Starting phenix.real_space_refine on Thu Feb 15 23:30:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/02_2024/7eju_31163.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/02_2024/7eju_31163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/02_2024/7eju_31163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/02_2024/7eju_31163.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/02_2024/7eju_31163.pdb" } 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 Residue "A ARG 19": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 186": "NH1" <-> "NH2" Residue "A ARG 236": "NH1" <-> "NH2" Residue "A ARG 243": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ARG 391": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A ARG 487": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A PHE 532": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 576": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A ARG 655": "NH1" <-> "NH2" Residue "A ARG 668": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "A ARG 788": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A TYR 991": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1128": "NH1" <-> "NH2" Residue "A ARG 1168": "NH1" <-> "NH2" Residue "A ARG 1215": "NH1" <-> "NH2" Residue "A ARG 1276": "NH1" <-> "NH2" Residue "A ARG 1472": "NH1" <-> "NH2" Residue "A ARG 1478": "NH1" <-> "NH2" Residue "A ARG 1558": "NH1" <-> "NH2" Residue "A ARG 1587": "NH1" <-> "NH2" Residue "A ARG 1590": "NH1" <-> "NH2" Residue "A ARG 1630": "NH1" <-> "NH2" Residue "A ARG 1768": "NH1" <-> "NH2" Residue "B ARG 60": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 7.58, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 5.36 Conformation dependent library (CDL) restraints added in 2.5 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: 1.60 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: 4.75 Time building geometry restraints manager: 5.78 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: 94.79 - 102.65: 68 102.65 - 110.51: 3717 110.51 - 118.37: 6973 118.37 - 126.23: 7857 126.23 - 134.09: 205 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 2.440 nonbonded pdb=" O LYS A 958 " pdb=" OG SER A 962 " model vdw 2.260 2.440 nonbonded pdb=" O ILE A 677 " pdb=" NH1 ARG A 691 " model vdw 2.279 2.520 nonbonded pdb=" OH TYR A 866 " pdb=" OE2 GLU A 888 " model vdw 2.292 2.440 nonbonded pdb=" OG SER A 121 " pdb=" OH TYR A 834 " model vdw 2.296 2.440 ... (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 ========== 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: 0.710 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: 4.380 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 41.080 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.970 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 18 poor density : 248 time to evaluate : 1.643 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: 0.2906 time to fit residues: 107.6490 Evaluate side-chains 175 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 170 time to evaluate : 1.636 ------------------------------------------------------------------------------- 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: 1.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 86 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 736 ASN A 787 ASN ** 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 A1428 ASN A1585 GLN A1784 ASN ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13964 Z= 0.157 Angle : 0.675 9.102 18820 Z= 0.347 Chirality : 0.042 0.157 2137 Planarity : 0.005 0.055 2376 Dihedral : 6.604 39.629 1840 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.81 % Favored : 87.13 % 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: -4.08 (0.18), residues: 1670 helix: -1.70 (0.17), residues: 752 sheet: -3.44 (0.42), residues: 110 loop : -3.68 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 155 HIS 0.012 0.001 HIS A 424 PHE 0.026 0.001 PHE A 43 TYR 0.013 0.001 TYR A 184 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 259 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 216 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 272 LEU cc_start: 0.8976 (mp) cc_final: 0.8583 (tt) REVERT: A 864 MET cc_start: 0.7162 (tmm) cc_final: 0.6854 (tmm) REVERT: A 1174 LYS cc_start: 0.7907 (mtmt) cc_final: 0.7557 (mtpp) REVERT: A 1751 LEU cc_start: 0.6519 (tp) cc_final: 0.6221 (mm) REVERT: B 33 LEU cc_start: 0.5724 (tm) cc_final: 0.5496 (tp) outliers start: 43 outliers final: 20 residues processed: 249 average time/residue: 0.2499 time to fit residues: 91.6480 Evaluate side-chains 195 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 175 time to evaluate : 1.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 333 CYS Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 485 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 686 LEU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 909 ASN Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 1285 SER 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 42 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 5.9990 chunk 136 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 422 ASN ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS A 900 GLN A 909 ASN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1733 ASN A1734 HIS A1784 ASN A1790 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1804 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13964 Z= 0.286 Angle : 0.728 8.793 18820 Z= 0.371 Chirality : 0.045 0.159 2137 Planarity : 0.005 0.045 2376 Dihedral : 6.424 49.574 1838 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.79 % Favored : 85.15 % Rotamer: