Starting phenix.real_space_refine on Sun Dec 10 06:59:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/12_2023/7eju_31163.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/12_2023/7eju_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_31163/12_2023/7eju_31163.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/12_2023/7eju_31163.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/12_2023/7eju_31163.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eju_31163/12_2023/7eju_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 7.51, 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: 5.26 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: 1.98 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: 4.76 Time building geometry restraints manager: 5.74 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: 1.560 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: 4.520 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 41.520 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.440 ------------------------------------------------------------------------------- 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 : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 4 residues processed: 264 average time/residue: 0.2879 time to fit residues: 107.2557 Evaluate side-chains 171 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.650 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1228 time to fit residues: 3.1756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 142 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 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: 0.8980 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 647 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7559 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13964 Z= 0.156 Angle : 0.673 9.186 18820 Z= 0.345 Chirality : 0.041 0.154 2137 Planarity : 0.005 0.056 2376 Dihedral : 6.258 36.609 1832 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.06 % Allowed : 12.46 % Favored : 87.49 % Rotamer: Outliers : 2.49 % Allowed : 10.68 % Favored : 86.83 % 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: -4.07 (0.18), residues: 1670 helix: -1.69 (0.17), residues: 752 sheet: -3.41 (0.42), residues: 110 loop : -3.67 (0.18), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 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 0.006 0.000 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 218 time to evaluate : 1.781 Fit side-chains revert: symmetry clash outliers start: 39 outliers final: 17 residues processed: 247 average time/residue: 0.2572 time to fit residues: 94.1565 Evaluate side-chains 191 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 174 time to evaluate : 1.747 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1447 time to fit residues: 6.7892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 chunk 127 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 166 optimal weight: 30.0000 chunk 136 optimal weight: 8.9990 chunk 152 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1230 HIS ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** B 73 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2123 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= 0.273 Angle : 0.724 10.983 18820 Z= 0.367 Chirality : 0.044 0.154 2137 Planarity : 0.005 0.046 2376 Dihedral : 6.094 37.120 1832 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 14.43 % Favored : 85.51 % Rotamer: Outliers : 2.94 % Allowed : 14.58 % 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: -3.64 (0.19), residues: 1670 helix: -1.17 (0.18), residues: 760 sheet: -3.08 (0.45), residues: 105 loop : -3.67 (0.18), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A1716 HIS 0.008 0.002 HIS A 471 PHE 0.023 0.002 PHE A1377 TYR 0.017 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 234 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 188 time to evaluate : 1.698 Fit side-chains revert: symmetry clash outliers start: 46 outliers final: 27 residues processed: 221 average time/residue: 0.2543 time to fit residues: 84.4433 Evaluate side-chains 196 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.641 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1286 time to fit residues: 8.9955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 151 optimal weight: 2.9990 chunk 115 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 17 optimal weight: 20.0000 chunk 73 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 154 optimal weight: 0.1980 chunk 163 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 44 optimal weight: 0.0980 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN A 909 ASN ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1711 ASN ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1804 GLN B 73 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13964 Z= 0.199 Angle : 0.663 9.238 18820 Z= 0.335 Chirality : 0.042 0.149 2137 Planarity : 0.004 0.044 2376 Dihedral : 5.777 34.719 1832 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.23 % Favored : 86.77 % Rotamer: Outliers : 2.56 % Allowed : 15.09 % Favored : 82.35 % 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: -3.22 (0.19), residues: 1670 helix: -0.74 (0.19), residues: 767 sheet: -2.83 (0.47), residues: 104 loop : -3.58 (0.19), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1716 HIS 0.005 0.001 HIS A1404 PHE 0.022 0.001 PHE A 43 TYR 0.012 0.001 TYR A 991 ARG 0.004 0.000 ARG A 691 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 191 time to evaluate : 1.563 Fit side-chains revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 221 average time/residue: 0.2645 time to fit residues: 86.5901 Evaluate side-chains 188 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 172 time to evaluate : 1.610 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1824 time to fit residues: 7.