Starting phenix.real_space_refine on Sat Feb 17 09:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7you_33987/02_2024/7you_33987.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7you_33987/02_2024/7you_33987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7you_33987/02_2024/7you_33987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7you_33987/02_2024/7you_33987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7you_33987/02_2024/7you_33987.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7you_33987/02_2024/7you_33987.pdb" } resolution = 3.41 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: 4 Type Number sf(0) Gaussians S 115 5.16 5 C 11587 2.51 5 N 3163 2.21 5 O 3401 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 111": "NH1" <-> "NH2" Residue "A ARG 112": "NH1" <-> "NH2" Residue "A ARG 123": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A ARG 191": "NH1" <-> "NH2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A ARG 258": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 405": "NH1" <-> "NH2" Residue "A ARG 442": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 532": "NH1" <-> "NH2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 633": "NH1" <-> "NH2" Residue "A ARG 677": "NH1" <-> "NH2" Residue "A ARG 714": "NH1" <-> "NH2" Residue "A ARG 739": "NH1" <-> "NH2" Residue "A ARG 783": "NH1" <-> "NH2" Residue "A ARG 799": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 962": "NH1" <-> "NH2" Residue "A ARG 1036": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1077": "NH1" <-> "NH2" Residue "A ARG 1080": "NH1" <-> "NH2" Residue "A ARG 1093": "NH1" <-> "NH2" Residue "A ARG 1101": "NH1" <-> "NH2" Residue "A ARG 1132": "NH1" <-> "NH2" Residue "A PHE 1167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1189": "NH1" <-> "NH2" Residue "A ARG 1201": "NH1" <-> "NH2" Residue "A ARG 1286": "NH1" <-> "NH2" Residue "A ARG 1370": "NH1" <-> "NH2" Residue "A ARG 1462": "NH1" <-> "NH2" Residue "A ARG 1554": "NH1" <-> "NH2" Residue "A PHE 1705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1745": "NH1" <-> "NH2" Residue "A PHE 1814": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1840": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 300": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 360": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18266 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 16338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2059, 16338 Classifications: {'peptide': 2059} Link IDs: {'PCIS': 1, 'PTRANS': 83, 'TRANS': 1974} Chain breaks: 16 Chain: "D" Number of atoms: 398 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 54, 393 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Conformer: "B" Number of residues, atoms: 54, 393 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} bond proxies already assigned to first conformer: 390 Chain: "C" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 344 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 302 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "E" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 884 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AALA D 301 " occ=0.50 ... (8 atoms not shown) pdb=" CB BALA D 301 " occ=0.50 Time building chain proxies: 9.94, per 1000 atoms: 0.54 Number of scatterers: 18266 At special positions: 0 Unit cell: (113.36, 143.52, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 115 16.00 O 3401 8.00 N 3163 7.00 C 11587 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A1112 " - pdb=" SG CYS A1350 " distance=2.01 Simple disulfide: pdb=" SG CYS A1157 " - pdb=" SG CYS A1160 " distance=2.03 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: 7.00 Conformation dependent library (CDL) restraints added in 3.6 seconds 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4422 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 9 sheets defined 57.3% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 9 through 13 removed outlier: 3.520A pdb=" N GLN A 12 " --> pdb=" O ALA A 9 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE A 13 " --> pdb=" O GLU A 10 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 9 through 13' Processing helix chain 'A' and resid 25 through 36 removed outlier: 4.017A pdb=" N LEU A 29 " --> pdb=" O VAL A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.810A pdb=" N SER A 52 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ARG A 53 " --> pdb=" O ILE A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.650A pdb=" N MET A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 100 removed outlier: 3.645A pdb=" N GLY A 100 " --> pdb=" O GLU A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 140 removed outlier: 4.113A pdb=" N LYS A 109 " --> pdb=" O ASP A 105 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ARG A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 151 through 160 Processing helix chain 'A' and resid 169 through 192 removed outlier: 4.070A pdb=" N THR A 192 " --> pdb=" O VAL A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 254 Processing helix chain 'A' and resid 257 through 279 removed outlier: 3.737A pdb=" N ALA A 261 " --> pdb=" O LEU A 257 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 263 " --> pdb=" O CYS A 259 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ASP A 277 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 279 " --> pdb=" O ALA A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 298 removed outlier: 3.650A pdb=" N ALA A 287 " --> pdb=" O TYR A 283 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LEU A 288 " --> pdb=" O ASP A 284 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N GLU A 290 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLY A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 299 through 301 No H-bonds generated for 'chain 'A' and resid 299 through 301' Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 327 through 342 Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.774A pdb=" N ALA A 351 " --> pdb=" O GLN A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 356 No H-bonds generated for 'chain 'A' and resid 354 through 356' Processing helix chain 'A' and resid 366 through 379 removed outlier: 4.099A pdb=" N GLN A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 408 Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.754A pdb=" N ILE A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 432 removed outlier: 3.593A pdb=" N ALA A 426 " --> pdb=" O GLY A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 443 Processing helix chain 'A' and resid 443 through 448 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'A' and resid 490 through 495 removed outlier: 3.666A pdb=" N LYS A 495 " --> pdb=" O GLU A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 Processing helix chain 'A' and resid 517 through 523 removed outlier: 3.540A pdb=" N GLU A 523 " --> pdb=" O TYR A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 533 Processing helix chain 'A' and resid 558 through 575 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 588 through 602 removed outlier: 3.739A pdb=" N THR A 593 " --> pdb=" O SER A 589 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU A 602 " --> pdb=" O ALA