Starting phenix.real_space_refine on Thu Jan 16 18:42:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r5o_18935/01_2025/8r5o_18935.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r5o_18935/01_2025/8r5o_18935.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r5o_18935/01_2025/8r5o_18935.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r5o_18935/01_2025/8r5o_18935.map" model { file = "/net/cci-nas-00/data/ceres_data/8r5o_18935/01_2025/8r5o_18935.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r5o_18935/01_2025/8r5o_18935.cif" } resolution = 2.49 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= 0.006 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 Zn 1 6.06 5 S 267 5.16 5 C 34604 2.51 5 N 9380 2.21 5 O 10219 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 54473 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 2449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2449 Classifications: {'peptide': 301} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 286} Chain breaks: 2 Chain: "B" Number of atoms: 1722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1722 Classifications: {'peptide': 216} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 205} Chain breaks: 1 Chain: "C" Number of atoms: 5170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 647, 5170 Classifications: {'peptide': 647} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 30, 'TRANS': 616} Chain breaks: 10 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 4468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 545, 4468 Classifications: {'peptide': 545} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 514} Chain breaks: 9 Chain: "E" Number of atoms: 7308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 912, 7308 Classifications: {'peptide': 912} Link IDs: {'PTRANS': 33, 'TRANS': 878} Chain breaks: 18 Chain: "F" Number of atoms: 4338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4338 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 21, 'TRANS': 515} Chain breaks: 3 Chain: "G" Number of atoms: 3040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3040 Classifications: {'peptide': 385} Link IDs: {'PTRANS': 8, 'TRANS': 376} Chain breaks: 2 Chain: "H" Number of atoms: 3701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3701 Classifications: {'peptide': 440} Link IDs: {'PCIS': 2, 'PTRANS': 32, 'TRANS': 405} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1771 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 202} Chain: "J" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1970 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 14, 'TRANS': 219} Chain breaks: 1 Chain: "K" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 3022 Classifications: {'peptide': 374} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 350} Chain: "L" Number of atoms: 3348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3348 Classifications: {'peptide': 408} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 381} Chain breaks: 2 Chain: "M" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1714 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 15, 'TRANS': 188} Chain: "N" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 201} Chain breaks: 1 Chain: "O" Number of atoms: 923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 923 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 107} Chain: "P" Number of atoms: 865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 865 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "Q" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1740 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 209} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 944 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 5, 'TRANS': 108} Chain breaks: 2 Chain: "S" Number of atoms: 3056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3056 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 364} Chain breaks: 1 Chain: "T" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 881 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "D" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "K" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "L" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "M" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "N" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 15516 SG CYS E 220 98.315 113.275 109.345 1.00 24.20 S ATOM 15985 SG CYS E 293 95.611 111.886 111.531 1.00 32.65 S ATOM 16043 SG CYS E 300 96.172 110.402 108.008 1.00 19.43 S ATOM 16068 SG CYS E 303 98.702 109.720 110.602 1.00 22.53 S Time building chain proxies: 21.78, per 1000 atoms: 0.40 Number of scatterers: 54473 At special positions: 0 Unit cell: (151, 210.5, 268, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 Fe 2 26.01 S 267 16.00 O 10219 8.00 N 9380 7.00 C 34604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 10.62 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E8001 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 220 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 300 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 303 " pdb="ZN ZN E8001 " - pdb=" SG CYS E 293 " Number of angles added : 6 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12546 Finding SS restraints... Secondary structure from input PDB file: 296 helices and 61 sheets defined 47.9% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'A' and resid 40 through 56 Processing helix chain 'A' and resid 83 through 93 Processing helix chain 'A' and resid 119 through 121 No H-bonds generated for 'chain 'A' and resid 119 through 121' Processing helix chain 'A' and resid 210 through 227 Processing helix chain 'A' and resid 228 through 231 Processing helix chain 'A' and resid 250 through 262 removed outlier: 3.543A pdb=" N HIS A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 273 through 277 Processing helix chain 'A' and resid 280 through 290 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 302 through 309 removed outlier: 3.829A pdb=" N LEU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE A 307 " --> pdb=" O GLN A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 327 removed outlier: 4.016A pdb=" N LYS A 318 " --> pdb=" O ILE A 314 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LYS A 319 " --> pdb=" O GLU A 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 56 removed outlier: 3.788A pdb=" N THR B 44 " --> pdb=" O GLY B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'B' and resid 210 through 227 Processing helix chain 'B' and resid 228 through 231 Processing helix chain 'C' and resid 16 through 29 Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 308 through 310 No H-bonds generated for 'chain 'C' and resid 308 through 310' Processing helix chain 'C' and resid 316 through 329 Processing helix chain 'C' and resid 362 through 372 Processing helix chain 'C' and resid 382 through 390 removed outlier: 4.427A pdb=" N GLY C 390 " --> pdb=" O GLN C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 418 Processing helix chain 'C' and resid 472 through 477 removed outlier: 4.099A pdb=" N GLU C 477 " --> pdb=" O PRO C 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 493 through 496 Processing helix chain 'C' and resid 513 through 515 No H-bonds generated for 'chain 'C' and resid 513 through 515' Processing helix chain 'C' and resid 529 through 533 Processing helix chain 'C' and resid 535 through 539 Processing helix chain 'C' and resid 540 through 552 removed outlier: 3.508A pdb=" N LEU C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 578 removed outlier: 4.065A pdb=" N GLY C 578 " --> pdb=" O ALA C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 682 Processing helix chain 'C' and resid 857 through 863 removed outlier: 4.146A pdb=" N SER C 861 " --> pdb=" O LEU C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 865 through 881 Processing helix chain 'C' and resid 889 through 893 Processing helix chain 'C' and resid 896 through 914 Processing helix chain 'C' and resid 915 through 919 Processing helix chain 'C' and resid 991 through 999 Processing helix chain 'C' and resid 1000 through 1009 Processing helix chain 'C' and resid 1039 through 1050 Processing helix chain 'D' and resid 16 through 25 removed outlier: 3.548A pdb=" N ALA D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 133 through 143 removed outlier: 4.186A pdb=" N LEU D 140 " --> pdb=" O GLU D 136 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 141 " --> pdb=" O LEU D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 179 Processing helix chain 'D' and resid 180 through 191 removed outlier: 4.091A pdb=" N ILE D 186 " --> pdb=" O GLN D 182 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N PHE D 187 " --> pdb=" O GLY D 183 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ASN D 189 " --> pdb=" O GLU D 185 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG D 190 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLU D 191 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 205 removed outlier: 3.770A pdb=" N ILE D 199 " --> pdb=" O GLY D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 225 removed outlier: 3.718A pdb=" N GLU D 225 " --> pdb=" O GLN D 221 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 257 removed outlier: 3.582A pdb=" N ARG D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 260 through 263 Processing helix chain 'D' and