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 136 optimal weight: 10.0000 chunk 92 optimal weight: 0.3980 chunk 2 optimal weight: 10.0000 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 0 optimal weight: 30.0000 chunk 83 optimal weight: 3.9990 chunk 146 optimal weight: 10.0000 chunk 41 optimal weight: 0.0060 overall best weight: 1.7800 ------------------------------------------------------------------------------- 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** ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13964 Z= 0.186 Angle : 0.656 9.738 18820 Z= 0.328 Chirality : 0.042 0.189 2137 Planarity : 0.004 0.043 2376 Dihedral : 5.548 33.118 1832 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.41 % Favored : 86.59 % Rotamer: Outliers : 2.75 % Allowed : 15.35 % Favored : 81.91 % 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: -3.03 (0.20), residues: 1670 helix: -0.55 (0.19), residues: 778 sheet: -3.69 (0.48), residues: 82 loop : -3.44 (0.19), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1716 HIS 0.004 0.001 HIS A1404 PHE 0.029 0.001 PHE A1492 TYR 0.011 0.001 TYR A 991 ARG 0.004 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 225 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 1.723 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 11 residues processed: 214 average time/residue: 0.2674 time to fit residues: 84.6624 Evaluate side-chains 182 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 171 time to evaluate : 1.642 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1332 time to fit residues: 5.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 54 optimal weight: 0.8980 chunk 147 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 163 optimal weight: 0.0970 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- 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** ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS A1733 ASN A1797 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2744 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= 0.220 Angle : 0.677 9.755 18820 Z= 0.339 Chirality : 0.043 0.157 2137 Planarity : 0.004 0.044 2376 Dihedral : 5.533 33.613 1832 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.06 % Allowed : 13.53 % Favored : 86.41 % Rotamer: Outliers : 2.17 % Allowed : 16.37 % Favored : 81.46 % 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: -2.94 (0.20), residues: 1670 helix: -0.52 (0.19), residues: 776 sheet: -2.51 (0.49), residues: 104 loop : -3.48 (0.19), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 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 544 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 210 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 1.747 Fit side-chains revert: symmetry clash outliers start: 34 outliers final: 17 residues processed: 202 average time/residue: 0.2832 time to fit residues: 83.9123 Evaluate side-chains 183 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 1.668 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1488 time to fit residues: 6.7592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 18 optimal weight: 9.9990 chunk 93 optimal weight: 0.2980 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 137 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 162 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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** A1019 GLN ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7651 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13964 Z= 0.197 Angle : 0.658 9.561 18820 Z= 0.330 Chirality : 0.042 0.156 2137 Planarity : 0.004 0.045 2376 Dihedral : 5.450 31.801 1832 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer: Outliers : 1.41 % Allowed : 17.52 % Favored : 81.07 % 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: -2.82 (0.20), residues: 1670 helix: -0.38 (0.19), residues: 775 sheet: -3.49 (0.50), residues: 82 loop : -3.32 (0.19), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1716 HIS 0.005 0.001 HIS A1357 PHE 0.027 0.001 PHE A1492 TYR 0.011 0.001 TYR A 544 ARG 0.004 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 207 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 185 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 9 residues processed: 203 average time/residue: 0.2542 time to fit residues: 77.0903 Evaluate side-chains 183 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 174 time to evaluate : 1.543 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1332 time to fit residues: 4.3305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 65 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 80 optimal weight: 5.9990 chunk 15 optimal weight: 20.0000 chunk 128 optimal weight: 2.9990 chunk 148 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- 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** ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13964 Z= 0.270 Angle : 0.707 10.791 18820 Z= 0.355 Chirality : 0.044 0.161 2137 Planarity : 0.004 0.045 2376 Dihedral : 5.598 33.163 