A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.944A pdb=" N ARG A 608 " --> pdb=" O ASN A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 666 removed outlier: 5.444A pdb=" N LEU A 656 " --> pdb=" O GLN A 652 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N PHE A 657 " --> pdb=" O THR A 653 " (cutoff:3.500A) Processing helix chain 'A' and resid 672 through 681 removed outlier: 3.859A pdb=" N LEU A 676 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 721 through 739 Processing helix chain 'A' and resid 766 through 792 removed outlier: 3.703A pdb=" N ILE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 829 removed outlier: 3.623A pdb=" N ASN A 827 " --> pdb=" O GLN A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 859 removed outlier: 3.730A pdb=" N SER A 845 " --> pdb=" O ASN A 841 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 859 " --> pdb=" O ARG A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 881 Processing helix chain 'A' and resid 901 through 910 Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.551A pdb=" N GLY A 916 " --> pdb=" O ALA A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 927 Processing helix chain 'A' and resid 933 through 948 removed outlier: 3.826A pdb=" N THR A 937 " --> pdb=" O ASP A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 4.412A pdb=" N MET A 956 " --> pdb=" O GLY A 952 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR A 957 " --> pdb=" O PRO A 953 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 960 " --> pdb=" O MET A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 975 removed outlier: 3.624A pdb=" N ASP A 975 " --> pdb=" O SER A 971 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1000 Processing helix chain 'A' and resid 1015 through 1029 Processing helix chain 'A' and resid 1034 through 1045 Processing helix chain 'A' and resid 1045 through 1055 Processing helix chain 'A' and resid 1060 through 1071 Processing helix chain 'A' and resid 1075 through 1083 Processing helix chain 'A' and resid 1083 through 1096 Processing helix chain 'A' and resid 1112 through 1130 Proline residue: A1127 - end of helix Processing helix chain 'A' and resid 1141 through 1146 removed outlier: 3.739A pdb=" N VAL A1146 " --> pdb=" O THR A1142 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1163 removed outlier: 4.102A pdb=" N GLY A1163 " --> pdb=" O CYS A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1212 through 1230 Processing helix chain 'A' and resid 1232 through 1244 Processing helix chain 'A' and resid 1250 through 1258 removed outlier: 3.880A pdb=" N LEU A1256 " --> pdb=" O GLU A1252 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1287 through 1291 removed outlier: 3.640A pdb=" N VAL A1291 " --> pdb=" O SER A1288 " (cutoff:3.500A) Processing helix chain 'A' and resid 1311 through 1327 Processing helix chain 'A' and resid 1385 through 1399 removed outlier: 4.496A pdb=" N ARG A1391 " --> pdb=" O GLY A1387 " (cutoff:3.500A) Processing helix chain 'A' and resid 1400 through 1402 No H-bonds generated for 'chain 'A' and resid 1400 through 1402' Processing helix chain 'A' and resid 1408 through 1421 Processing helix chain 'A' and resid 1462 through 1482 removed outlier: 4.160A pdb=" N TYR A1466 " --> pdb=" O ARG A1462 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TYR A1477 " --> pdb=" O LEU A1473 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN A1478 " --> pdb=" O ASP A1474 " (cutoff:3.500A) Processing helix chain 'A' and resid 1489 through 1500 Processing helix chain 'A' and resid 1506 through 1513 Processing helix chain 'A' and resid 1515 through 1525 Processing helix chain 'A' and resid 1538 through 1542 Processing helix chain 'A' and resid 1543 through 1562 Processing helix chain 'A' and resid 1580 through 1597 Processing helix chain 'A' and resid 1610 through 1623 Processing helix chain 'A' and resid 1635 through 1641 removed outlier: 3.582A pdb=" N SER A1641 " --> pdb=" O ASP A1637 " (cutoff:3.500A) Processing helix chain 'A' and resid 1650 through 1665 removed outlier: 3.770A pdb=" N SER A1658 " --> pdb=" O MET A1654 " (cutoff:3.500A) Processing helix chain 'A' and resid 1667 through 1675 removed outlier: 3.566A pdb=" N MET A1675 " --> pdb=" O ILE A1671 " (cutoff:3.500A) Processing helix chain 'A' and resid 1696 through 1700 removed outlier: 3.558A pdb=" N MET A1700 " --> pdb=" O GLN A1697 " (cutoff:3.500A) Processing helix chain 'A' and resid 1739 through 1744 Processing helix chain 'A' and resid 1756 through 1762 Processing helix chain 'A' and resid 1763 through 1768 removed outlier: 3.820A pdb=" N ARG A1767 " --> pdb=" O VAL A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1792 Processing helix chain 'A' and resid 1804 through 1808 removed outlier: 3.903A pdb=" N ASN A1808 " --> pdb=" O ASN A1805 " (cutoff:3.500A) Processing helix chain 'A' and resid 1818 through 1823 removed outlier: 3.553A pdb=" N ASN A1823 " --> pdb=" O THR A1819 " (cutoff:3.500A) Processing helix chain 'A' and resid 1824 through 1832 Processing helix chain 'A' and resid 1859 through 1870 removed outlier: 3.702A pdb=" N VAL A1863 " --> pdb=" O SER A1859 " (cutoff:3.500A) Processing helix chain 'A' and resid 1889 through 1907 Processing helix chain 'A' and resid 1922 through 1934 Processing helix chain 'A' and resid 1945 through 1949 removed outlier: 3.656A pdb=" N ALA A1948 " --> pdb=" O ASN A1945 " (cutoff:3.500A) Processing helix chain 'A' and resid 1966 through 1983 Processing helix chain 'A' and resid 1989 through 2012 Processing helix chain 'A' and resid 2014 through 2023 Processing helix chain 'A' and resid 2040 through 2046 removed outlier: 4.010A pdb=" N LEU A2046 " --> pdb=" O ALA A2043 " (cutoff:3.500A) Processing helix chain 'A' and resid 2054 through 2076 removed outlier: 3.855A pdb=" N GLU A2075 " --> pdb=" O VAL A2071 " (cutoff:3.500A) Processing helix chain 'A' and resid 2095 through 2117 Processing helix chain 'A' and resid 2122 through 2135 removed outlier: 3.656A pdb=" N GLY A2135 " --> pdb=" O LEU A2131 " (cutoff:3.500A) Processing helix chain 'A' and resid 2138 through 2143 removed outlier: 3.596A pdb=" N LEU A2142 " --> pdb=" O SER A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2144 through 2151 Processing helix chain 'A' and resid 2154 through 2162 removed outlier: 3.529A pdb=" N LEU A2158 " --> pdb=" O CYS A2154 " (cutoff:3.500A) Processing helix chain 'A' and resid 2162 through 2172 removed outlier: 4.217A pdb=" N LYS A2166 " --> pdb=" O LEU A2162 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER A2172 " --> pdb=" O ARG A2168 " (cutoff:3.500A) Processing helix chain 'A' and resid 2180 through 2197 removed outlier: 3.612A pdb=" N GLN A2184 " --> pdb=" O THR A2180 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 281 removed outlier: 4.393A pdb=" N SER D 264 " --> pdb=" O PRO D 260 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N THR D 271 " --> pdb=" O GLN D 267 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA D 278 " --> pdb=" O ALA D 274 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLY D 281 " --> pdb=" O GLU D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 304 removed outlier: 3.524A pdb=" N ARG D 300 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS D 304 " --> pdb=" O ARG D 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 