG 0.005 0.000 ARG A 691 *********************** 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 250 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 180 time to evaluate : 1.742 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7332 (tp) REVERT: A 182 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5484 (tt0) REVERT: A 262 GLN cc_start: 0.6429 (mp10) cc_final: 0.5886 (mp10) REVERT: A 272 LEU cc_start: 0.9040 (mp) cc_final: 0.8555 (tt) REVERT: A 707 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8318 (ttmm) REVERT: A 854 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7722 (ttpt) REVERT: A 1174 LYS cc_start: 0.7918 (mtmt) cc_final: 0.7637 (mtpp) outliers start: 70 outliers final: 45 residues processed: 239 average time/residue: 0.2576 time to fit residues: 91.1581 Evaluate side-chains 223 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 174 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 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 510 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 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 1769 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 137 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 162 optimal weight: 0.0050 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 0.3980 chunk 100 optimal weight: 2.9990 overall best weight: 1.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1019 GLN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13964 Z= 0.166 Angle : 0.649 10.487 18820 Z= 0.325 Chirality : 0.042 0.283 2137 Planarity : 0.004 0.039 2376 Dihedral : 5.665 55.274 1838 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.22 % Favored : 87.78 % Rotamer: Outliers : 4.16 % Allowed : 15.73 % Favored : 80.12 % 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: -2.68 (0.20), residues: 1670 helix: -0.31 (0.19), residues: 769 sheet: -2.65 (0.50), residues: 101 loop : -3.27 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1716 HIS 0.004 0.001 HIS A1232 PHE 0.028 0.001 PHE A1492 TYR 0.015 0.001 TYR A1311 ARG 0.004 0.000 ARG A 908 *********************** 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 253 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 188 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7241 (tp) REVERT: A 56 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6595 (mm-30) REVERT: A 182 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.5463 (tt0) REVERT: A 262 GLN cc_start: 0.6355 (mp10) cc_final: 0.5814 (mp10) REVERT: A 272 LEU cc_start: 0.9004 (mp) cc_final: 0.8516 (tt) REVERT: A 707 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8317 (ttmm) REVERT: A 1174 LYS cc_start: 0.7915 (mtmt) cc_final: 0.7631 (mtpp) outliers start: 65 outliers final: 43 residues processed: 240 average time/residue: 0.2656 time to fit residues: 94.5150 Evaluate side-chains 226 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 179 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 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 798 LYS 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 962 SER Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 1020 GLU Chi-restraints excluded: chain A residue 1100 SER Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 0.5980 chunk 80 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 128 optimal weight: 0.9980 chunk 148 optimal weight: 0.0870 overall best weight: 0.7360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1428 ASN A1804 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13964 Z= 0.149 Angle : 0.640 10.158 18820 Z= 0.319 Chirality : 0.041 0.282 2137 Planarity : 0.004 0.042 2376 Dihedral : 5.314 44.521 1836 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 3.64 % Allowed : 16.37 % Favored : 79.99 % 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: -2.46 (0.20), residues: 1670 helix: -0.05 (0.19), residues: 766 sheet: -3.59 (0.54), residues: 75 loop : -3.12 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1716 HIS 0.004 0.001 HIS A1357 PHE 0.022 0.001 PHE A 43 TYR 0.015 0.001 TYR A1311 ARG 0.004 0.000 ARG A 375 *********************** 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 257 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 200 time to evaluate : 1.641 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7159 (tp) REVERT: A 155 TRP cc_start: 0.5197 (p-90) cc_final: 0.4817 (p-90) REVERT: A 182 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.5406 (tt0) REVERT: A 262 GLN cc_start: 0.6337 (mp10) cc_final: 0.5817 (mp10) REVERT: A 272 LEU cc_start: 0.8987 (mp) cc_final: 0.8549 (tt) REVERT: A 707 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8314 (ttmm) REVERT: A 854 LYS cc_start: 0.8031 (OUTLIER) cc_final: 0.7673 (ttpt) REVERT: A 1174 LYS cc_start: 0.7893 (mtmt) cc_final: 0.7607 (mtpp) outliers start: 57 outliers final: 40 residues processed: 246 average time/residue: 0.2972 time to fit residues: 109.8698 Evaluate side-chains 229 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 185 time to evaluate : 1.694 ------------------------------------------------------------------------------- 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 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 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 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 982 LEU 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 1322 VAL Chi-restraints excluded: chain A residue 1357 HIS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1785 LEU Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 2.9990 chunk 142 optimal weight: 0.0770 chunk 151 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 143 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.0144 ------------------------------------------------------------------------------- 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** A1357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13964 Z= 0.200 Angle : 0.670 10.566 18820 Z= 0.334 Chirality : 0.043 0.316 2137 Planarity : 0.004 0.043 2376 Dihedral : 5.390 46.194 1836 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 3.13 % Allowed : 17.20 % Favored : 79.67 % 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: -2.54 (0.20), residues: 1670 helix: -0.17 (0.19), residues: 782 sheet: -3.54 (0.52), residues: 79 loop : -3.15 (0.20), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1716 HIS 0.007 0.001 HIS A1357 PHE 0.035 0.001 PHE A1492 TYR 0.019 0.001 TYR A1301 ARG 0.005 0.000 ARG A 691 *********************** 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 237 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 188 time to evaluate : 1.492 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7207 (tp) REVERT: A 182 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5621 (tt0) REVERT: A 262 GLN cc_start: 0.6363 (mp10) cc_final: 0.5895 (mp10) REVERT: A 272 LEU cc_start: 0.9027 (mp) cc_final: 0.8522 (tt) REVERT: A 707 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8338 (ttmm) REVERT: A 854 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7655 (ttpt) REVERT: A 1033 GLN cc_start: 0.5614 (tp40) cc_final: 0.4867 (mt0) REVERT: A 1174 LYS cc_start: 0.7905 (mtmt) cc_final: 0.7612 (mtpp) REVERT: A 1454 THR cc_start: 0.7900 (m) cc_final: 0.7686 (m) outliers start: 49 outliers final: 40 residues processed: 231 average time/residue: 0.2753 time to fit residues: 94.1639 Evaluate side-chains 224 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 1.614 ------------------------------------------------------------------------------- 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 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 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 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 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 111 optimal weight: 7.9990 chunk 168 optimal weight: 0.7980 chunk 154 optimal weight: 0.0010 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13964 Z= 0.184 Angle : 0.664 10.523 18820 Z= 0.331 Chirality : 0.043 0.326 2137 Planarity : 0.004 0.043 2376 Dihedral : 5.396 46.190 1836 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 3.20 % Allowed : 17.20 % Favored : 79.60 % 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: -2.40 (0.20), residues: 1670 helix: -0.05 (0.19), residues: 773 sheet: -3.49 (0.52), residues: 81 loop : -3.05 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1716 HIS 0.004 0.001 HIS A1404 PHE 0.021 0.001 PHE A 43 TYR 0.016 0.001 TYR A1301 ARG 0.004 0.000 ARG A 691 ********************** 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 233 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 183 time to evaluate : 2.103 Fit side-chains revert: symmetry clash REVERT: A 182 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.5502 (tt0) REVERT: A 262 GLN cc_start: 0.6364 (mp10) cc_final: 0.5870 (mp10) REVERT: A 272 LEU cc_start: 0.9017 (mp) cc_final: 0.8525 (tt) REVERT: A 707 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8327 (ttmm) REVERT: A 854 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7661 (ttpt) REVERT: A 1174 LYS cc_start: 0.7926 (mtmt) cc_final: 0.7632 (mtpp) outliers start: 50 outliers final: 42 residues processed: 225 average time/residue: 0.3583 time to fit residues: 123.5758 Evaluate side-chains 223 residues out of total 1565 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 178 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 182 GLN Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 456 VAL Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 751 MET Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 888 GLU Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 957 ILE Chi-restraints excluded: chain A residue 962 SER Chi-restraints excluded: chain A residue 982 LEU Chi-restraints excluded: chain A residue 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 1322 VAL Chi-restraints excluded: chain A residue 1357 HIS Chi-restraints excluded: chain A residue 1414 LEU Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain A residue 1801 ILE Chi-restraints excluded: chain B residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 19 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 117 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** 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** A1357 HIS A1734 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.174843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.138461 restraints weight = 15612.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.140723 restraints weight = 13212.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.142176 restraints weight = 10246.352| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13964 Z= 0.346 Angle : 0.783 12.495 18820 Z= 0.392 Chirality : 0.047 0.167 2137 Planarity : 0.005 0.041 2376 Dihedral : 5.874 50.540 1836 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.91 % Favored : 85.03 % Rotamer: Outliers : 3.32 % Allowed : 17.58 % Favored : 79.09 % 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: -2.95 (0.19), residues: 1670 helix: -0.56 (0.18), residues: 790 sheet: -3.68 (0.50), residues: 78 loop : -3.34 (0.19), residues: 802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1716 HIS 0.017 0.002 HIS A1357 PHE 0.035 0.002 PHE A1492 TYR 0.016 0.002 TYR A 544 ARG 0.006 0.001 ARG A 691 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3228.63 seconds wall clock time: 59 minutes 50.87 seconds (3590.87 seconds total)