1832 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.06 % Allowed : 15.09 % Favored : 84.85 % Rotamer: Outliers : 1.21 % Allowed : 18.54 % Favored : 80.24 % 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: -2.97 (0.19), residues: 1670 helix: -0.57 (0.18), residues: 786 sheet: -2.59 (0.49), residues: 105 loop : -3.48 (0.19), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1716 HIS 0.007 0.001 HIS A1404 PHE 0.021 0.002 PHE A 43 TYR 0.014 0.001 TYR A 544 ARG 0.006 0.000 ARG A 691 *********************** 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 193 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.788 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 187 average time/residue: 0.2721 time to fit residues: 75.6282 Evaluate side-chains 175 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 169 time to evaluate : 1.601 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1375 time to fit residues: 3.8716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 156 optimal weight: 4.9990 chunk 142 optimal weight: 0.9980 chunk 151 optimal weight: 2.9990 chunk 91 optimal weight: 0.0060 chunk 66 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 137 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 627 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1240 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1357 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13964 Z= 0.154 Angle : 0.639 9.738 18820 Z= 0.320 Chirality : 0.041 0.265 2137 Planarity : 0.004 0.040 2376 Dihedral : 5.233 30.678 1832 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.51 % Favored : 87.49 % Rotamer: Outliers : 0.45 % Allowed : 19.63 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.20), residues: 1670 helix: -0.10 (0.19), residues: 769 sheet: -3.53 (0.51), residues: 80 loop : -3.18 (0.19), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 155 HIS 0.004 0.001 HIS A 646 PHE 0.021 0.001 PHE A 43 TYR 0.010 0.001 TYR A 991 ARG 0.006 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 203 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 196 time to evaluate : 1.716 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 202 average time/residue: 0.2515 time to fit residues: 76.3443 Evaluate side-chains 182 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.625 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1325 time to fit residues: 3.5015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 97 optimal weight: 9.9990 chunk 76 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 168 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 134 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 82 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 912 GLN A1230 HIS ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1240 ASN ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13964 Z= 0.447 Angle : 0.840 12.567 18820 Z= 0.422 Chirality : 0.050 0.332 2137 Planarity : 0.005 0.043 2376 Dihedral : 5.954 33.894 1832 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 16.41 % Favored : 83.53 % Rotamer: Outliers : 0.51 % Allowed : 19.63 % 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: -3.25 (0.19), residues: 1670 helix: -0.80 (0.18), residues: 777 sheet: -3.78 (0.47), residues: 87 loop : -3.46 (0.19), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1716 HIS 0.011 0.002 HIS A1404 PHE 0.026 0.003 PHE A1386 TYR 0.019 0.002 TYR A 544 ARG 0.008 0.001 ARG A 691 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3340 Ramachandran restraints generated. 1670 Oldfield, 0 Emsley, 1670 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.722 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 175 average time/residue: 0.2611 time to fit residues: 69.5622 Evaluate side-chains 168 residues out of total 1565 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 1.606 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1364 time to fit residues: 3.2372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 169 random chunks: chunk 41 optimal weight: 0.4980 chunk 123 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 37 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 137 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 912 GLN ** A1232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1797 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.178895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.143864 restraints weight = 15519.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.145333 restraints weight = 13085.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146809 restraints weight = 10055.688| |-----------------------------------------------------------------------------| r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13964 Z= 0.183 Angle : 0.687 11.138 18820 Z= 0.343 Chirality : 0.043 0.293 2137 Planarity : 0.004 0.044 2376 Dihedral : 5.510 32.254 1832 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 0.13 % Allowed : 20.40 % Favored : 79.48 % 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: -2.79 (0.20), residues: 1670 helix: -0.34 (0.19), residues: 778 sheet: -3.53 (0.50), residues: 84 loop : -3.33 (0.19), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1716 HIS 0.005 0.001 HIS A 646 PHE 0.024 0.001 PHE A1104 TYR 0.010 0.001 TYR A 991 ARG 0.004 0.000 ARG A 375 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2929.70 seconds wall clock time: 54 minutes 11.55 seconds (3251.55 seconds total)