286 removed outlier: 4.187A pdb=" N GLU C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N VAL C 275 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N MET C 276 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU C 277 " --> pdb=" O VAL C 273 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 292 removed outlier: 3.610A pdb=" N ALA C 291 " --> pdb=" O PRO C 288 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN C 292 " --> pdb=" O GLY C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 288 through 292' Processing helix chain 'C' and resid 298 through 305 removed outlier: 3.628A pdb=" N SER C 305 " --> pdb=" O ALA C 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 279 removed outlier: 3.707A pdb=" N ILE B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 267 " --> pdb=" O ARG B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 Processing helix chain 'E' and resid 275 through 280 removed outlier: 3.957A pdb=" N ASN E 279 " --> pdb=" O VAL E 275 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU E 280 " --> pdb=" O MET E 276 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 275 through 280' Processing helix chain 'E' and resid 295 through 302 removed outlier: 3.701A pdb=" N LEU E 299 " --> pdb=" O SER E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 removed outlier: 4.365A pdb=" N ILE E 342 " --> pdb=" O PRO E 338 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS E 343 " --> pdb=" O SER E 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 338 through 343' Processing helix chain 'E' and resid 352 through 366 removed outlier: 3.684A pdb=" N ARG E 356 " --> pdb=" O ILE E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.501A pdb=" N LYS E 379 " --> pdb=" O LYS E 375 " (cutoff:3.500A) Processing helix chain 'E' and resid 388 through 397 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.545A pdb=" N THR A 87 " --> pdb=" O PHE A 226 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N CYS A 228 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 382 through 385 removed outlier: 6.490A pdb=" N LYS B 284 " --> pdb=" O LEU E 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 556 removed outlier: 6.374A pdb=" N TYR A 540 " --> pdb=" O GLY A 686 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 744 through 749 Processing sheet with id=AA5, first strand: chain 'A' and resid 807 through 810 removed outlier: 4.632A pdb=" N ILE A 814 " --> pdb=" O LEU A 821 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1147 through 1151 Processing sheet with id=AA7, first strand: chain 'A' and resid 1176 through 1177 Processing sheet with id=AA8, first strand: chain 'A' and resid 1705 through 1708 removed outlier: 3.804A pdb=" N PHE A1705 " --> pdb=" O SER A1944 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A1944 " --> pdb=" O PHE A1705 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N CYS A1955 " --> pdb=" O LYS A1917 " (cutoff:3.500A) removed outlier: 4.896A pdb=" N LYS A1917 " --> pdb=" O CYS A1955 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL A1957 " --> pdb=" O ILE A1915 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ILE A1915 " --> pdb=" O VAL A1957 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N PHE A1959 " --> pdb=" O VAL A1913 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N VAL A1913 " --> pdb=" O PHE A1959 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N MET A1961 " --> pdb=" O GLY A1911 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N SER A1876 " --> pdb=" O GLY A1911 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ASN A1773 " --> pdb=" O SER A1876 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N LEU A1878 " --> pdb=" O ASN A1773 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU A1775 " --> pdb=" O LEU A1878 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N CYS A1880 " --> pdb=" O LEU A1775 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU A1777 " --> pdb=" O CYS A1880 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER A1774 " --> pdb=" O TYR A1798 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TYR A1799 " --> pdb=" O ARG A1845 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1705 through 1708 removed outlier: 3.804A pdb=" N PHE A1705 " --> pdb=" O SER A1944 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER A1944 " --> pdb=" O PHE A1705 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL A1960 " --> pdb=" O VAL A1938 " (cutoff:3.500A) 893 hydrogen bonds defined for protein. 2545 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: 8.19 Time building geometry restraints manager: 7.59 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: 5710 1.34 - 1.46: 4000 1.46 - 1.58: 8714 1.58 - 1.71: 0 1.71 - 1.83: 186 Bond restraints: 18610 Sorted by residual: bond pdb=" C ALA A 577 " pdb=" N PRO A 578 " ideal model delta sigma weight residual 1.334 1.372 -0.038 8.40e-03 1.42e+04 2.05e+01 bond pdb=" CG1 ILE A 117 " pdb=" CD1 ILE A 117 " ideal model delta sigma weight residual 1.513 1.411 0.102 3.90e-02 6.57e+02 6.85e+00 bond pdb=" CA ILE C 259 " pdb=" C ILE C 259 " ideal model delta sigma weight residual 1.525 1.580 -0.055 2.10e-02 2.27e+03 6.74e+00 bond pdb=" CG LEU A 926 " pdb=" CD2 LEU A 926 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.70e+00 bond pdb=" CG1 ILE A 955 " pdb=" CD1 ILE A 955 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.28e+00 ... (remaining 18605 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.79: 434 105.79 - 112.86: 10072 112.86 - 119.92: 6609 119.92 - 126.99: 7870 126.99 - 134.06: 209 Bond angle restraints: 25194 Sorted by residual: angle pdb=" N LEU A1423 " pdb=" CA LEU A1423 " pdb=" C LEU A1423 " ideal model delta sigma weight residual 113.18 104.17 9.01 1.33e+00 5.65e-01 4.59e+01 angle pdb=" CA LEU A1008 " pdb=" CB LEU A1008 " pdb=" CG LEU A1008 " ideal model delta sigma weight residual 116.30 133.07 -16.77 3.50e+00 8.16e-02 2.30e+01 angle pdb=" CA CYS A1157 " pdb=" CB CYS A1157 " pdb=" SG CYS A1157 " ideal model delta sigma weight residual 114.40 124.93 -10.53 2.30e+00 1.89e-01 2.10e+01 angle pdb=" C ASP A 706 " pdb=" N ASP A 707 " pdb=" CA ASP A 707 " ideal model delta sigma weight residual 121.54 130.13 -8.59 1.91e+00 2.74e-01 2.02e+01 angle pdb=" C ASN A 463 " pdb=" N LEU A 464 " pdb=" CA LEU A 464 " ideal model delta sigma weight residual 121.54 130.05 -8.51 1.91e+00 2.74e-01 1.99e+01 ... (remaining 25189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 10766 16.30 - 32.61: 481 32.61 - 48.91: 98 48.91 - 65.22: 6 65.22 - 81.52: 12 Dihedral angle restraints: 11363 sinusoidal: 4560 harmonic: 6803 Sorted by residual: dihedral pdb=" CB CYS A1157 " pdb=" SG CYS A1157 " pdb=" SG CYS A1160 " pdb=" CB CYS A1160 " ideal model delta sinusoidal sigma weight residual 93.00 163.27 -70.27 1 1.00e+01 1.00e-02 6.36e+01 dihedral pdb=" CA ASP A 706 " pdb=" C ASP A 706 " pdb=" N ASP A 707 " pdb=" CA ASP A 707 " ideal model delta harmonic sigma weight residual 180.00 -149.65 -30.35 0 5.00e+00 4.00e-02 3.68e+01 dihedral pdb=" CA LEU A 796 " pdb=" C LEU A 796 " pdb=" N LYS A 797 " pdb=" CA LYS A 797 " ideal model delta harmonic sigma weight residual -180.00 -150.35 -29.65 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 