Outliers : 4.16 % Allowed : 13.36 % Favored : 82.48 % 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: -3.67 (0.19), residues: 1670 helix: -1.20 (0.18), residues: 760 sheet: -3.11 (0.45), residues: 105 loop : -3.69 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A1716 HIS 0.010 0.002 HIS A 471 PHE 0.024 0.002 PHE A1377 TYR 0.015 0.002 TYR A1311 ARG 0.006 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 250 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 185 time to evaluate : 1.678 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7480 (tp) REVERT: A 182 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.5394 (tm130) REVERT: A 272 LEU cc_start: 0.9051 (mp) cc_final: 0.8601 (tt) REVERT: A 1174 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7625 (mtpp) REVERT: A 1711 ASN cc_start: 0.5755 (OUTLIER) cc_final: 0.5292 (p0) REVERT: A 1751 LEU cc_start: 0.6587 (tp) cc_final: 0.6298 (mm) outliers start: 65 outliers final: 39 residues processed: 232 average time/residue: 0.2510 time to fit residues: 87.1053 Evaluate side-chains 213 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 171 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 94 THR Chi-restraints excluded: chain A residue 125 ASN 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 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 493 SER Chi-restraints excluded: chain A residue 537 ASN 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 825 ASP 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 1105 THR Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1214 ASP 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 1515 ILE Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1711 ASN Chi-restraints excluded: chain B residue 47 THR 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: 0.0670 chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 154 optimal weight: 0.0970 chunk 163 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 146 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13964 Z= 0.183 Angle : 0.647 8.704 18820 Z= 0.327 Chirality : 0.042 0.151 2137 Planarity : 0.004 0.044 2376 Dihedral : 5.996 47.219 1838 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 4.54 % Allowed : 14.19 % Favored : 81.27 % 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: -3.16 (0.19), residues: 1670 helix: -0.67 (0.19), residues: 761 sheet: -2.84 (0.47), residues: 104 loop : -3.55 (0.19), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1716 HIS 0.005 0.001 HIS A1404 PHE 0.023 0.001 PHE A 43 TYR 0.011 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 265 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 194 time to evaluate : 1.659 Fit side-chains REVERT: A 38 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7404 (tp) REVERT: A 182 GLN cc_start: 0.7272 (OUTLIER) cc_final: 0.6705 (tp40) REVERT: A 272 LEU cc_start: 0.9021 (mp) cc_final: 0.8568 (tt) REVERT: A 707 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8347 (ttmm) REVERT: A 1174 LYS cc_start: 0.7865 (mtmt) cc_final: 0.7595 (mtpp) REVERT: A 1711 ASN cc_start: 0.5835 (OUTLIER) cc_final: 0.5323 (p0) REVERT: A 1751 LEU cc_start: 0.6540 (tp) cc_final: 0.6267 (mm) outliers start: 71 outliers final: 42 residues processed: 250 average time/residue: 0.2520 time to fit residues: 92.9067 Evaluate side-chains 219 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 173 time to evaluate : 1.662 ------------------------------------------------------------------------------- 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 401 LEU Chi-restraints excluded: chain A residue 407 MET 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 493 SER Chi-restraints excluded: chain A residue 537 ASN 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 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 897 THR 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 1105 THR Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1138 LYS 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 1466 ASP Chi-restraints excluded: chain A residue 1544 LEU Chi-restraints excluded: chain A residue 1559 LEU Chi-restraints excluded: chain A residue 1711 ASN 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 136 optimal weight: 8.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 139 optimal weight: 6.9990 chunk 112 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 83 optimal weight: 1.9990 chunk 146 optimal weight: 9.9990 chunk 41 optimal weight: 0.9980 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN A1230 HIS A1357 HIS A1797 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13964 Z= 0.269 Angle : 0.702 9.828 18820 Z= 0.353 Chirality : 0.044 0.199 2137 Planarity : 0.004 0.044 2376 Dihedral : 6.049 50.688 1838 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.31 % Favored : 85.63 % Rotamer: Outliers : 5.69 % Allowed : 14.45 % Favored : 79.86 % 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: -3.13 (0.19), residues: 1670 helix: -0.67 (0.19), residues: 765 sheet: -2.82 (0.47), residues: 105 loop : -3.51 (0.19), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1716 HIS 0.006 0.001 HIS A1404 PHE 0.028 0.002 PHE A1492 TYR 0.014 0.001 TYR A 544 ARG 0.005 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 270 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 181 time to evaluate : 1.688 Fit side-chains REVERT: A 38 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7429 (tp) REVERT: A 182 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.5510 (tt0) REVERT: A 272 LEU cc_start: 0.9056 (mp) cc_final: 0.8581 (tt) REVERT: A 439 ASP cc_start: 0.7946 (OUTLIER) cc_final: 0.7588 (p0) REVERT: A 707 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8360 (ttmm) REVERT: A 1174 LYS cc_start: 0.7909 (mtmt) cc_final: 0.7623 (mtpp) REVERT: A 1711 ASN cc_start: 0.5917 (OUTLIER) cc_final: 0.5408 (p0) REVERT: A 1751 LEU cc_start: 0.6602 (tp) cc_final: 0.6312 (mm) outliers start: 89 outliers final: 57 residues processed: 250 average time/residue: 0.2583 time to fit residues: 95.1706 Evaluate side-chains 240 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 178 time to evaluate : 1.496 ------------------------------------------------------------------------------- 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 125 ASN 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 407 MET Chi-restraints excluded: chain A residue 439 ASP 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 493 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 ASN 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 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 897 THR 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 1105 THR Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1138 LYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1430 VAL Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 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 1711 ASN Chi-restraints excluded: chain A residue 1733 ASN 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 Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 47 THR 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 54 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 163 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 75 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 3.9990 chunk 157 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 A1019 GLN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13964 Z= 0.241 Angle : 0.680 10.085 18820 Z= 0.343 Chirality : 0.043 0.162 2137 Planarity : 0.004 0.045 2376 Dihedral : 5.987 53.300 1838 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.77 % Favored : 86.17 % Rotamer: Outliers : 5.56 % Allowed : 14.77 % 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: -3.04 (0.20), residues: 1670 helix: -0.58 (0.19), residues: 769 sheet: -2.70 (0.49), residues: 104 loop : -3.51 (0.19), residues: 797 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 0.012 0.001 TYR A 991 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 268 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 181 time to evaluate : 1.613 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7391 (tp) REVERT: A 125 ASN cc_start: 0.8397 (OUTLIER) cc_final: 0.8192 (t0) REVERT: A 182 GLN cc_start: 0.7070 (OUTLIER) cc_final: 0.5352 (tt0) REVERT: A 184 TYR cc_start: 0.6414 (m-80) cc_final: 0.6148 (m-80) REVERT: A 272 LEU cc_start: 0.9064 (mp) cc_final: 0.8572 (tt) REVERT: A 371 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6669 (mt) REVERT: A 439 ASP cc_start: 0.7922 (OUTLIER) cc_final: 0.7575 (p0) REVERT: A 707 LYS cc_start: 0.8714 (OUTLIER) cc_final: 0.8338 (ttmm) REVERT: A 854 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: A 1174 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7647 (mtpp) REVERT: A 1751 LEU cc_start: 0.6569 (tp) cc_final: 0.6284 (mm) outliers start: 87 outliers final: 60 residues processed: 247 average time/residue: 0.2531 time to fit residues: 92.0814 Evaluate side-chains 242 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 175 time to evaluate : 1.634 ------------------------------------------------------------------------------- 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 125 ASN 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 371 ILE Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 407 MET Chi-restraints excluded: chain A residue 439 ASP 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 493 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 ASN 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 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 897 THR Chi-restraints excluded: chain A residue 900 GLN 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 1138 LYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1223 VAL 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 1430 VAL 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 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 1733 ASN Chi-restraints excluded: chain A residue 1769 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 47 THR 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 18 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 137 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 162 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- 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 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 13964 Z= 0.289 Angle : 0.716 10.631 18820 Z= 0.361 Chirality : 0.044 0.159 2137 Planarity : 0.004 0.046 2376 Dihedral : 6.096 56.784 1838 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.09 % Favored : 84.85 % Rotamer: Outliers : 5.31 % Allowed : 15.79 % Favored : 78.90 % 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: -3.14 (0.19), residues: 1670 helix: -0.66 (0.18), residues: 770 sheet: -2.70 (0.49), residues: 105 loop : -3.58 (0.19), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1716 HIS 0.006 0.001 HIS A1404 PHE 0.026 0.002 PHE A1492 TYR 0.014 0.002 TYR A 544 ARG 0.006 0.000 ARG A 691 *********************** 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 260 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 177 time to evaluate : 1.548 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7408 (tp) REVERT: A 182 