resid 273 through 277 Processing helix chain 'D' and resid 292 through 310 Processing helix chain 'D' and resid 322 through 337 Processing helix chain 'D' and resid 355 through 361 Processing helix chain 'D' and resid 398 through 406 removed outlier: 3.838A pdb=" N GLU D 404 " --> pdb=" O GLU D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 Processing helix chain 'D' and resid 422 through 432 Processing helix chain 'D' and resid 435 through 446 removed outlier: 3.759A pdb=" N GLU D 439 " --> pdb=" O PRO D 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 533 through 544 Processing helix chain 'D' and resid 548 through 552 Processing helix chain 'D' and resid 583 through 593 Processing helix chain 'D' and resid 655 through 676 Processing helix chain 'E' and resid 15 through 31 Processing helix chain 'E' and resid 31 through 54 Processing helix chain 'E' and resid 67 through 88 Processing helix chain 'E' and resid 92 through 123 removed outlier: 3.611A pdb=" N TRP E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ASN E 116 " --> pdb=" O ARG E 112 " (cutoff:3.500A) Proline residue: E 117 - end of helix Processing helix chain 'E' and resid 126 through 134 removed outlier: 3.675A pdb=" N SER E 132 " --> pdb=" O VAL E 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 174 through 211 removed outlier: 3.840A pdb=" N TYR E 183 " --> pdb=" O ILE E 179 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY E 184 " --> pdb=" O ILE E 180 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 280 Processing helix chain 'E' and resid 301 through 305 Processing helix chain 'E' and resid 319 through 330 Processing helix chain 'E' and resid 365 through 369 removed outlier: 3.592A pdb=" N VAL E 369 " --> pdb=" O GLU E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 566 through 570 Processing helix chain 'E' and resid 885 through 889 Processing helix chain 'E' and resid 986 through 990 Processing helix chain 'E' and resid 999 through 1007 removed outlier: 3.926A pdb=" N ILE E1004 " --> pdb=" O GLN E1000 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E1007 " --> pdb=" O VAL E1003 " (cutoff:3.500A) Processing helix chain 'E' and resid 1008 through 1013 removed outlier: 4.539A pdb=" N LYS E1013 " --> pdb=" O ASP E1010 " (cutoff:3.500A) Processing helix chain 'E' and resid 1146 through 1155 Processing helix chain 'E' and resid 1163 through 1180 removed outlier: 3.556A pdb=" N CYS E1175 " --> pdb=" O GLY E1171 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR E1177 " --> pdb=" O ASN E1173 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N ARG E1178 " --> pdb=" O ARG E1174 " (cutoff:3.500A) Processing helix chain 'E' and resid 1184 through 1212 Processing helix chain 'E' and resid 1217 through 1229 removed outlier: 3.929A pdb=" N ILE E1221 " --> pdb=" O HIS E1217 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN E1227 " --> pdb=" O ILE E1223 " (cutoff:3.500A) Processing helix chain 'E' and resid 1251 through 1261 Processing helix chain 'E' and resid 1273 through 1279 Processing helix chain 'E' and resid 1283 through 1289 Processing helix chain 'E' and resid 1292 through 1303 removed outlier: 3.592A pdb=" N ARG E1303 " --> pdb=" O LYS E1299 " (cutoff:3.500A) Processing helix chain 'E' and resid 1311 through 1319 removed outlier: 4.101A pdb=" N ASN E1315 " --> pdb=" O GLY E1311 " (cutoff:3.500A) Processing helix chain 'E' and resid 1324 through 1328 Processing helix chain 'F' and resid 64 through 83 Processing helix chain 'F' and resid 86 through 101 Processing helix chain 'F' and resid 105 through 119 Processing helix chain 'F' and resid 121 through 135 Processing helix chain 'F' and resid 140 through 154 Processing helix chain 'F' and resid 156 through 170 Processing helix chain 'F' and resid 174 through 188 Processing helix chain 'F' and resid 190 through 204 Processing helix chain 'F' and resid 209 through 223 Processing helix chain 'F' and resid 225 through 240 Processing helix chain 'F' and resid 244 through 256 removed outlier: 3.852A pdb=" N VAL F 254 " --> pdb=" O CYS F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 260 through 273 removed outlier: 4.020A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR F 267 " --> pdb=" O VAL F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 275 through 279 Processing helix chain 'F' and resid 281 through 294 Processing helix chain 'F' and resid 300 through 314 Processing helix chain 'F' and resid 321 through 335 removed outlier: 3.616A pdb=" N HIS F 325 " --> pdb=" O ASN F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 337 through 350 removed outlier: 3.967A pdb=" N ASN F 350 " --> pdb=" O ARG F 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 360 Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 366 through 378 Processing helix chain 'F' and resid 380 through 394 Processing helix chain 'F' and resid 431 through 439 Processing helix chain 'F' and resid 459 through 463 Processing helix chain 'F' and resid 474 through 495 removed outlier: 3.555A pdb=" N HIS F 487 " --> pdb=" O TRP F 483 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 616 Processing helix chain 'F' and resid 744 through 755 Processing helix chain 'F' and resid 759 through 763 Processing helix chain 'F' and resid 765 through 770 Processing helix chain 'F' and resid 774 through 778 Processing helix chain 'F' and resid 787 through 805 Processing helix chain 'F' and resid 810 through 817 Processing helix chain 'F' and resid 836 through 840 Processing helix chain 'G' and resid 421 through 434 Processing helix chain 'G' and resid 435 through 449 Processing helix chain 'G' and resid 454 through 468 Processing helix chain 'G' and resid 470 through 484 removed outlier: 3.985A pdb=" N HIS G 482 " --> pdb=" O PHE G 478 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G 483 " --> pdb=" O ASN G 479 " (cutoff:3.500A) Processing helix chain 'G' and resid 489 through 504 removed outlier: 3.508A pdb=" N PHE G 493 " --> pdb=" O SER G 489 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU G 497 " --> pdb=" O PHE G 493 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY G 503 " --> pdb=" O SER G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 505 through 519 removed outlier: 3.797A pdb=" N ASN G 518 " --> pdb=" O SER G 514 " (cutoff:3.500A) Processing helix chain 'G' and resid 524 through 538 removed outlier: 3.554A pdb=" N PHE G 528 " --> pdb=" O ASN G 524 " (cutoff:3.500A) Processing helix chain 'G' and resid 540 through 554 removed outlier: 3.590A pdb=" N GLU G 552 " --> pdb=" O TYR G 548 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS G 553 " --> pdb=" O VAL G 549 " (cutoff:3.500A) Processing helix chain 'G' and resid 559 through 573 removed outlier: 3.596A pdb=" N VAL G 569 " --> pdb=" O ALA G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 575 through 589 removed outlier: 3.593A pdb=" N LYS G 587 " --> pdb=" O PHE G 583 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER G 589 " --> pdb=" O GLU G 585 " (cutoff:3.500A) Processing helix chain 'G' and resid 594 through 608 removed outlier: 3.511A pdb=" N THR G 608 " --> pdb=" O VAL G 604 " (cutoff:3.500A) Processing helix chain 'G' and resid 610 through 624 removed outlier: 3.725A pdb=" N GLU G 620 " --> pdb=" O GLU G 616 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER G 623 " --> pdb=" O GLU G 619 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASN G 624 " --> pdb=" O GLU G 620 " (cutoff:3.500A) Processing helix chain 'G' and resid 627 through 639 removed outlier: 3.760A pdb=" N GLN G 631 " --> pdb=" O SER G 627 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS G 638 " --> pdb=" O GLY G 634 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLY G 639 " --> pdb=" O GLN G 635 " (cutoff:3.500A) Processing helix chain 'G' and resid 644 through 646 No H-bonds generated for 'chain 'G' and resid 644 through 646' Processing helix chain 'G' and resid 647 through 658 Processing helix chain 'G' and resid 660 through 679 removed outlier: 4.298A pdb=" N LEU G 664 " --> pdb=" O GLU G 660 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ARG G 667 " --> pdb=" O GLY G 663 " (cutoff:3.500A) Processing helix chain 'G' and resid 681 through 695 removed outlier: 3.775A pdb=" N LYS G 694 " --> pdb=" O ASN G 690 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG G 695 " --> pdb=" O GLU G 691 " (cutoff:3.500A) Processing helix chain 'G' and resid 717 through 735 removed outlier: 3.501A pdb=" N ASP G 734 " --> pdb=" O ASN G 730 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE G 735 " --> pdb=" O ASP G 731 " (cutoff:3.500A) Processing helix chain 'G' and resid 753 through 757 removed outlier: 3.513A pdb=" N LYS G 757 " --> pdb=" O GLN G 754 " (cutoff:3.500A) Processing helix chain 'G' and resid 760 through 763 Processing helix chain 'G' and resid 764 through 779 removed outlier: 3.546A pdb=" N ASP G 776 " --> pdb=" O SER G 772 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS G 777 " --> pdb=" O PHE G 773 " (cutoff:3.500A) Processing helix chain 'G' and resid 796 through 801 removed outlier: 3.930A pdb=" N GLN G 801 " --> pdb=" O SER G 797 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 80 Processing helix chain 'H' and resid 89 through 99 Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 120 through 131 Processing helix chain 'H' and resid 134 through 142 removed outlier: 3.524A pdb=" N GLN H 142 " --> pdb=" O TRP