11360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2175 0.061 - 0.122: 641 0.122 - 0.183: 94 0.183 - 0.244: 7 0.244 - 0.305: 3 Chirality restraints: 2920 Sorted by residual: chirality pdb=" CB ILE D 310 " pdb=" CA ILE D 310 " pdb=" CG1 ILE D 310 " pdb=" CG2 ILE D 310 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CB VAL A1037 " pdb=" CA VAL A1037 " pdb=" CG1 VAL A1037 " pdb=" CG2 VAL A1037 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB ILE A 674 " pdb=" CA ILE A 674 " pdb=" CG1 ILE A 674 " pdb=" CG2 ILE A 674 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.48e+00 ... (remaining 2917 not shown) Planarity restraints: 3198 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 395 " -0.022 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE A 395 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 395 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE A 395 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 395 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 PHE A 395 " -0.016 2.00e-02 2.50e+03 pdb=" CZ PHE A 395 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 33 " -0.019 2.00e-02 2.50e+03 2.18e-02 1.19e+01 pdb=" CG TRP A 33 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A 33 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 33 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 33 " -0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 33 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 33 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 265 " -0.015 2.00e-02 2.50e+03 2.93e-02 8.59e+00 pdb=" C ASP A 265 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 265 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP A 266 " -0.017 2.00e-02 2.50e+03 ... (remaining 3195 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 5177 2.81 - 3.33: 16964 3.33 - 3.86: 30406 3.86 - 4.38: 35315 4.38 - 4.90: 60005 Nonbonded interactions: 147867 Sorted by model distance: nonbonded pdb=" OD1 ASN A1489 " pdb=" OG SER A2062 " model vdw 2.288 2.440 nonbonded pdb=" OH TYR A1480 " pdb=" O PRO A1604 " model vdw 2.288 2.440 nonbonded pdb=" OG SER A1108 " pdb=" OD1 ASP A1110 " model vdw 2.306 2.440 nonbonded pdb=" O PHE A1167 " pdb=" OG SER A1297 " model vdw 2.311 2.440 nonbonded pdb=" OE2 GLU A 301 " pdb=" OG SER A 804 " model vdw 2.313 2.440 ... (remaining 147862 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = (chain 'C' and resid 261 through 301) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.870 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: 4.830 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 52.200 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.100 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 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 : 0.008 0.102 18610 Z= 0.531 Angle : 1.004 16.768 25194 Z= 0.533 Chirality : 0.056 0.305 2920 Planarity : 0.008 0.067 3198 Dihedral : 10.413 81.521 6935 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.34 % Allowed : 3.46 % Favored : 96.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -3.52 (0.14), residues: 2280 helix: -2.13 (0.11), residues: 1168 sheet: -1.01 (0.45), residues: 121 loop : -2.67 (0.17), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP A 33 HIS 0.014 0.003 HIS A1927 PHE 0.058 0.003 PHE A 395 TYR 0.038 0.003 TYR A 868 ARG 0.009 0.001 ARG A1286 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 461 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 PHE cc_start: 0.8687 (t80) cc_final: 0.8443 (t80) REVERT: A 596 MET cc_start: 0.8581 (mmp) cc_final: 0.8348 (mmm) REVERT: A 647 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8716 (pp) REVERT: A 1065 LYS cc_start: 0.8670 (mtmt) cc_final: 0.8468 (mttt) REVERT: A 1394 LEU cc_start: 0.8174 (mm) cc_final: 0.7806 (tt) REVERT: A 1451 TRP cc_start: 0.7261 (m-10) cc_final: 0.6934 (m-90) REVERT: A 1465 GLU cc_start: 0.8450 (mt-10) cc_final: 0.7892 (pt0) REVERT: A 1506 LEU cc_start: 0.7887 (mt) cc_final: 0.7657 (mp) REVERT: A 1653 TYR cc_start: 0.8276 (t80) cc_final: 0.7940 (t80) REVERT: A 1785 MET cc_start: 0.8917 (ttp) cc_final: 0.8256 (ttp) REVERT: A 1807 MET cc_start: 0.8247 (mtt) cc_final: 0.7985 (mtp) REVERT: A 1856 ASP cc_start: 0.8021 (t0) cc_final: 0.7669 (t0) REVERT: A 1884 ILE cc_start: 0.8998 (mt) cc_final: 0.8612 (mp) REVERT: A 1933 PHE cc_start: 0.9154 (m-80) cc_final: 0.8563 (m-80) REVERT: A 2170 MET cc_start: 0.6236 (mtt) cc_final: 0.5942 (mtp) REVERT: A 2199 TYR cc_start: 0.5404 (m-80) cc_final: 0.5110 (m-80) REVERT: C 273 VAL cc_start: 0.9082 (t) cc_final: 0.8872 (p) REVERT: E 282 MET cc_start: 0.8658 (mmt) cc_final: 0.7741 (mmt) REVERT: E 283 MET cc_start: 0.8647 (mmm) cc_final: 0.8090 (mmm) REVERT: E 300 ARG cc_start: 0.7498 (mmt-90) cc_final: 0.7002 (mpt90) REVERT: E 342 ILE cc_start: 0.7715 (mm) cc_final: 0.7468 (mm) REVERT: E 355 GLU cc_start: 0.7726 (mp0) cc_final: 0.7467 (mp0) REVERT: E 394 ARG cc_start: 0.8048 (ptp90) cc_final: 0.7784 (mtm110) outliers start: 7 outliers final: 2 residues processed: 466 average time/residue: 0.3907 time to fit residues: 255.8739 Evaluate side-chains 280 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 277 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 20.0000 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 117 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 180 optimal weight: 8.9990 chunk 69 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 134 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 GLN A 183 GLN ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 314 ASN ** A 328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN A 487 ASN A 496 ASN A 565 GLN ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN A 662 ASN A 789 ASN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 906 HIS A 974 ASN A1088 HIS ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1447 ASN A1457 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 HIS A1794 HIS A1820 GLN ** A1823 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1831 GLN A1879 HIS A2048 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN B 268 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18610 Z= 0.266 Angle : 0.636 9.641 25194 Z= 0.323 Chirality : 0.043 0.198 2920 Planarity : 0.005 0.054 3198 Dihedral : 5.560 31.878 2518 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.34 % Allowed : 9.07 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: -1.58 (0.17), residues: 2280 helix: -0.28 (0.14), residues: 1196 sheet: -0.42 (0.45), residues: 124 loop : -2.11 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 33 HIS 0.006 0.001 HIS A1927 PHE 0.023 0.002 PHE A 395 TYR 0.022 0.002 TYR A1400 ARG 0.008 0.001 ARG A2024 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 302 time to evaluate : 2.