Starting phenix.real_space_refine on Mon Jun 16 08:47:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7you_33987/06_2025/7you_33987.cif Found real_map, /net/cci-nas-00/data/ceres_data/7you_33987/06_2025/7you_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/cci-nas-00/data/ceres_data/7you_33987/06_2025/7you_33987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7you_33987/06_2025/7you_33987.map" model { file = "/net/cci-nas-00/data/ceres_data/7you_33987/06_2025/7you_33987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7you_33987/06_2025/7you_33987.cif" } 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. Time to flip 49 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 10.00, per 1000 atoms: 0.55 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.41 Conformation dependent library (CDL) restraints added in 2.2 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: 2.19 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: 7.40 Time building geometry restraints manager: 5.12 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: 0.00 - 3.35: 24829 3.35 - 6.71: 329 6.71 - 10.06: 30 10.06 - 13.41: 4 13.41 - 16.77: 2 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 3.040 nonbonded pdb=" OH TYR A1480 " pdb=" O PRO A1604 " model vdw 2.288 3.040 nonbonded pdb=" OG SER A1108 " pdb=" OD1 ASP A1110 " model vdw 2.306 3.040 nonbonded pdb=" O PHE A1167 " pdb=" OG SER A1297 " model vdw 2.311 3.040 nonbonded pdb=" OE2 GLU A 301 " pdb=" OG SER A 804 " model vdw 2.313 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 1.430 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: 0.030 Extract box with map and model: 0.990 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 41.560 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.640 ------------------------------------------------------------------------------- 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 18612 Z= 0.347 Angle : 1.006 16.768 25198 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 Details of bonding type rmsd hydrogen bonds : bond 0.15266 ( 887) hydrogen bonds : angle 6.42826 ( 2545) SS BOND : bond 0.01258 ( 2) SS BOND : angle 4.07460 ( 4) covalent geometry : bond 0.00822 (18610) covalent geometry : angle 1.00436 (25194) *********************** 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 to be fit. rotamer outliers: 7 poor density : 461 time to evaluate : 1.956 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: 0.4014 time to fit residues: 267.5938 Evaluate side-chains 280 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 2.626 ------------------------------------------------------------------------------- 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: 5.9990 chunk 96 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 180 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 109 optimal weight: 0.9980 chunk 134 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 314 ASN A 347 GLN A 496 ASN A 565 GLN A 581 GLN A 652 GLN A 662 ASN ** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN A 906 HIS A 974 ASN A1088 HIS ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 ASN A1315 GLN A1447 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** ** A1707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1759 HIS A1794 HIS A1820 GLN A1879 HIS A2048 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.118297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.082153 restraints weight = 62756.319| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 3.84 r_work: 0.2949 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 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 = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18612 Z= 0.160 Angle : 0.640 9.402 25198 Z= 0.326 Chirality : 0.043 0.226 2920 Planarity : 0.005 0.054 3198 Dihedral : 5.588 30.295 2518 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.00 % Allowed : 8.98 % Favored : 89.02 % 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: -1.62 (0.17), residues: 2280 helix: -0.31 (0.14), residues: 1189 sheet: -0.48 (0.45), residues: 126 loop : -2.10 (0.19), residues: 965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 33 HIS 0.006 0.001 HIS A 669 PHE 0.021 0.001 PHE A 395 TYR 0.020 0.002 TYR A1400 ARG 0.008 0.001 ARG A1845 Details of bonding type rmsd hydrogen bonds : bond 0.04058 ( 887) hydrogen bonds : angle 4.49187 ( 2545) SS BOND : bond 0.00411 ( 2) SS BOND : angle 2.24355 ( 4) covalent geometry : bond 0.00367 (18610) covalent geometry : angle 0.63938 (25194) *********************** 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 363 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 322 time to evaluate : 2.