H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 179 through 188 Processing helix chain 'H' and resid 189 through 195 removed outlier: 3.713A pdb=" N MET H 193 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 198 through 202 removed outlier: 3.590A pdb=" N LEU H 202 " --> pdb=" O LEU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 217 removed outlier: 3.928A pdb=" N THR H 213 " --> pdb=" O GLU H 210 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP H 215 " --> pdb=" O ALA H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 219 through 248 removed outlier: 5.807A pdb=" N ASP H 238 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ARG H 239 " --> pdb=" O ALA H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 268 through 272 Processing helix chain 'H' and resid 308 through 314 removed outlier: 4.287A pdb=" N TRP H 312 " --> pdb=" O ASN H 308 " (cutoff:3.500A) Processing helix chain 'H' and resid 349 through 353 Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 391 through 395 Processing helix chain 'H' and resid 403 through 424 Processing helix chain 'H' and resid 468 through 472 removed outlier: 3.662A pdb=" N GLU H 471 " --> pdb=" O SER H 468 " (cutoff:3.500A) Processing helix chain 'H' and resid 473 through 484 Processing helix chain 'H' and resid 503 through 538 Processing helix chain 'I' and resid 67 through 77 Processing helix chain 'I' and resid 77 through 91 Processing helix chain 'I' and resid 100 through 110 removed outlier: 3.568A pdb=" N ASN I 110 " --> pdb=" O LYS I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 113 No H-bonds generated for 'chain 'I' and resid 111 through 113' Processing helix chain 'I' and resid 117 through 133 removed outlier: 3.508A pdb=" N TYR I 125 " --> pdb=" O ALA I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 155 Processing helix chain 'I' and resid 156 through 171 Processing helix chain 'I' and resid 198 through 203 Processing helix chain 'I' and resid 213 through 216 Processing helix chain 'I' and resid 217 through 222 Processing helix chain 'I' and resid 224 through 236 Processing helix chain 'I' and resid 238 through 250 Processing helix chain 'J' and resid 205 through 210 Processing helix chain 'J' and resid 234 through 238 Processing helix chain 'J' and resid 254 through 266 removed outlier: 3.670A pdb=" N VAL J 258 " --> pdb=" O ASP J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 277 through 307 removed outlier: 5.754A pdb=" N HIS J 289 " --> pdb=" O ARG J 285 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N LEU J 290 " --> pdb=" O ALA J 286 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE J 291 " --> pdb=" O ARG J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 313 Processing helix chain 'J' and resid 314 through 316 No H-bonds generated for 'chain 'J' and resid 314 through 316' Processing helix chain 'J' and resid 324 through 336 Processing helix chain 'J' and resid 338 through 348 Processing helix chain 'J' and resid 351 through 359 Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 368 through 373 Processing helix chain 'J' and resid 375 through 380 Processing helix chain 'J' and resid 381 through 383 No H-bonds generated for 'chain 'J' and resid 381 through 383' Processing helix chain 'J' and resid 390 through 393 Processing helix chain 'J' and resid 415 through 423 Processing helix chain 'K' and resid 118 through 122 Processing helix chain 'K' and resid 123 through 128 Processing helix chain 'K' and resid 130 through 134 Processing helix chain 'K' and resid 139 through 150 removed outlier: 3.845A pdb=" N VAL K 143 " --> pdb=" O PRO K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 163 through 176 Processing helix chain 'K' and resid 200 through 204 removed outlier: 3.693A pdb=" N GLY K 203 " --> pdb=" O PHE K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 217 Processing helix chain 'K' and resid 219 through 223 Processing helix chain 'K' and resid 224 through 231 Processing helix chain 'K' and resid 239 through 242 Processing helix chain 'K' and resid 243 through 260 removed outlier: 3.528A pdb=" N LYS K 252 " --> pdb=" O SER K 248 " (cutoff:3.500A) Processing helix chain 'K' and resid 271 through 276 Processing helix chain 'K' and resid 277 through 292 removed outlier: 4.767A pdb=" N LYS K 287 " --> pdb=" O LYS K 283 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N SER K 288 " --> pdb=" O LEU K 284 " (cutoff:3.500A) Processing helix chain 'K' and resid 299 through 307 Processing helix chain 'K' and resid 307 through 316 removed outlier: 3.751A pdb=" N TYR K 311 " --> pdb=" O ASP K 307 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 330 removed outlier: 3.756A pdb=" N THR K 329 " --> pdb=" O ASP K 325 