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7424 (tpp-160) cc_final: 0.7221 (mmm160) REVERT: A 236 MET cc_start: 0.8977 (ttp) cc_final: 0.8691 (ttp) REVERT: A 313 PHE cc_start: 0.8664 (t80) cc_final: 0.8445 (t80) REVERT: A 647 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8741 (pp) REVERT: A 909 VAL cc_start: 0.9388 (m) cc_final: 0.9183 (t) REVERT: A 961 THR cc_start: 0.9217 (OUTLIER) cc_final: 0.8934 (p) REVERT: A 1052 GLN cc_start: 0.8707 (tt0) cc_final: 0.8413 (mt0) REVERT: A 1254 LEU cc_start: 0.9059 (tp) cc_final: 0.8837 (tp) REVERT: A 1413 MET cc_start: 0.7950 (mtm) cc_final: 0.7178 (mmm) REVERT: A 1465 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8247 (mt-10) REVERT: A 1506 LEU cc_start: 0.7902 (mt) cc_final: 0.7673 (mp) REVERT: A 1738 GLN cc_start: 0.7933 (mp10) cc_final: 0.7701 (pm20) REVERT: A 1785 MET cc_start: 0.8923 (ttp) cc_final: 0.8518 (ttp) REVERT: A 1798 TYR cc_start: 0.7775 (m-80) cc_final: 0.7443 (m-80) REVERT: A 1807 MET cc_start: 0.8248 (mtt) cc_final: 0.7944 (mtp) REVERT: A 1833 GLU cc_start: 0.8339 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 1873 ARG cc_start: 0.6375 (mmm-85) cc_final: 0.5914 (mmm-85) REVERT: A 1920 TYR cc_start: 0.8036 (t80) cc_final: 0.7727 (t80) REVERT: A 1933 PHE cc_start: 0.9079 (m-80) cc_final: 0.8560 (m-80) REVERT: A 1953 MET cc_start: 0.7749 (mtm) cc_final: 0.6989 (mtm) REVERT: A 1976 MET cc_start: 0.8490 (tmm) cc_final: 0.8243 (mtp) REVERT: A 2021 LEU cc_start: 0.8222 (mm) cc_final: 0.7860 (mm) REVERT: D 268 GLN cc_start: 0.7862 (mt0) cc_final: 0.7573 (mt0) REVERT: D 283 MET cc_start: 0.8145 (mmt) cc_final: 0.7941 (mmm) REVERT: C 266 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8509 (tp) REVERT: C 273 VAL cc_start: 0.8867 (t) cc_final: 0.8377 (p) REVERT: C 277 GLU cc_start: 0.8903 (mp0) cc_final: 0.8109 (mp0) REVERT: B 262 MET cc_start: 0.6887 (tpp) cc_final: 0.6644 (tpp) REVERT: E 282 MET cc_start: 0.8607 (mmt) cc_final: 0.7882 (mmm) REVERT: E 342 ILE cc_start: 0.7811 (mm) cc_final: 0.7407 (mm) REVERT: E 355 GLU cc_start: 0.7863 (mp0) cc_final: 0.7447 (mp0) REVERT: E 357 ASP cc_start: 0.8443 (m-30) cc_final: 0.8226 (m-30) REVERT: E 394 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7712 (mtm110) outliers start: 48 outliers final: 24 residues processed: 335 average time/residue: 0.3234 time to fit residues: 163.3789 Evaluate side-chains 293 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 266 time to evaluate : 2.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1740 VAL Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 chunk 173 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 209 optimal weight: 4.9990 chunk 226 optimal weight: 1.9990 chunk 186 optimal weight: 7.9990 chunk 207 optimal weight: 0.0670 chunk 71 optimal weight: 2.9990 chunk 167 optimal weight: 10.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1515 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1660 ASN A1759 HIS A1808 ASN A1813 HIS ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 18610 Z= 0.333 Angle : 0.644 11.743 25194 Z= 0.324 Chirality : 0.043 0.174 2920 Planarity : 0.005 0.047 3198 Dihedral : 5.338 37.660 2518 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 3.17 % Allowed : 10.63 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: -0.80 (0.18), residues: 2280 helix: 0.39 (0.15), residues: 1206 sheet: -0.15 (0.45), residues: 126 loop : -1.80 (0.20), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 33 HIS 0.006 0.001 HIS A1759 PHE 0.021 0.002 PHE A 395 TYR 0.019 0.002 TYR A 868 ARG 0.007 0.001 ARG A1873 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 267 time to evaluate : 2.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7426 (tpp-160) cc_final: 0.7178 (mmm160) REVERT: A 236 MET cc_start: 0.8995 (ttp) cc_final: 0.8766 (ttp) REVERT: A 647 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 1052 GLN cc_start: 0.8662 (tt0) cc_final: 0.8431 (mt0) REVERT: A 1413 MET cc_start: 0.7915 (mtm) cc_final: 0.7169 (mmm) REVERT: A 1450 ASN cc_start: 0.6813 (t0) cc_final: 0.6527 (t0) REVERT: A 1465 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8299 (mt-10) REVERT: A 1506 LEU cc_start: 0.7956 (mt) cc_final: 0.7724 (mp) REVERT: A 1785 MET cc_start: 0.8908 (ttp) cc_final: 0.8519 (ttp) REVERT: A 1807 MET cc_start: 0.8279 (mtt) cc_final: 0.8005 (mtp) REVERT: A 1833 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8196 (mt-10) REVERT: A 1853 GLU cc_start: 0.8298 (mt-10) cc_final: 0.8051 (mm-30) REVERT: A 1933 PHE cc_start: 0.9067 (m-80) cc_final: 0.8517 (m-80) REVERT: A 1953 MET cc_start: 0.7341 (mtm) cc_final: 0.6949 (mtm) REVERT: A 1954 GLU cc_start: 0.8588 (tt0) cc_final: 0.8318 (tt0) REVERT: D 286 LEU cc_start: 0.8546 (tt) cc_final: 0.8045 (tt) REVERT: D 297 SER cc_start: 0.8128 (p) cc_final: 0.7750 (t) REVERT: E 282 MET cc_start: 0.8603 (mmt) cc_final: 0.7771 (mmm) REVERT: E 283 MET cc_start: 0.8805 (mmm) cc_final: 0.7810 (mmm) REVERT: E 342 ILE cc_start: 0.7699 (mm) cc_final: 0.7451 (mm) REVERT: E 355 GLU cc_start: 0.7860 (mp0) cc_final: 0.7431 (mp0) REVERT: E 357 ASP cc_start: 0.8511 (m-30) cc_final: 0.8281 (m-30) REVERT: E 394 ARG cc_start: 0.8146 (ptp90) cc_final: 0.7785 (mtm110) outliers start: 65 outliers final: 41 residues processed: 314 average time/residue: 0.3281 time to fit residues: 157.2671 Evaluate side-chains 295 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 253 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 798 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 954 ASN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 1.9990 chunk 157 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 23 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 209 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 199 optimal weight: 20.0000 chunk 59 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN A1034 HIS ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18610 Z= 0.248 Angle : 0.588 10.514 25194 Z= 0.295 Chirality : 0.042 0.163 2920 Planarity : 0.004 0.040 3198 Dihedral : 4.998 38.417 2518 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.32 % Allowed : 11.17 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: -0.31 (0.18), residues: 2280 helix: 0.82 (0.15), residues: 1210 sheet: 0.13 (0.46), residues: 122 loop : -1.62 (0.21), residues: 948 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1754 HIS 0.006 0.001 HIS A1927 PHE 0.015 0.001 PHE A 395 TYR 0.021 0.001 TYR A1920 ARG 0.004 0.000 ARG A 997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 271 time to evaluate : 2.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7437 (tpp-160) cc_final: 0.7176 (mmm160) REVERT: A 236 MET cc_start: 0.8971 (ttp) cc_final: 0.8749 (ttp) REVERT: A 383 MET cc_start: 0.8635 (ttm) cc_final: 0.8334 (ttm) REVERT: A 520 LYS cc_start: 0.8603 (pptt) cc_final: 0.8361 (pptt) REVERT: A 587 GLN cc_start: 0.7472 (mt0) cc_final: 0.7027 (mm-40) REVERT: A 647 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8812 (pp) REVERT: A 961 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8762 (p) REVERT: A 1052 GLN cc_start: 0.8638 (tt0) cc_final: 0.8392 (mt0) REVERT: A 1413 MET cc_start: 0.7946 (mtm) cc_final: 0.7114 (mmm) REVERT: A 1450 ASN cc_start: 0.6956 (t0) cc_final: 0.6689 (t0) REVERT: A 1465 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 1506 LEU cc_start: 0.7869 (mt) cc_final: 0.7565 (mp) REVERT: A 1785 MET cc_start: 0.8848 (ttp) cc_final: 0.8644 (ttp) REVERT: A 1807 MET cc_start: 0.8278 (mtt) cc_final: 0.7980 (mtp) REVERT: A 1933 PHE cc_start: 0.9051 (m-80) cc_final: 0.8524 (m-80) REVERT: A 1953 MET cc_start: 0.7398 (mtm) cc_final: 0.6852 (mtm) REVERT: A 1954 GLU cc_start: 0.8600 (tt0) cc_final: 0.8347 (tt0) REVERT: A 1961 MET cc_start: 0.6096 (ttp) cc_final: 0.5542 (ttp) REVERT: A 2188 MET cc_start: 0.8900 (mmt) cc_final: 0.8312 (tpp) REVERT: D 286 LEU cc_start: 0.8579 (tt) cc_final: 0.8070 (tt) REVERT: D 297 SER cc_start: 0.8068 (p) cc_final: 0.7803 (t) REVERT: E 276 MET cc_start: 0.4450 (mmm) cc_final: 0.4179 (mmm) REVERT: E 282 MET cc_start: 0.8609 (mmt) cc_final: 0.7884 (mmm) REVERT: E 283 MET cc_start: 0.8760 (mmm) cc_final: 0.7765 (mmm) REVERT: E 355 GLU cc_start: 0.7833 (mp0) cc_final: 0.7452 (mp0) REVERT: E 357 ASP cc_start: 0.8452 (m-30) cc_final: 0.8208 (m-30) REVERT: E 379 LYS cc_start: 0.9096 (pttt) cc_final: 0.8835 (ptpp) REVERT: E 394 ARG cc_start: 0.8095 (ptp90) cc_final: 0.7739 (mtm110) outliers start: 68 outliers final: 44 residues processed: 320 average time/residue: 0.3198 time to fit residues: 153.9597 Evaluate side-chains 296 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 250 time to evaluate : 2.