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7920 (tpp-160) cc_final: 0.7453 (mmm160) REVERT: A 272 ASP cc_start: 0.8819 (m-30) cc_final: 0.8615 (m-30) REVERT: A 466 MET cc_start: 0.8936 (mtp) cc_final: 0.8724 (mtp) REVERT: A 587 GLN cc_start: 0.7631 (mt0) cc_final: 0.6733 (tp40) REVERT: A 647 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9003 (pp) REVERT: A 812 LYS cc_start: 0.9084 (mttm) cc_final: 0.8826 (mtmm) REVERT: A 1052 GLN cc_start: 0.9073 (tt0) cc_final: 0.8786 (mt0) REVERT: A 1065 LYS cc_start: 0.9000 (mtmt) cc_final: 0.8749 (mttp) REVERT: A 1254 LEU cc_start: 0.9149 (tp) cc_final: 0.8912 (tp) REVERT: A 1394 LEU cc_start: 0.7992 (mm) cc_final: 0.7658 (tt) REVERT: A 1413 MET cc_start: 0.7981 (mtm) cc_final: 0.7231 (mmm) REVERT: A 1450 ASN cc_start: 0.7359 (t0) cc_final: 0.7071 (t0) REVERT: A 1452 ILE cc_start: 0.9179 (tt) cc_final: 0.8835 (tt) REVERT: A 1465 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8295 (mt-10) REVERT: A 1506 LEU cc_start: 0.7859 (mt) cc_final: 0.7616 (mp) REVERT: A 1738 GLN cc_start: 0.7969 (mp10) cc_final: 0.7746 (pm20) REVERT: A 1785 MET cc_start: 0.9074 (ttp) cc_final: 0.8679 (ttp) REVERT: A 1798 TYR cc_start: 0.8000 (m-80) cc_final: 0.7667 (m-80) REVERT: A 1807 MET cc_start: 0.8376 (mtt) cc_final: 0.8051 (mtp) REVERT: A 1851 ASN cc_start: 0.7790 (OUTLIER) cc_final: 0.7497 (m110) REVERT: A 1908 VAL cc_start: 0.8958 (t) cc_final: 0.8585 (t) REVERT: A 1920 TYR cc_start: 0.8191 (t80) cc_final: 0.7857 (t80) REVERT: A 1933 PHE cc_start: 0.9051 (m-80) cc_final: 0.8464 (m-80) REVERT: A 1976 MET cc_start: 0.8618 (tmm) cc_final: 0.8211 (mtp) REVERT: A 2021 LEU cc_start: 0.8245 (mm) cc_final: 0.7876 (mm) REVERT: D 268 GLN cc_start: 0.7711 (mt0) cc_final: 0.7441 (mt0) REVERT: D 283 MET cc_start: 0.8323 (mmt) cc_final: 0.8057 (mmm) REVERT: D 298 ASP cc_start: 0.6872 (m-30) cc_final: 0.6585 (t0) REVERT: C 265 GLU cc_start: 0.7434 (mp0) cc_final: 0.7092 (mp0) REVERT: C 266 ILE cc_start: 0.8803 (OUTLIER) cc_final: 0.8603 (tp) REVERT: C 273 VAL cc_start: 0.9017 (t) cc_final: 0.8574 (p) REVERT: C 277 GLU cc_start: 0.9019 (mp0) cc_final: 0.8289 (mp0) REVERT: E 342 ILE cc_start: 0.7774 (mm) cc_final: 0.7367 (mm) REVERT: E 355 GLU cc_start: 0.8419 (mp0) cc_final: 0.7994 (mp0) REVERT: E 357 ASP cc_start: 0.8684 (m-30) cc_final: 0.8434 (m-30) REVERT: E 394 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7865 (mtm110) outliers start: 41 outliers final: 15 residues processed: 349 average time/residue: 0.3221 time to fit residues: 170.5112 Evaluate side-chains 289 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1804 SER Chi-restraints excluded: chain A residue 1851 ASN 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 351 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 49 optimal weight: 1.9990 chunk 29 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 overall best weight: 3.0046 ------------------------------------------------------------------------------- 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 581 GLN ** A 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 974 ASN ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1457 ASN A1500 ASN A1515 HIS ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1707 HIS A2063 HIS A2104 GLN B 268 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.116089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.079903 restraints weight = 68959.151| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.92 r_work: 0.2892 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2896 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2896 r_free = 0.2896 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2896 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 18612 Z= 0.223 Angle : 0.656 9.242 25198 Z= 0.331 Chirality : 0.044 0.168 2920 Planarity : 0.005 0.091 3198 Dihedral : 5.388 36.176 2518 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 2.88 % Allowed : 10.63 % Favored : 86.49 % 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: -0.92 (0.17), residues: 2280 helix: 0.34 (0.15), residues: 1193 sheet: -0.31 (0.44), residues: 129 loop : -1.88 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 33 HIS 0.006 0.001 HIS A1927 PHE 0.026 0.002 PHE A1821 TYR 0.018 0.002 TYR A 977 ARG 0.006 0.001 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 887) hydrogen bonds : angle 4.28927 ( 2545) SS BOND : bond 0.00381 ( 2) SS BOND : angle 2.10307 ( 4) covalent geometry : bond 0.00520 (18610) covalent geometry : angle 0.65551 (25194) *********************** 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 333 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 274 time to evaluate : 3.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7978 (tpp-160) cc_final: 0.7589 (mmm160) REVERT: A 236 MET cc_start: 0.9293 (ttp) cc_final: 0.9067 (ttp) REVERT: A 272 ASP cc_start: 0.9040 (m-30) cc_final: 0.8827 (m-30) REVERT: A 587 GLN cc_start: 0.7522 (mt0) cc_final: 0.6721 (tp40) REVERT: A 647 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8977 (pp) REVERT: A 762 ARG cc_start: 0.8535 (ttp-110) cc_final: 0.8310 (mtm110) REVERT: A 1052 GLN cc_start: 0.9055 (tt0) cc_final: 0.8840 (mt0) REVERT: A 1065 LYS cc_start: 0.9025 (mtmt) cc_final: 0.8760 (mttp) REVERT: A 1413 MET cc_start: 0.7982 (mtm) cc_final: 0.7262 (mmm) REVERT: A 1465 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8392 (mt-10) REVERT: A 1494 MET cc_start: 0.6097 (mmm) cc_final: 0.5434 (mmp) REVERT: A 1506 LEU cc_start: 0.7958 (mt) cc_final: 0.7703 (mp) REVERT: A 1785 MET cc_start: 0.9060 (ttp) cc_final: 0.8820 (ttp) REVERT: A 1807 MET cc_start: 0.8539 (mtt) cc_final: 0.8227 (mtp) REVERT: A 1933 PHE cc_start: 0.9078 (m-80) cc_final: 0.8528 (m-80) REVERT: D 262 MET cc_start: 0.7902 (mmp) cc_final: 0.7368 (mmp) REVERT: D 298 ASP cc_start: 0.7115 (m-30) cc_final: 0.6698 (t0) REVERT: C 265 GLU cc_start: 0.7728 (mp0) cc_final: 0.7288 (mp0) REVERT: C 273 VAL cc_start: 0.9074 (t) cc_final: 0.8715 (p) REVERT: C 276 MET cc_start: 0.8848 (mmp) cc_final: 0.8485 (ttp) REVERT: C 277 GLU cc_start: 