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.5481 (tt0) REVERT: A 272 LEU cc_start: 0.9097 (mp) cc_final: 0.8592 (tt) REVERT: A 439 ASP cc_start: 0.7916 (OUTLIER) cc_final: 0.7562 (p0) REVERT: A 707 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8331 (ttmm) REVERT: A 854 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7758 (ttpt) REVERT: A 1174 LYS cc_start: 0.7924 (mtmt) cc_final: 0.7634 (mtpp) REVERT: A 1751 LEU cc_start: 0.6557 (tp) cc_final: 0.6284 (mm) outliers start: 83 outliers final: 64 residues processed: 241 average time/residue: 0.2562 time to fit residues: 90.7817 Evaluate side-chains 239 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 170 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 407 MET Chi-restraints excluded: chain A residue 439 ASP 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 493 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 ASN 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 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 897 THR Chi-restraints excluded: chain A residue 900 GLN 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 1138 LYS Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1234 VAL Chi-restraints excluded: chain A residue 1285 SER Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1387 VAL Chi-restraints excluded: chain A residue 1430 VAL 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 1733 ASN 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 128 optimal weight: 1.9990 chunk 148 optimal weight: 0.0870 overall best weight: 0.9162 ------------------------------------------------------------------------------- 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** 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: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 13964 Z= 0.150 Angle : 0.631 9.073 18820 Z= 0.318 Chirality : 0.041 0.304 2137 Planarity : 0.004 0.041 2376 Dihedral : 5.664 59.025 1838 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.40 % Favored : 87.60 % Rotamer: Outliers : 4.03 % Allowed : 17.07 % Favored : 78.90 % 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: -2.72 (0.20), residues: 1670 helix: -0.24 (0.19), residues: 770 sheet: -3.68 (0.53), residues: 75 loop : -3.31 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 155 HIS 0.004 0.001 HIS A1357 PHE 0.022 0.001 PHE A 43 TYR 0.010 0.001 TYR A1120 ARG 0.007 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 252 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 189 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7215 (tp) REVERT: A 184 TYR cc_start: 0.6380 (m-80) cc_final: 0.6013 (m-80) REVERT: A 272 LEU cc_start: 0.9021 (mp) cc_final: 0.8607 (tt) REVERT: A 707 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8315 (ttmm) REVERT: A 854 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7703 (ttpt) REVERT: A 1174 LYS cc_start: 0.7911 (mtmt) cc_final: 0.7628 (mtpp) REVERT: A 1751 LEU cc_start: 0.6571 (tp) cc_final: 0.6305 (mm) outliers start: 63 outliers final: 45 residues processed: 238 average time/residue: 0.2554 time to fit residues: 89.8950 Evaluate side-chains 227 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 179 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 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 493 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 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 897 THR Chi-restraints excluded: chain A residue 900 GLN 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 1020 GLU Chi-restraints excluded: chain A residue 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1138 LYS Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1230 HIS Chi-restraints excluded: chain A residue 1322 VAL 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 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 B residue 36 ARG Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 160 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 909 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13964 Z= 0.235 Angle : 0.682 10.217 18820 Z= 0.342 Chirality : 0.043 0.311 2137 Planarity : 0.004 0.041 2376 Dihedral : 5.589 47.707 1836 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.13 % Favored : 85.81 % Rotamer: Outliers : 3.84 % Allowed : 17.97 % Favored : 78.20 % 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: -2.85 (0.20), residues: 1670 helix: -0.37 (0.19), residues: 785 sheet: -3.56 (0.50), residues: 82 loop : -3.41 (0.19), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A1716 HIS 0.008 0.001 HIS A1232 PHE 0.030 0.002 PHE A1492 TYR 0.025 0.001 TYR A 687 ARG 0.009 0.000 ARG A 375 *********************** 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 236 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 176 time to evaluate : 1.687 Fit side-chains revert: symmetry clash REVERT: A 38 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7252 (tp) REVERT: A 184 TYR cc_start: 0.6356 (m-80) cc_final: 0.6029 (m-80) REVERT: A 272 LEU cc_start: 0.9051 (mp) cc_final: 0.8633 (tt) REVERT: A 439 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7583 (p0) REVERT: A 707 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8325 (ttmm) REVERT: A 854 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7732 (ttpt) REVERT: A 1174 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7642 (mtpp) REVERT: A 1724 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5505 (ppt170) REVERT: A 1751 LEU cc_start: 0.6557 (tp) cc_final: 0.6311 (mm) outliers start: 60 outliers final: 48 residues processed: 224 average time/residue: 0.2646 time to fit residues: 87.2379 Evaluate side-chains 227 