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 764 ASP Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1324 ILE Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1378 MET Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1813 HIS Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 91 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 153 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 ASN ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1851 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18610 Z= 0.304 Angle : 0.615 9.781 25194 Z= 0.308 Chirality : 0.043 0.285 2920 Planarity : 0.004 0.042 3198 Dihedral : 4.995 40.331 2518 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.37 % Allowed : 12.44 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: -0.14 (0.18), residues: 2280 helix: 0.93 (0.15), residues: 1211 sheet: 0.25 (0.47), residues: 122 loop : -1.52 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 169 HIS 0.004 0.001 HIS A 178 PHE 0.018 0.001 PHE A1814 TYR 0.023 0.002 TYR A1920 ARG 0.005 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 251 time to evaluate : 2.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8986 (ttp) cc_final: 0.8779 (ttp) REVERT: A 266 ASP cc_start: 0.7801 (m-30) cc_final: 0.7527 (m-30) REVERT: A 587 GLN cc_start: 0.7470 (mt0) cc_final: 0.6985 (mm-40) REVERT: A 647 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8802 (pp) REVERT: A 961 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8809 (p) REVERT: A 1052 GLN cc_start: 0.8667 (tt0) cc_final: 0.8320 (mt0) REVERT: A 1265 ASN cc_start: 0.8246 (OUTLIER) cc_final: 0.7712 (p0) REVERT: A 1413 MET cc_start: 0.8023 (mtm) cc_final: 0.7185 (mmm) REVERT: A 1450 ASN cc_start: 0.7018 (t0) cc_final: 0.6710 (t0) REVERT: A 1465 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8304 (mt-10) REVERT: A 1506 LEU cc_start: 0.7900 (mt) cc_final: 0.7636 (mp) REVERT: A 1807 MET cc_start: 0.8329 (mtt) cc_final: 0.8093 (mtp) REVERT: A 1881 ASP cc_start: 0.8387 (t0) cc_final: 0.8164 (t0) REVERT: A 1933 PHE cc_start: 0.9085 (m-80) cc_final: 0.8580 (m-80) REVERT: A 1953 MET cc_start: 0.7419 (mtm) cc_final: 0.6955 (mtm) REVERT: A 1954 GLU cc_start: 0.8520 (tt0) cc_final: 0.8265 (tt0) REVERT: A 2170 MET cc_start: 0.5748 (mtp) cc_final: 0.5524 (mtp) REVERT: D 286 LEU cc_start: 0.8606 (tt) cc_final: 0.8107 (tt) REVERT: D 297 SER cc_start: 0.8088 (p) cc_final: 0.7831 (t) REVERT: C 262 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.7365 (mpp) REVERT: E 283 MET cc_start: 0.8764 (mmm) cc_final: 0.7747 (mmm) REVERT: E 355 GLU cc_start: 0.7824 (mp0) cc_final: 0.7471 (mp0) REVERT: E 357 ASP cc_start: 0.8479 (m-30) cc_final: 0.8244 (m-30) REVERT: E 379 LYS cc_start: 0.9122 (pttt) cc_final: 0.8907 (ptpp) REVERT: E 394 ARG cc_start: 0.8094 (ptp90) cc_final: 0.7725 (mtm110) outliers start: 69 outliers final: 47 residues processed: 302 average time/residue: 0.3107 time to fit residues: 143.0495 Evaluate side-chains 293 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 242 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1378 MET Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1787 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1813 HIS Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 269 LEU Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 279 ASN Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 130 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 chunk 222 optimal weight: 3.9990 chunk 184 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 18 optimal weight: 6.9990 chunk 73 optimal weight: 0.9980 chunk 116 optimal weight: 10.0000 overall best weight: 2.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1899 ASN ** A1906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 18610 Z= 0.257 Angle : 0.603 13.193 25194 Z= 0.299 Chirality : 0.042 0.327 2920 Planarity : 0.004 0.077 3198 Dihedral : 4.880 41.910 2518 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.37 % Allowed : 13.32 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: 0.02 (0.18), residues: 2280 helix: 1.09 (0.15), residues: 1215 sheet: 0.35 (0.47), residues: 122 loop : -1.48 (0.21), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 169 HIS 0.004 0.001 HIS A 27 PHE 0.014 0.001 PHE A1705 TYR 0.024 0.001 TYR A1920 ARG 0.007 0.000 ARG A1873 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 254 time to evaluate : 2.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.8973 (ttp) cc_final: 0.8766 (ttp) REVERT: A 266 ASP cc_start: 0.7791 (m-30) cc_final: 0.7486 (m-30) REVERT: A 587 GLN cc_start: 0.7367 (mt0) cc_final: 0.6891 (mm-40) REVERT: A 647 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8769 (pp) REVERT: A 961 THR cc_start: 0.9250 (OUTLIER) cc_final: 0.8897 (p) REVERT: A 1052 GLN cc_start: 0.8662 (tt0) cc_final: 0.8309 (mt0) REVERT: A 1265 ASN cc_start: 0.8208 (OUTLIER) cc_final: 0.7901 (p0) REVERT: A 1413 MET cc_start: 0.8137 (mtm) cc_final: 0.7255 (mmm) REVERT: A 1450 ASN cc_start: 0.7076 (t0) cc_final: 0.6734 (t0) REVERT: A 1465 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8225 (mt-10) REVERT: A 1506 LEU cc_start: 0.8043 (mt) cc_final: 0.7792 (mp) REVERT: A 1802 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8927 (tp) REVERT: A 1807 MET cc_start: 0.8316 (mtt) cc_final: 0.8082 (mtp) REVERT: A 1881 ASP cc_start: 0.8351 (t0) cc_final: 0.8138 (t0) REVERT: A 1933 PHE cc_start: 0.9070 (m-80) cc_final: 0.8595 (m-80) REVERT: A 1953 MET cc_start: 0.7408 (mtm) cc_final: 0.6917 (mtm) REVERT: A 1954 GLU cc_start: 0.8503 (tt0) cc_final: 0.8250 (tt0) REVERT: D 286 LEU cc_start: 0.8628 (tt) cc_final: 0.8368 (tt) REVERT: D 297 SER cc_start: 0.8090 (p) cc_final: 0.7840 (t) REVERT: C 262 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7421 (mpp) REVERT: E 282 MET cc_start: 0.8673 (mmt) cc_final: 0.7751 (mmp) REVERT: E 355 GLU cc_start: 0.7828 (mp0) cc_final: 0.7438 (mp0) REVERT: E 357 ASP cc_start: 0.8434 (m-30) cc_final: 0.8223 (m-30) REVERT: E 394 ARG cc_start: 0.8052 (ptp90) cc_final: 0.7739 (mtm110) outliers start: 69 outliers final: 46 residues processed: 307 average time/residue: 0.3228 time to fit residues: 149.8349 Evaluate side-chains 295 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 244 time to evaluate : 2.