0.8997 (mp0) cc_final: 0.8229 (mp0) REVERT: E 282 MET cc_start: 0.8690 (mmt) cc_final: 0.7976 (mmm) REVERT: E 342 ILE cc_start: 0.7789 (mm) cc_final: 0.7576 (mm) REVERT: E 355 GLU cc_start: 0.8453 (mp0) cc_final: 0.7980 (mp0) REVERT: E 357 ASP cc_start: 0.8739 (m-30) cc_final: 0.8504 (m-30) REVERT: E 368 MET cc_start: 0.7702 (ttp) cc_final: 0.7427 (ttp) REVERT: E 394 ARG cc_start: 0.8257 (ptp90) cc_final: 0.7889 (mtm110) outliers start: 59 outliers final: 33 residues processed: 318 average time/residue: 0.3514 time to fit residues: 174.7393 Evaluate side-chains 290 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 256 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP 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 954 ASN 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 1324 ILE 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 1542 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 1802 LEU Chi-restraints excluded: chain A residue 1804 SER Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 308 VAL 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 96 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 229 optimal weight: 8.9990 chunk 9 optimal weight: 0.9980 chunk 201 optimal weight: 6.9990 chunk 143 optimal weight: 10.0000 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 11 optimal weight: 0.5980 chunk 220 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 583 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 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** ** A1707 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1808 ASN D 268 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.082523 restraints weight = 58118.724| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.73 r_work: 0.2962 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 18612 Z= 0.114 Angle : 0.575 11.819 25198 Z= 0.286 Chirality : 0.041 0.177 2920 Planarity : 0.004 0.051 3198 Dihedral : 4.892 37.668 2518 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.24 % Allowed : 11.56 % 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: -0.27 (0.18), residues: 2280 helix: 0.89 (0.15), residues: 1198 sheet: 0.04 (0.45), residues: 127 loop : -1.61 (0.20), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1754 HIS 0.005 0.001 HIS A 27 PHE 0.029 0.001 PHE A1821 TYR 0.021 0.001 TYR A1920 ARG 0.012 0.000 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.03320 ( 887) hydrogen bonds : angle 3.96973 ( 2545) SS BOND : bond 0.00329 ( 2) SS BOND : angle 1.84340 ( 4) covalent geometry : bond 0.00264 (18610) covalent geometry : angle 0.57427 (25194) *********************** 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 334 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 2.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7984 (tpp-160) cc_final: 0.7639 (mmm160) REVERT: A 236 MET cc_start: 0.9223 (ttp) cc_final: 0.9007 (ttp) REVERT: A 587 GLN cc_start: 0.7392 (mt0) cc_final: 0.6663 (tp40) REVERT: A 647 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9065 (pp) REVERT: A 663 GLN cc_start: 0.8813 (mt0) cc_final: 0.8442 (mt0) REVERT: A 1052 GLN cc_start: 0.8968 (tt0) cc_final: 0.8691 (mt0) REVERT: A 1065 LYS cc_start: 0.8972 (mtmt) cc_final: 0.8708 (mttp) REVERT: A 1413 MET cc_start: 0.7984 (mtm) cc_final: 0.7170 (mmm) REVERT: A 1450 ASN cc_start: 0.7358 (t0) cc_final: 0.7123 (t0) REVERT: A 1465 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8233 (mt-10) REVERT: A 1494 MET cc_start: 0.6117 (mmm) cc_final: 0.5499 (mmp) REVERT: A 1506 LEU cc_start: 0.7812 (mt) cc_final: 0.7446 (mp) REVERT: A 1798 TYR cc_start: 0.8006 (m-80) cc_final: 0.7611 (m-80) REVERT: A 1807 MET cc_start: 0.8524 (mtt) cc_final: 0.8154 (mtp) REVERT: A 1933 PHE cc_start: 0.9043 (m-80) cc_final: 0.8477 (m-80) REVERT: A 2024 ARG cc_start: 0.7990 (tpt-90) cc_final: 0.7585 (tpt-90) REVERT: A 2188 MET cc_start: 0.8846 (mmt) cc_final: 0.8246 (tpp) REVERT: A 2199 TYR cc_start: 0.5527 (m-80) cc_final: 0.5261 (m-10) REVERT: D 283 MET cc_start: 0.8346 (mmp) cc_final: 0.8115 (mmm) REVERT: D 286 LEU cc_start: 0.8618 (tt) cc_final: 0.8208 (tt) REVERT: D 298 ASP cc_start: 0.6988 (m-30) cc_final: 0.6730 (t0) REVERT: C 273 VAL cc_start: 0.9030 (t) cc_final: 0.8525 (p) REVERT: C 276 MET cc_start: 0.8830 (mmp) cc_final: 0.8468 (ttp) REVERT: C 277 GLU cc_start: 0.8981 (mp0) cc_final: 0.8105 (mp0) REVERT: C 284 LYS cc_start: 0.9211 (mttt) cc_final: 0.8963 (mttt) REVERT: E 282 MET cc_start: 0.8529 (mmt) cc_final: 0.7845 (mmt) REVERT: E 342 ILE cc_start: 0.7716 (mm) cc_final: 0.7490 (mm) REVERT: E 355 GLU cc_start: 0.8447 (mp0) cc_final: 0.7945 (mp0) REVERT: E 357 ASP cc_start: 0.8594 (m-30) cc_final: 0.8327 (m-30) REVERT: E 368 MET cc_start: 0.7580 (ttp) cc_final: 0.7274 (ttp) REVERT: E 379 LYS cc_start: 0.9251 (pttt) cc_final: 0.8945 (ptpp) REVERT: E 394 ARG cc_start: 0.8200 (ptp90) cc_final: 0.7812 (mtm110) outliers start: 46 outliers final: 31 residues processed: 321 average time/residue: 0.3124 time to fit residues: 152.4729 Evaluate side-chains 295 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 263 time to evaluate : 2.