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS K 330 " --> pdb=" O PHE K 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 330' Processing helix chain 'K' and resid 339 through 344 Processing helix chain 'K' and resid 345 through 347 No H-bonds generated for 'chain 'K' and resid 345 through 347' Processing helix chain 'K' and resid 391 through 407 removed outlier: 3.716A pdb=" N THR K 406 " --> pdb=" O ARG K 402 " (cutoff:3.500A) Processing helix chain 'K' and resid 408 through 412 removed outlier: 3.557A pdb=" N PHE K 411 " --> pdb=" O PRO K 408 " (cutoff:3.500A) Processing helix chain 'K' and resid 413 through 432 removed outlier: 3.797A pdb=" N PHE K 423 " --> pdb=" O ARG K 419 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA K 424 " --> pdb=" O GLN K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 436 through 441 Processing helix chain 'K' and resid 443 through 455 Processing helix chain 'K' and resid 456 through 460 Processing helix chain 'L' and resid 76 through 85 removed outlier: 4.162A pdb=" N TYR L 80 " --> pdb=" O ASP L 76 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY L 83 " --> pdb=" O PHE L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 125 through 127 No H-bonds generated for 'chain 'L' and resid 125 through 127' Processing helix chain 'L' and resid 147 through 155 removed outlier: 4.182A pdb=" N ASP L 151 " --> pdb=" O HIS L 147 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 176 Processing helix chain 'L' and resid 179 through 185 removed outlier: 4.214A pdb=" N LEU L 183 " --> pdb=" O HIS L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 186 through 188 No H-bonds generated for 'chain 'L' and resid 186 through 188' Processing helix chain 'L' and resid 196 through 200 Processing helix chain 'L' and resid 201 through 206 Processing helix chain 'L' and resid 210 through 232 Processing helix chain 'L' and resid 237 through 242 Processing helix chain 'L' and resid 246 through 260 Processing helix chain 'L' and resid 329 through 338 Processing helix chain 'L' and resid 359 through 366 Processing helix chain 'L' and resid 371 through 375 removed outlier: 3.810A pdb=" N TYR L 375 " --> pdb=" O PRO L 372 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 399 Processing helix chain 'L' and resid 410 through 430 removed outlier: 3.544A pdb=" N LYS L 416 " --> pdb=" O SER L 412 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 446 Processing helix chain 'L' and resid 450 through 480 Processing helix chain 'M' and resid 137 through 139 No H-bonds generated for 'chain 'M' and resid 137 through 139' Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 276 through 278 No H-bonds generated for 'chain 'M' and resid 276 through 278' Processing helix chain 'M' and resid 297 through 299 No H-bonds generated for 'chain 'M' and resid 297 through 299' Processing helix chain 'M' and resid 301 through 323 Processing helix chain 'M' and resid 327 through 330 Processing helix chain 'N' and resid 65 through 73 Processing helix chain 'N' and resid 75 through 88 Processing helix chain 'N' and resid 99 through 107 removed outlier: 3.546A pdb=" N ASN N 107 " --> pdb=" O LEU N 103 " (cutoff:3.500A) Processing helix chain 'N' and resid 108 through 110 No H-bonds generated for 'chain 'N' and resid 108 through 110' Processing helix chain 'N' and resid 114 through 130 Processing helix chain 'N' and resid 140 through 152 Processing helix chain 'N' and resid 153 through 168 Processing helix chain 'N' and resid 210 through 215 Processing helix chain 'N' and resid 225 through 228 Processing helix chain 'N' and resid 229 through 234 Processing helix chain 'N' and resid 236 through 248 Processing helix chain 'N' and resid 250 through 270 Processing helix chain 'O' and resid 83 through 93 Processing helix chain 'O' and resid 108 through 125 removed outlier: 3.886A pdb=" N ILE O 112 " --> pdb=" O CYS O 108 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU O 113 " --> pdb=" O GLY O 109 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLN O 116 " --> pdb=" O ILE O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 146 Processing helix chain 'O' and resid 173 through 185 Processing helix chain 'P' and resid 83 through 93 removed outlier: 3.540A pdb=" N GLY P 93 " --> pdb=" O ASP P 89 " (cutoff:3.500A) Processing helix chain 'P' and resid 108 through 125 removed outlier: 3.582A pdb=" N ILE P 112 " --> pdb=" O CYS P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 146 Processing helix chain 'P' and resid 173 through 185 removed outlier: 3.623A pdb=" N MET P 177 " --> pdb=" O PRO P 173 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET P 185 " --> pdb=" O ILE P 181 " (cutoff:3.500A) Processing helix