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 839 SER Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1740 VAL Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1813 HIS Chi-restraints excluded: chain A residue 1873 ARG Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 0.0050 chunk 25 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 125 optimal weight: 8.9990 chunk 187 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 221 optimal weight: 9.9990 chunk 138 optimal weight: 3.9990 chunk 135 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 581 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18610 Z= 0.160 Angle : 0.559 14.147 25194 Z= 0.273 Chirality : 0.040 0.373 2920 Planarity : 0.004 0.039 3198 Dihedral : 4.537 39.434 2518 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 2.73 % Allowed : 14.00 % Favored : 83.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: 0.36 (0.18), residues: 2280 helix: 1.41 (0.15), residues: 1216 sheet: 0.43 (0.46), residues: 122 loop : -1.40 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1754 HIS 0.005 0.001 HIS A 27 PHE 0.011 0.001 PHE A 781 TYR 0.022 0.001 TYR A1920 ARG 0.007 0.000 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 269 time to evaluate : 2.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 GLN cc_start: 0.7308 (mt0) cc_final: 0.6862 (mm-40) REVERT: A 647 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8857 (pp) REVERT: A 961 THR cc_start: 0.9194 (OUTLIER) cc_final: 0.8891 (p) REVERT: A 1052 GLN cc_start: 0.8628 (tt0) cc_final: 0.8265 (mt0) REVERT: A 1413 MET cc_start: 0.8026 (mtm) cc_final: 0.7212 (mmm) REVERT: A 1450 ASN cc_start: 0.7054 (t0) cc_final: 0.6718 (t0) REVERT: A 1506 LEU cc_start: 0.7942 (mt) cc_final: 0.7689 (mp) REVERT: A 1791 HIS cc_start: 0.8894 (m-70) cc_final: 0.8605 (m-70) REVERT: A 1807 MET cc_start: 0.8422 (mtt) cc_final: 0.8165 (mtp) REVERT: A 1922 MET cc_start: 0.7412 (mmt) cc_final: 0.7033 (mpp) REVERT: A 1933 PHE cc_start: 0.9041 (m-80) cc_final: 0.8558 (m-80) REVERT: A 1953 MET cc_start: 0.7425 (mtm) cc_final: 0.6946 (mtm) REVERT: A 1954 GLU cc_start: 0.8475 (tt0) cc_final: 0.8237 (tt0) REVERT: A 1975 ARG cc_start: 0.7922 (ptm160) cc_final: 0.6950 (tpt90) REVERT: A 1976 MET cc_start: 0.8718 (tmm) cc_final: 0.8183 (mtp) REVERT: A 2021 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 2188 MET cc_start: 0.8908 (mmt) cc_final: 0.8335 (tpp) REVERT: D 286 LEU cc_start: 0.8683 (tt) cc_final: 0.8331 (tt) REVERT: E 282 MET cc_start: 0.8500 (mmt) cc_final: 0.7591 (mmp) REVERT: E 355 GLU cc_start: 0.7791 (mp0) cc_final: 0.7402 (mp0) REVERT: E 357 ASP cc_start: 0.8383 (m-30) cc_final: 0.8134 (m-30) REVERT: E 379 LYS cc_start: 0.9117 (pttt) cc_final: 0.8876 (pttm) REVERT: E 394 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7749 (mtm110) outliers start: 56 outliers final: 33 residues processed: 311 average time/residue: 0.3298 time to fit residues: 154.0817 Evaluate side-chains 281 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 245 time to evaluate : 2.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 120 HIS Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1188 MET Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1740 VAL Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1873 ARG Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 381 ASP Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 132 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 174 optimal weight: 0.5980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 HIS ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 487 ASN A 581 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 HIS ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN C 279 ASN E 333 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 18610 Z= 0.180 Angle : 0.584 15.368 25194 Z= 0.284 Chirality : 0.041 0.385 2920 Planarity : 0.004 0.040 3198 Dihedral : 4.461 38.236 2518 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.68 % Allowed : 14.78 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: 0.45 (0.18), residues: 2280 helix: 1.49 (0.15), residues: 1216 sheet: 0.52 (0.46), residues: 122 loop : -1.38 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 169 HIS 0.012 0.001 HIS A 120 PHE 0.016 0.001 PHE A 313 TYR 0.023 0.001 TYR A1920 ARG 0.006 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 255 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 587 GLN cc_start: 0.7327 (mt0) cc_final: 0.6831 (mm-40) REVERT: A 647 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8913 (pp) REVERT: A 961 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8917 (p) REVERT: A 1052 GLN cc_start: 0.8588 (tt0) cc_final: 0.8304 (mt0) REVERT: A 1220 ARG cc_start: 0.7797 (tpp-160) cc_final: 0.7476 (tpp-160) REVERT: A 1413 MET cc_start: 0.8018 (mtm) cc_final: 0.7205 (mmm) REVERT: A 1450 ASN cc_start: 0.7026 (t0) cc_final: 0.6693 (t0) REVERT: A 1465 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7845 (pt0) REVERT: A 1506 LEU cc_start: 0.7979 (mt) cc_final: 0.7709 (mp) REVERT: A 1654 MET cc_start: 0.7407 (mmt) cc_final: 0.7117 (mmt) REVERT: A 1791 HIS cc_start: 0.8877 (m-70) cc_final: 0.8560 (m-70) REVERT: A 1802 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8903 (tp) REVERT: A 1807 MET cc_start: 0.8435 (mtt) cc_final: 0.8183 (mtp) REVERT: A 1933 PHE cc_start: 0.9036 (m-80) cc_final: 0.8579 (m-80) REVERT: A 1953 MET cc_start: 0.7435 (mtm) cc_final: 0.6973 (mtm) REVERT: A 1954 GLU cc_start: 0.8475 (tt0) cc_final: 0.8240 (tt0) REVERT: A 2188 MET cc_start: 0.8899 (mmt) cc_final: 0.8533 (mmt) REVERT: D 286 LEU cc_start: 0.8724 (tt) cc_final: 0.8377 (tt) REVERT: E 282 MET cc_start: 0.8485 (mmt) cc_final: 0.7594 (mmp) REVERT: E 355 GLU cc_start: 0.7788 (mp0) cc_final: 0.7453 (mp0) REVERT: E 357 ASP cc_start: 0.8399 (m-30) cc_final: 0.8158 (m-30) REVERT: E 394 ARG cc_start: 0.8090 (ptp90) cc_final: 0.7745 (mtm110) outliers start: 55 outliers final: 39 residues processed: 296 average time/residue: 0.3223 time to fit residues: 143.8359 Evaluate side-chains 286 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 244 time to evaluate : 2.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1188 MET Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1740 VAL Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1802 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1873 ARG Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 3.9990 chunk 212 optimal weight: 0.8980 chunk 193 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 162 optimal weight: 10.0000 chunk 63 optimal weight: 3.9990 chunk 186 optimal weight: 7.9990 chunk 195 optimal weight: 20.0000 chunk 205 optimal weight: 6.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2036 GLN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 18610 Z= 0.388 Angle : 0.690 14.782 25194 Z= 0.341 Chirality : 0.045 0.383 2920 Planarity : 0.004 0.043 3198 Dihedral : 4.910 42.696 2518 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.68 % Allowed : 15.02 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: 0.22 (0.18), residues: 2280 helix: 1.23 (0.15), residues: 1208 sheet: 0.67 (0.47), residues: 120 loop : -1.37 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 169 HIS 0.012 0.001 HIS A1759 PHE 0.021 0.002 PHE A 313 TYR 0.031 0.002 TYR A1920 ARG 0.008 0.001 ARG C 263 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 237 time to evaluate : 2.