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP 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 954 ASN Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1096 VAL Chi-restraints excluded: chain A residue 1207 LYS Chi-restraints excluded: chain A residue 1324 ILE 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 1804 SER Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain D residue 259 ILE 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 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 104 optimal weight: 0.9990 chunk 43 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 92 optimal weight: 7.9990 chunk 93 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 188 optimal weight: 9.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A1034 HIS ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 ASN ** A1523 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1707 HIS A1759 HIS ** A1906 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.117416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081037 restraints weight = 70785.307| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 4.11 r_work: 0.2920 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2922 r_free = 0.2922 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 18612 Z= 0.144 Angle : 0.590 13.857 25198 Z= 0.292 Chirality : 0.042 0.277 2920 Planarity : 0.004 0.044 3198 Dihedral : 4.764 37.490 2518 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.88 % Allowed : 12.29 % Favored : 84.83 % 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: -0.03 (0.18), residues: 2280 helix: 1.04 (0.15), residues: 1211 sheet: 0.23 (0.46), residues: 123 loop : -1.48 (0.21), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1754 HIS 0.004 0.001 HIS A 27 PHE 0.032 0.001 PHE A1821 TYR 0.019 0.001 TYR A1920 ARG 0.008 0.000 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.03355 ( 887) hydrogen bonds : angle 3.89653 ( 2545) SS BOND : bond 0.00817 ( 2) SS BOND : angle 1.93091 ( 4) covalent geometry : bond 0.00341 (18610) covalent geometry : angle 0.58923 (25194) *********************** 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 330 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 271 time to evaluate : 2.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7995 (tpp-160) cc_final: 0.7587 (mmm160) REVERT: A 236 MET cc_start: 0.9270 (ttp) cc_final: 0.9058 (ttp) REVERT: A 587 GLN cc_start: 0.7498 (mt0) cc_final: 0.6636 (tp40) REVERT: A 647 LEU cc_start: 0.9386 (OUTLIER) cc_final: 0.9095 (pp) REVERT: A 954 ASN cc_start: 0.8823 (OUTLIER) cc_final: 0.8534 (p0) REVERT: A 1052 GLN cc_start: 0.9030 (tt0) cc_final: 0.8762 (mt0) REVERT: A 1065 LYS cc_start: 0.8980 (mtmt) cc_final: 0.8729 (mttp) REVERT: A 1413 MET cc_start: 0.7970 (mtm) cc_final: 0.7145 (mmm) REVERT: A 1465 GLU cc_start: 0.8598 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 1506 LEU cc_start: 0.7765 (mt) cc_final: 0.7483 (mp) REVERT: A 1654 MET cc_start: 0.7494 (mmt) cc_final: 0.7098 (mmt) REVERT: A 1707 HIS cc_start: 0.7392 (OUTLIER) cc_final: 0.7102 (t-170) REVERT: A 1807 MET cc_start: 0.8460 (mtt) cc_final: 0.8137 (mtp) REVERT: A 1933 PHE cc_start: 0.9031 (m-80) cc_final: 0.8533 (m-80) REVERT: A 1976 MET cc_start: 0.8734 (tmm) cc_final: 0.8321 (mtp) REVERT: A 2199 TYR cc_start: 0.5469 (m-80) cc_final: 0.5246 (m-10) REVERT: D 283 MET cc_start: 0.8428 (mmp) cc_final: 0.8222 (mmm) REVERT: D 286 LEU cc_start: 0.8689 (tt) cc_final: 0.8299 (tt) REVERT: D 298 ASP cc_start: 0.7071 (m-30) cc_final: 0.6796 (t0) REVERT: C 273 VAL cc_start: 0.9053 (t) cc_final: 0.8516 (p) REVERT: C 277 GLU cc_start: 0.9004 (mp0) cc_final: 0.8110 (mp0) REVERT: C 284 LYS cc_start: 0.9204 (mttt) cc_final: 0.8979 (mttt) REVERT: E 355 GLU cc_start: 0.8376 (mp0) cc_final: 0.7949 (mp0) REVERT: E 357 ASP cc_start: 0.8666 (m-30) cc_final: 0.8370 (m-30) REVERT: E 394 ARG cc_start: 0.8234 (ptp90) cc_final: 0.7881 (mtm110) outliers start: 59 outliers final: 35 residues processed: 314 average time/residue: 0.3015 time to fit residues: 145.0186 Evaluate side-chains 290 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 252 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER 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 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP 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 954 ASN 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 1339 ILE Chi-restraints excluded: chain A residue 1492 LEU Chi-restraints excluded: chain A residue 1523 HIS Chi-restraints excluded: chain A residue 1707 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 1996 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2180 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain C residue 296 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 62 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 144 optimal weight: 0.5980 chunk 72 optimal weight: 0.0570 chunk 211 optimal weight: 3.9990 chunk 187 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 GLN A 663 GLN ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1707 HIS ** A1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1811 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.119024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.082333 restraints weight = 77344.738| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 4.36 r_work: 0.2943 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18612 Z= 0.103 Angle : 0.571 14.886 25198 Z= 0.280 Chirality : 0.041 0.290 2920 Planarity : 0.004 0.058 3198 Dihedral : 4.544 37.207 2518 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.54 % Allowed : 13.27 % 