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 174 time to evaluate : 1.564 ------------------------------------------------------------------------------- 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 333 CYS Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 401 LEU Chi-restraints excluded: chain A residue 439 ASP 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 493 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 707 LYS Chi-restraints excluded: chain A residue 764 LYS Chi-restraints excluded: chain A residue 785 LEU Chi-restraints excluded: chain A residue 798 LYS Chi-restraints excluded: chain A residue 847 MET Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 891 VAL Chi-restraints excluded: chain A residue 897 THR Chi-restraints excluded: chain A residue 900 GLN 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 1132 VAL Chi-restraints excluded: chain A residue 1137 THR Chi-restraints excluded: chain A residue 1138 LYS Chi-restraints excluded: chain A residue 1184 CYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1322 VAL Chi-restraints excluded: chain A residue 1357 HIS 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 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1724 ARG Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 111 optimal weight: 7.9990 chunk 168 optimal weight: 0.0010 chunk 154 optimal weight: 0.0570 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 6.9990 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 0.3980 chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 6.9990 overall best weight: 0.6706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 909 ASN A1230 HIS ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13964 Z= 0.147 Angle : 0.645 11.318 18820 Z= 0.321 Chirality : 0.041 0.293 2137 Planarity : 0.004 0.040 2376 Dihedral : 5.346 44.694 1836 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.68 % Favored : 88.32 % Rotamer: Outliers : 3.71 % Allowed : 18.35 % Favored : 77.94 % 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: -2.50 (0.20), residues: 1670 helix: -0.04 (0.19), residues: 776 sheet: -3.55 (0.54), residues: 77 loop : -3.22 (0.19), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 155 HIS 0.007 0.001 HIS A1357 PHE 0.022 0.001 PHE A 43 TYR 0.022 0.001 TYR A 687 ARG 0.011 0.000 ARG A 375 ********************** 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 257 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 199 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6378 (tpp) cc_final: 0.6150 (tpp) REVERT: A 38 LEU cc_start: 0.7389 (OUTLIER) cc_final: 0.7140 (tp) REVERT: A 102 GLU cc_start: 0.7395 (mp0) cc_final: 0.7125 (mp0) REVERT: A 184 TYR cc_start: 0.6263 (m-80) cc_final: 0.5970 (m-80) REVERT: A 272 LEU cc_start: 0.8981 (mp) cc_final: 0.8587 (tt) REVERT: A 291 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 563 VAL cc_start: 0.8000 (OUTLIER) cc_final: 0.7691 (p) REVERT: A 707 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8306 (ttmm) REVERT: A 854 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7671 (ttpt) REVERT: A 1174 LYS cc_start: 0.7897 (mtmt) cc_final: 0.7604 (mtpp) REVERT: A 1724 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.5320 (ppt170) REVERT: A 1751 LEU cc_start: 0.6564 (tp) cc_final: 0.6293 (mm) outliers start: 58 outliers final: 41 residues processed: 242 average time/residue: 0.2754 time to fit residues: 98.4953 Evaluate side-chains 231 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 184 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 291 LEU 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 493 SER Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 707 LYS 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 897 THR 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 1138 LYS Chi-restraints excluded: chain A residue 1214 ASP Chi-restraints excluded: chain A residue 1223 VAL 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 1559 LEU Chi-restraints excluded: chain A residue 1624 MET Chi-restraints excluded: chain A residue 1724 ARG Chi-restraints excluded: chain A residue 1730 LEU Chi-restraints excluded: chain A residue 1781 MET Chi-restraints excluded: chain B residue 36 ARG Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 47 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 134 optimal weight: 4.9990 chunk 56 optimal weight: 0.8980 chunk 137 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 A1019 GLN A1113 ASN ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS B 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.182640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146892 restraints weight = 15395.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.150464 restraints weight = 12940.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.151552 restraints weight = 8937.732| |-----------------------------------------------------------------------------| r_work (final): 0.3780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 13964 Z= 0.157 Angle : 0.642 11.433 18820 Z= 0.319 Chirality : 0.041 0.285 2137 Planarity : 0.004 0.040 2376 Dihedral : 5.254 44.569 1836 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 3.45 % Allowed : 18.29 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.37 (0.20), residues: 1670 helix: 0.13 (0.19), residues: 767 sheet: -3.58 (0.51), residues: 82 loop : -3.18 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1716 HIS 0.006 0.001 HIS A1232 PHE 0.022 0.001 PHE A 43 TYR 0.022 0.001 TYR A 687 ARG 0.011 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3100.96 seconds wall clock time: 56 minutes 57.47 seconds (3417.47 seconds total)