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.9044 (ttp) cc_final: 0.8808 (ttp) REVERT: A 581 GLN cc_start: 0.7325 (OUTLIER) cc_final: 0.6883 (tt0) REVERT: A 587 GLN cc_start: 0.7535 (mt0) cc_final: 0.6989 (mm-40) REVERT: A 647 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.8780 (pp) REVERT: A 961 THR cc_start: 0.9249 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 1052 GLN cc_start: 0.8696 (tt0) cc_final: 0.8344 (mt0) REVERT: A 1265 ASN cc_start: 0.8339 (OUTLIER) cc_final: 0.8031 (p0) REVERT: A 1450 ASN cc_start: 0.7290 (t0) cc_final: 0.6842 (t0) REVERT: A 1465 GLU cc_start: 0.8254 (mt-10) cc_final: 0.7952 (pt0) REVERT: A 1506 LEU cc_start: 0.8089 (mt) cc_final: 0.7800 (mp) REVERT: A 1807 MET cc_start: 0.8393 (mtt) cc_final: 0.8190 (mtp) REVERT: A 1920 TYR cc_start: 0.8104 (t80) cc_final: 0.7538 (t80) REVERT: A 1933 PHE cc_start: 0.9061 (m-80) cc_final: 0.8575 (m-80) REVERT: A 1953 MET cc_start: 0.7312 (mtm) cc_final: 0.6805 (mtm) REVERT: A 1975 ARG cc_start: 0.8011 (ptm160) cc_final: 0.6942 (tpt90) REVERT: A 1976 MET cc_start: 0.8670 (tmm) cc_final: 0.8129 (mtp) REVERT: D 286 LEU cc_start: 0.8654 (tt) cc_final: 0.8393 (tt) REVERT: D 297 SER cc_start: 0.8144 (p) cc_final: 0.7930 (t) REVERT: E 282 MET cc_start: 0.8720 (mmt) cc_final: 0.7808 (mmp) REVERT: E 355 GLU cc_start: 0.7801 (mp0) cc_final: 0.7427 (mp0) REVERT: E 357 ASP cc_start: 0.8474 (m-30) cc_final: 0.8252 (m-30) REVERT: E 394 ARG cc_start: 0.8050 (ptp90) cc_final: 0.7711 (mtm110) outliers start: 55 outliers final: 42 residues processed: 278 average time/residue: 0.3233 time to fit residues: 135.0376 Evaluate side-chains 279 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 233 time to evaluate : 2.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1103 ASN Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1265 ASN Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1740 VAL Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1813 HIS Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1873 ARG Chi-restraints excluded: chain A residue 1943 LEU Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 5.9990 chunk 218 optimal weight: 0.0370 chunk 133 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 229 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 4.9990 overall best weight: 2.3864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1171 HIS ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 18610 Z= 0.279 Angle : 0.653 15.720 25194 Z= 0.318 Chirality : 0.043 0.401 2920 Planarity : 0.004 0.041 3198 Dihedral : 4.828 40.913 2518 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.20 % Allowed : 15.71 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: 0.31 (0.18), residues: 2280 helix: 1.31 (0.15), residues: 1200 sheet: 0.75 (0.48), residues: 120 loop : -1.33 (0.20), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 169 HIS 0.021 0.001 HIS A1906 PHE 0.023 0.001 PHE A 313 TYR 0.026 0.002 TYR A1920 ARG 0.014 0.000 ARG C 263 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4560 Ramachandran restraints generated. 2280 Oldfield, 0 Emsley, 2280 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 238 time to evaluate : 2.216 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 236 MET cc_start: 0.9019 (ttp) cc_final: 0.8783 (ttp) REVERT: A 581 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: A 587 GLN cc_start: 0.7496 (mt0) cc_final: 0.6963 (mm-40) REVERT: A 647 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8808 (pp) REVERT: A 961 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8965 (p) REVERT: A 1052 GLN cc_start: 0.8649 (tt0) cc_final: 0.8300 (mt0) REVERT: A 1220 ARG cc_start: 0.7621 (tpp-160) cc_final: 0.7185 (tpp-160) REVERT: A 1450 ASN cc_start: 0.7161 (t0) cc_final: 0.6735 (t0) REVERT: A 1465 GLU cc_start: 0.8286 (mt-10) cc_final: 0.7998 (pt0) REVERT: A 1506 LEU cc_start: 0.8037 (mt) cc_final: 0.7753 (mp) REVERT: A 1917 LYS cc_start: 0.8154 (ttpp) cc_final: 0.7771 (ttmt) REVERT: A 1933 PHE cc_start: 0.9064 (m-80) cc_final: 0.8564 (m-80) REVERT: A 1953 MET cc_start: 0.7332 (mtm) cc_final: 0.6874 (mtm) REVERT: A 1975 ARG cc_start: 0.8025 (ptm160) cc_final: 0.6943 (tpt90) REVERT: A 1976 MET cc_start: 0.8668 (tmm) cc_final: 0.8136 (mtp) REVERT: A 2188 MET cc_start: 0.8762 (mmt) cc_final: 0.8202 (tpp) REVERT: D 286 LEU cc_start: 0.8663 (tt) cc_final: 0.8397 (tt) REVERT: D 297 SER cc_start: 0.8083 (p) cc_final: 0.7867 (t) REVERT: B 282 MET cc_start: 0.6974 (mmp) cc_final: 0.6726 (mmp) REVERT: E 282 MET cc_start: 0.8720 (mmt) cc_final: 0.7796 (mmp) REVERT: E 355 GLU cc_start: 0.7786 (mp0) cc_final: 0.7407 (mp0) REVERT: E 357 ASP cc_start: 0.8436 (m-30) cc_final: 0.8225 (m-30) REVERT: E 394 ARG cc_start: 0.8058 (ptp90) cc_final: 0.7728 (mtm110) outliers start: 45 outliers final: 40 residues processed: 273 average time/residue: 0.3313 time to fit residues: 136.7030 Evaluate side-chains 280 residues out of total 2050 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 237 time to evaluate : 2.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 325 LEU Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 581 GLN Chi-restraints excluded: chain A residue 590 ILE Chi-restraints excluded: chain A residue 647 LEU Chi-restraints excluded: chain A residue 740 SER Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 920 ASN Chi-restraints excluded: chain A residue 928 THR Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1112 CYS Chi-restraints excluded: chain A residue 1188 MET Chi-restraints excluded: chain A residue 1331 THR Chi-restraints excluded: chain A residue 1339 ILE Chi-restraints excluded: chain A residue 1463 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1740 VAL Chi-restraints excluded: chain A residue 1749 THR Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1813 HIS Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 1873 ARG Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2121 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain D residue 262 MET Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 335 VAL Chi-restraints excluded: chain E residue 388 GLU Chi-restraints excluded: chain E residue 389 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 187 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN ** A 827 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 859 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.116084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081252 restraints weight = 46935.932| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 3.17 r_work: 0.2944 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 18610 Z= 0.246 Angle : 0.635 15.469 25194 Z= 0.308 Chirality : 0.042 0.411 2920 Planarity : 0.004 0.040 3198 Dihedral : 4.728 39.586 2518 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 2.34 % Allowed : 15.76 % Favored : 81.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.00 % Cis-general : 0.00 % 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: 0.42 (0.18), residues: 2280 helix: 1.43 (0.15), residues: 1192 sheet: 0.92 (0.48), residues: 116 loop : -1.32 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 169 HIS 0.018 0.001 HIS A1906 PHE 0.021 0.001 PHE A 313 TYR 0.019 0.001 TYR A1920 ARG 0.013 0.000 ARG C 263 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4095.58 seconds wall clock time: 75 minutes 18.09 seconds (4518.09 seconds total)