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: 0.24 (0.18), residues: 2280 helix: 1.32 (0.15), residues: 1200 sheet: 0.36 (0.46), residues: 123 loop : -1.41 (0.20), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1754 HIS 0.021 0.001 HIS A1707 PHE 0.033 0.001 PHE A1821 TYR 0.019 0.001 TYR A1920 ARG 0.006 0.000 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 887) hydrogen bonds : angle 3.76842 ( 2545) SS BOND : bond 0.00928 ( 2) SS BOND : angle 2.07926 ( 4) covalent geometry : bond 0.00236 (18610) covalent geometry : angle 0.57073 (25194) *********************** 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 332 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 280 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7980 (tpp-160) cc_final: 0.7669 (mmm160) REVERT: A 587 GLN cc_start: 0.7416 (mt0) cc_final: 0.6584 (tp40) REVERT: A 954 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8598 (p0) REVERT: A 1052 GLN cc_start: 0.9005 (tt0) cc_final: 0.8740 (mt0) REVERT: A 1065 LYS cc_start: 0.8993 (mtmt) cc_final: 0.8713 (mttp) REVERT: A 1394 LEU cc_start: 0.8138 (mm) cc_final: 0.7786 (tt) REVERT: A 1413 MET cc_start: 0.8046 (mtm) cc_final: 0.7218 (mmm) REVERT: A 1506 LEU cc_start: 0.7755 (mt) cc_final: 0.7461 (mp) REVERT: A 1617 MET cc_start: 0.8214 (tpp) cc_final: 0.7906 (tmm) REVERT: A 1755 TYR cc_start: 0.7589 (m-80) cc_final: 0.7137 (m-10) REVERT: A 1807 MET cc_start: 0.8555 (mtt) cc_final: 0.8225 (mtp) REVERT: A 1933 PHE cc_start: 0.9043 (m-80) cc_final: 0.8540 (m-80) REVERT: A 1953 MET cc_start: 0.7257 (mtm) cc_final: 0.6841 (ttm) REVERT: A 2199 TYR cc_start: 0.5373 (m-80) cc_final: 0.5152 (m-10) REVERT: D 286 LEU cc_start: 0.8710 (tt) cc_final: 0.8365 (tt) REVERT: D 298 ASP cc_start: 0.7045 (m-30) cc_final: 0.6721 (t0) REVERT: C 273 VAL cc_start: 0.9085 (t) cc_final: 0.8459 (p) REVERT: C 277 GLU cc_start: 0.9006 (mp0) cc_final: 0.8060 (mp0) REVERT: E 282 MET cc_start: 0.8554 (mmt) cc_final: 0.7861 (mmt) REVERT: E 355 GLU cc_start: 0.8314 (mp0) cc_final: 0.7877 (mp0) REVERT: E 357 ASP cc_start: 0.8577 (m-30) cc_final: 0.8310 (m-30) REVERT: E 394 ARG cc_start: 0.8213 (ptp90) cc_final: 0.7852 (mtm110) outliers start: 52 outliers final: 35 residues processed: 318 average time/residue: 0.4290 time to fit residues: 214.5416 Evaluate side-chains 284 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER 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 389 ILE Chi-restraints excluded: chain A residue 475 HIS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU Chi-restraints excluded: chain A residue 954 ASN 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 1339 ILE Chi-restraints excluded: chain A residue 1452 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 1996 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2180 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain C residue 296 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 91 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 189 optimal weight: 7.9990 chunk 131 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 181 optimal weight: 0.1980 chunk 89 optimal weight: 7.9990 chunk 209 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 53 optimal weight: 0.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 340 ASN A 581 GLN ** A1171 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** ** A1791 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.118191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083152 restraints weight = 46000.239| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.21 r_work: 0.2980 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2983 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18612 Z= 0.123 Angle : 0.584 14.950 25198 Z= 0.289 Chirality : 0.041 0.282 2920 Planarity : 0.004 0.043 3198 Dihedral : 4.404 37.521 2516 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.29 % Allowed : 13.95 % Favored : 83.76 % 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: 0.35 (0.18), residues: 2280 helix: 1.37 (0.15), residues: 1207 sheet: 0.46 (0.45), residues: 123 loop : -1.32 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 169 HIS 0.006 0.001 HIS A1791 PHE 0.034 0.001 PHE A1821 TYR 0.019 0.001 TYR A1920 ARG 0.007 0.000 ARG D 300 Details of bonding type rmsd hydrogen bonds : bond 0.03130 ( 887) hydrogen bonds : angle 3.74567 ( 2545) SS BOND : bond 0.00671 ( 2) SS BOND : angle 2.00381 ( 4) covalent geometry : bond 0.00288 (18610) covalent geometry : angle 0.58372 (25194) *********************** 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 310 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 263 time to evaluate : 2.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7895 (tpp-160) cc_final: 0.7618 (mmm160) REVERT: A 520 LYS cc_start: 0.8792 (pptt) cc_final: 0.8432 (pptt) REVERT: A 587 GLN cc_start: 0.7439 (mt0) cc_final: 0.6653 (tp40) REVERT: A 1052 GLN cc_start: 0.8921 (tt0) cc_final: 0.8647 (mt0) REVERT: A 1065 LYS cc_start: 0.8941 (mtmt) cc_final: 0.8678 (mttt) REVERT: A 1413 MET cc_start: 0.8009 (mtm) cc_final: 0.7218 (mmm) REVERT: A 1465 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7799 (mp0) REVERT: A 1506 LEU cc_start: 0.7736 (mt) cc_final: 0.7443 (mp) REVERT: A 1617 MET cc_start: 0.8229 (tpp) cc_final: 0.7937 (tmm) REVERT: A 1755 TYR cc_start: 0.7485 (m-80) cc_final: 0.7043 (m-10) REVERT: A 1807 MET cc_start: 0.8556 (mtt) cc_final: 0.8264 (mtp) REVERT: A 1933 PHE cc_start: 0.9030 (m-80) cc_final: 0.8533 (m-80) REVERT: A 1975 ARG cc_start: 0.7895 (ptm160) cc_final: 0.6931 (tpt90) REVERT: A 1976 MET cc_start: 0.8729 (tmm) cc_final: 0.8027 (mtp) REVERT: D 286 LEU cc_start: 0.8710 (tt) cc_final: 0.8341 (tt) REVERT: D 298 ASP cc_start: 0.6946 (m-30) cc_final: 0.6688 (t0) REVERT: E 282 MET cc_start: 0.8536 (mmt) cc_final: 0.7838 (mmt) REVERT: E 355 GLU cc_start: 0.8268 (mp0) cc_final: 0.7845 (mp0) REVERT: E 357 ASP cc_start: 0.8538 (m-30) cc_final: 0.8274 (m-30) REVERT: E 394 ARG cc_start: 0.8217 (ptp90) cc_final: 0.7846 (mtm110) outliers start: 47 outliers final: 35 residues processed: 297 average time/residue: 0.4173 time to fit residues: 196.3814 Evaluate side-chains 286 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 2.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER 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 599 MET Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU 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 1339 ILE Chi-restraints excluded: chain A residue 1452 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 1903 ILE Chi-restraints excluded: chain A residue 1996 LEU Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2180 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 93 optimal weight: 0.0670 chunk 213 optimal weight: 10.0000 chunk 209 optimal weight: 0.4980 chunk 97 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 198 optimal weight: 9.9990 chunk 120 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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 ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1315 GLN ** A1530 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN D 279 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.118957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083334 restraints weight = 55286.808| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.61 r_work: 0.2980 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18612 Z= 0.110 Angle : 0.583 12.321 25198 Z= 0.287 Chirality : 0.041 0.304 2920 Planarity : 0.004 0.048 3198 Dihedral : 4.283 36.099 2516 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.29 % Allowed : 14.44 % 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: 0.49 (0.18), residues: 2280 helix: 1.49 (0.15), residues: 1200 sheet: 0.36 (0.44), residues: 130 loop : -1.23 (0.21), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1451 HIS 0.008 0.001 HIS A1791 PHE 0.035 0.001 PHE A1821 TYR 0.022 0.001 TYR A1920 ARG 0.009 0.000 ARG A1873 Details of bonding type rmsd hydrogen bonds : bond 0.02998 ( 887) hydrogen bonds : angle 3.67150 ( 2545) SS BOND : bond 0.00453 ( 2) SS BOND : angle 1.83364 ( 4) covalent geometry : bond 0.00258 (18610) covalent geometry : angle 0.58255 (25194) *********************** 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 317 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 270 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7868 (tpp-160) cc_final: 0.7650 (mmm160) REVERT: A 520 LYS cc_start: 0.8787 (pptt) cc_final: 0.8538 (pptt) REVERT: A 587 GLN cc_start: 0.7410 (mt0) cc_final: 0.6678 (tp40) REVERT: A 1052 GLN cc_start: 0.8913 (tt0) cc_final: 0.8650 (mt0) REVERT: A 1065 LYS cc_start: 0.8930 (mtmt) cc_final: 0.8674 (mttp) REVERT: A 1413 MET cc_start: 0.7993 (mtm) cc_final: 0.7192 (mmm) REVERT: A 1465 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7902 (pt0) REVERT: A 1654 MET cc_start: 0.7260 (mmt) cc_final: 0.6996 (mmt) REVERT: A 1755 TYR cc_start: 0.7454 (m-80) cc_final: 0.7048 (m-80) REVERT: A 1807 MET cc_start: 0.8552 (mtt) cc_final: 0.8255 (mtp) REVERT: A 1933 PHE cc_start: 0.9068 (m-80) cc_final: 0.8535 (m-80) REVERT: A 1953 MET cc_start: 0.7276 (mtm) cc_final: 0.6857 (ttm) REVERT: A 1976 MET cc_start: 0.8747 (tmm) cc_final: 0.8118 (mtp) REVERT: A 2021 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8143 (mm) REVERT: A 2024 ARG cc_start: 0.8018 (tpt-90) cc_final: 0.7689 (tpt-90) REVERT: A 2171 PHE cc_start: 0.7208 (OUTLIER) cc_final: 0.6942 (m-80) REVERT: A 2188 MET cc_start: 0.8929 (mmt) cc_final: 0.8662 (mmt) REVERT: D 286 LEU cc_start: 0.8719 (tt) cc_final: 0.8376 (tt) REVERT: D 298 ASP cc_start: 0.7001 (m-30) cc_final: 0.6726 (t0) REVERT: B 270 LYS cc_start: 0.7842 (tmtt) cc_final: 0.7599 (pttt) REVERT: E 282 MET cc_start: 0.8483 (mmt) cc_final: 0.7571 (mmp) REVERT: E 355 GLU cc_start: 0.8285 (mp0) cc_final: 0.7821 (mp0) REVERT: E 357 ASP cc_start: 0.8536 (m-30) cc_final: 0.8273 (m-30) REVERT: E 394 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7813 (mtm110) outliers start: 47 outliers final: 34 residues processed: 304 average time/residue: 0.3061 time to fit residues: 143.4969 Evaluate side-chains 288 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 252 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER 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 748 VAL Chi-restraints excluded: chain A residue 831 LEU 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 1339 ILE Chi-restraints excluded: chain A residue 1452 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 1804 SER Chi-restraints excluded: chain A residue 2021 LEU Chi-restraints excluded: chain A residue 2171 PHE Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 306 HIS Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 296 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 286 LEU 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 74 optimal weight: 4.9990 chunk 222 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 214 optimal weight: 10.0000 chunk 116 optimal weight: 0.4980 chunk 203 optimal weight: 4.9990 chunk 163 optimal weight: 5.9990 chunk 224 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 121 optimal weight: 0.4980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 496 ASN A 581 GLN ** A1171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1489 ASN ** A1534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1759 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 268 GLN D 279 ASN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.119103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082746 restraints weight = 70525.439| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 4.14 r_work: 0.2953 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2955 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2955 r_free = 0.2955 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2955 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 18612 Z= 0.112 Angle : 0.592 12.212 25198 Z= 0.290 Chirality : 0.041 0.281 2920 Planarity : 0.004 0.048 3198 Dihedral : 4.233 35.890 2516 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.15 % Allowed : 15.07 % Favored : 82.78 % 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: 0.58 (0.18), residues: 2280 helix: 1.55 (0.15), residues: 1201 sheet: 0.38 (0.43), residues: 130 loop : -1.16 (0.21), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1451 HIS 0.007 0.001 HIS A1791 PHE 0.036 0.001 PHE A1821 TYR 0.017 0.001 TYR A 698 ARG 0.010 0.000 ARG A1873 Details of bonding type rmsd hydrogen bonds : bond 0.02978 ( 887) hydrogen bonds : angle 3.67403 ( 2545) SS BOND : bond 0.00446 ( 2) SS BOND : angle 2.27843 ( 4) covalent geometry : bond 0.00264 (18610) covalent geometry : angle 0.59096 (25194) *********************** 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 297 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 2.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 ARG cc_start: 0.7903 (tpp-160) cc_final: 0.7678 (mmm160) REVERT: A 520 LYS cc_start: 0.8802 (pptt) cc_final: 0.8534 (pptt) REVERT: A 587 GLN cc_start: 0.7443 (mt0) cc_final: 0.6639 (tp40) REVERT: A 1052 GLN cc_start: 0.8934 (tt0) cc_final: 0.8691 (mt0) REVERT: A 1065 LYS cc_start: 0.8955 (mtmt) cc_final: 0.8704 (mttp) REVERT: A 1413 MET cc_start: 0.7975 (mtm) cc_final: 0.7186 (mmm) REVERT: A 1465 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7978 (pt0) REVERT: A 1617 MET cc_start: 0.8170 (tpp) cc_final: 0.7884 (tmm) REVERT: A 1654 MET cc_start: 0.7289 (mmt) cc_final: 0.7058 (mmt) REVERT: A 1807 MET cc_start: 0.8475 (mtt) cc_final: 0.8190 (mtp) REVERT: A 1920 TYR cc_start: 0.8302 (t80) cc_final: 0.7531 (t80) REVERT: A 1922 MET cc_start: 0.7415 (mmt) cc_final: 0.7079 (mpp) REVERT: A 1933 PHE cc_start: 0.9081 (m-80) cc_final: 0.8555 (m-80) REVERT: A 1953 MET cc_start: 0.7362 (mtm) cc_final: 0.6967 (ttm) REVERT: A 1976 MET cc_start: 0.8749 (tmm) cc_final: 0.8114 (mtp) REVERT: A 2024 ARG cc_start: 0.8000 (tpt-90) cc_final: 0.7683 (tpt-90) REVERT: A 2188 MET cc_start: 0.8900 (mmt) cc_final: 0.8635 (mmt) REVERT: D 286 LEU cc_start: 0.8765 (tt) cc_final: 0.8439 (tt) REVERT: D 298 ASP cc_start: 0.7061 (m-30) cc_final: 0.6759 (t0) REVERT: C 265 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: E 282 MET cc_start: 0.8491 (mmt) cc_final: 0.7577 (mmp) REVERT: E 355 GLU cc_start: 0.8309 (mp0) cc_final: 0.7858 (mp0) REVERT: E 357 ASP cc_start: 0.8575 (m-30) cc_final: 0.8308 (m-30) REVERT: E 394 ARG cc_start: 0.8186 (ptp90) cc_final: 0.7778 (mtm110) outliers start: 44 outliers final: 35 residues processed: 286 average time/residue: 0.3101 time to fit residues: 137.2831 Evaluate side-chains 284 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 248 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 117 ILE Chi-restraints excluded: chain A residue 236 MET 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 748 VAL Chi-restraints excluded: chain A residue 831 LEU 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 1339 ILE Chi-restraints excluded: chain A residue 1452 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 2027 ASP Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2180 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain B residue 271 THR Chi-restraints excluded: chain E residue 285 ILE Chi-restraints excluded: chain E residue 286 LEU 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 118 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 134 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 177 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 127 optimal weight: 0.0870 chunk 131 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- 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 ** A1171 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** D 268 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.118419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.081998 restraints weight = 75053.358| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 4.27 r_work: 0.2930 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 18612 Z= 0.130 Angle : 0.600 11.421 25198 Z= 0.296 Chirality : 0.042 0.274 2920 Planarity : 0.004 0.043 3198 Dihedral : 4.265 36.190 2516 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 1.90 % Allowed : 15.32 % Favored : 82.78 % 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: 0.61 (0.18), residues: 2280 helix: 1.56 (0.15), residues: 1202 sheet: 0.65 (0.44), residues: 121 loop : -1.16 (0.21), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1451 HIS 0.007 0.001 HIS A1791 PHE 0.037 0.001 PHE A1821 TYR 0.015 0.001 TYR A1920 ARG 0.010 0.000 ARG A1873 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 887) hydrogen bonds : angle 3.69453 ( 2545) SS BOND : bond 0.00477 ( 2) SS BOND : angle 2.19320 ( 4) covalent geometry : bond 0.00310 (18610) covalent geometry : angle 0.59981 (25194) ********************** 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 291 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 252 time to evaluate : 2.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.9162 (m-30) cc_final: 0.8686 (p0) REVERT: A 193 ARG cc_start: 0.7930 (tpp-160) cc_final: 0.7698 (mmm160) REVERT: A 520 LYS cc_start: 0.8817 (pptt) cc_final: 0.8522 (pptt) REVERT: A 581 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7270 (pp30) REVERT: A 587 GLN cc_start: 0.7659 (mt0) cc_final: 0.6683 (tp40) REVERT: A 873 MET cc_start: 0.9516 (mmt) cc_final: 0.9256 (mmt) REVERT: A 1052 GLN cc_start: 0.8953 (tt0) cc_final: 0.8701 (mt0) REVERT: A 1413 MET cc_start: 0.7968 (mtm) cc_final: 0.7182 (mmm) REVERT: A 1465 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7994 (pt0) REVERT: A 1617 MET cc_start: 0.8166 (tpp) cc_final: 0.7875 (tmm) REVERT: A 1654 MET cc_start: 0.7341 (mmt) cc_final: 0.7123 (mmt) REVERT: A 1770 ARG cc_start: 0.6902 (mpp80) cc_final: 0.6637 (ptp90) REVERT: A 1807 MET cc_start: 0.8586 (mtt) cc_final: 0.8319 (mtp) REVERT: A 1920 TYR cc_start: 0.8251 (t80) cc_final: 0.7982 (t80) REVERT: A 1922 MET cc_start: 0.7452 (mmt) cc_final: 0.7137 (mpp) REVERT: A 1933 PHE cc_start: 0.9089 (m-80) cc_final: 0.8541 (m-80) REVERT: A 1953 MET cc_start: 0.7341 (mtm) cc_final: 0.6937 (ttm) REVERT: A 1976 MET cc_start: 0.8751 (tmm) cc_final: 0.8111 (mtp) REVERT: A 2024 ARG cc_start: 0.8042 (tpt-90) cc_final: 0.7817 (tpt-90) REVERT: A 2170 MET cc_start: 0.6213 (ppp) cc_final: 0.5036 (mtm) REVERT: A 2188 MET cc_start: 0.8933 (mmt) cc_final: 0.8718 (mmt) REVERT: D 286 LEU cc_start: 0.8736 (tt) cc_final: 0.8371 (tt) REVERT: D 298 ASP cc_start: 0.7076 (m-30) cc_final: 0.6765 (t0) REVERT: C 265 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7278 (mp0) REVERT: E 282 MET cc_start: 0.8526 (mmt) cc_final: 0.7789 (mmt) REVERT: E 355 GLU cc_start: 0.8317 (mp0) cc_final: 0.7860 (mp0) REVERT: E 357 ASP cc_start: 0.8608 (m-30) cc_final: 0.8351 (m-30) REVERT: E 394 ARG cc_start: 0.8199 (ptp90) cc_final: 0.7785 (mtm110) outliers start: 39 outliers final: 34 residues processed: 282 average time/residue: 0.3173 time to fit residues: 139.2592 Evaluate side-chains 281 residues out of total 2050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 245 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 61 SER 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 592 LEU Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 831 LEU 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 1339 ILE Chi-restraints excluded: chain A residue 1452 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 1804 SER Chi-restraints excluded: chain A residue 1863 VAL Chi-restraints excluded: chain A residue 2027 ASP Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2176 MET Chi-restraints excluded: chain A residue 2180 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain C residue 286 LEU 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 175 optimal weight: 10.0000 chunk 89 optimal weight: 0.9990 chunk 147 optimal weight: 0.3980 chunk 13 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 186 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 overall best weight: 2.0788 ------------------------------------------------------------------------------- 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 A1061 ASN ** A1171 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** D 268 GLN ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.117079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081259 restraints weight = 58358.216| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 3.67 r_work: 0.2932 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 18612 Z= 0.166 Angle : 0.630 11.073 25198 Z= 0.311 Chirality : 0.043 0.273 2920 Planarity : 0.004 0.041 3198 Dihedral : 4.385 37.650 2516 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.90 % Allowed : 15.22 % Favored : 82.88 % 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: 0.53 (0.18), residues: 2280 helix: 1.50 (0.15), residues: 1207 sheet: 0.51 (0.44), residues: 126 loop : -1.21 (0.21), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1451 HIS 0.007 0.001 HIS A1791 PHE 0.037 0.001 PHE A1821 TYR 0.016 0.001 TYR A1920 ARG 0.013 0.000 ARG C 263 Details of bonding type rmsd hydrogen bonds : bond 0.03285 ( 887) hydrogen bonds : angle 3.77558 ( 2545) SS BOND : bond 0.00526 ( 2) SS BOND : angle 2.27051 ( 4) covalent geometry : bond 0.00396 (18610) covalent geometry : angle 0.62896 (25194) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10897.41 seconds wall clock time: 192 minutes 30.72 seconds (11550.72 seconds total)