chain 'Q' and resid 351 through 361 Processing helix chain 'Q' and resid 540 through 548 removed outlier: 3.725A pdb=" N TYR Q 544 " --> pdb=" O ARG Q 540 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ASN Q 545 " --> pdb=" O HIS Q 541 " (cutoff:3.500A) Processing helix chain 'Q' and resid 595 through 608 Processing helix chain 'Q' and resid 628 through 640 removed outlier: 3.662A pdb=" N THR Q 633 " --> pdb=" O ARG Q 629 " (cutoff:3.500A) Processing helix chain 'Q' and resid 654 through 664 Processing helix chain 'Q' and resid 665 through 667 No H-bonds generated for 'chain 'Q' and resid 665 through 667' Processing helix chain 'Q' and resid 669 through 679 Processing helix chain 'Q' and resid 696 through 706 Processing helix chain 'Q' and resid 735 through 753 removed outlier: 3.531A pdb=" N GLN Q 745 " --> pdb=" O ARG Q 741 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ASP Q 748 " --> pdb=" O LEU Q 744 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU Q 749 " --> pdb=" O GLN Q 745 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU Q 750 " --> pdb=" O TYR Q 746 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 79 Processing helix chain 'R' and resid 79 through 91 removed outlier: 3.790A pdb=" N THR R 83 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 114 Processing helix chain 'R' and resid 123 through 136 removed outlier: 3.514A pdb=" N LEU R 136 " --> pdb=" O ARG R 132 " (cutoff:3.500A) Processing helix chain 'R' and resid 141 through 145 Processing helix chain 'S' and resid 193 through 197 Processing helix chain 'S' and resid 225 through 232 Processing helix chain 'S' and resid 249 through 260 Processing helix chain 'S' and resid 273 through 286 Processing helix chain 'S' and resid 322 through 326 Processing helix chain 'S' and resid 328 through 332 Processing helix chain 'S' and resid 333 through 340 Processing helix chain 'S' and resid 348 through 351 Processing helix chain 'S' and resid 352 through 369 removed outlier: 3.535A pdb=" N THR S 358 " --> pdb=" O LYS S 354 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 Processing helix chain 'S' and resid 386 through 400 removed outlier: 4.994A pdb=" N GLU S 396 " --> pdb=" O SER S 392 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N VAL S 397 " --> pdb=" O LEU S 393 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU S 400 " --> pdb=" O GLU S 396 " (cutoff:3.500A) Processing helix chain 'S' and resid 408 through 415 Processing helix chain 'S' and resid 429 through 433 Processing helix chain 'S' and resid 437 through 442 removed outlier: 3.795A pdb=" N VAL S 441 " --> pdb=" O GLU S 437 " (cutoff:3.500A) Processing helix chain 'S' and resid 443 through 445 No H-bonds generated for 'chain 'S' and resid 443 through 445' Processing helix chain 'S' and resid 487 through 505 removed outlier: 3.563A pdb=" N GLY S 491 " --> pdb=" O MET S 487 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL S 504 " --> pdb=" O ARG S 500 " (cutoff:3.500A) Processing helix chain 'S' and resid 506 through 509 removed outlier: 3.875A pdb=" N MET S 509 " --> pdb=" O PRO S 506 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 506 through 509' Processing helix chain 'S' and resid 511 through 538 removed outlier: 3.547A pdb=" N GLN S 535 " --> pdb=" O TRP S 531 " (cutoff:3.500A) Processing helix chain 'S' and resid 568 through 573 Processing helix chain 'T' and resid 40 through 46 Processing helix chain 'T' and resid 54 through 62 Processing helix chain 'T' and resid 63 through 66 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 24 removed outlier: 5.363A pdb=" N TRP A 15 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N SER A 35 " --> pdb=" O TRP A 15 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N CYS A 17 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ILE A 33 " --> pdb=" O CYS A 17 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU A 27 " --> pdb=" O ASP A 23 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N TYR A 29 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR A 205 " --> pdb=" O TYR A 29 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N ARG A 31 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ILE A 203 " --> pdb=" O ARG A 31 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N ILE A 33 " --> pdb=" O ILE A 201 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ILE A 201 " --> pdb=" O ILE A 33 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N SER A 35 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU A 199 " --> pdb=" O SER A 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASN A 181 " --> pdb=" O TRP A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 171 removed outlier: 6.622A pdb=" N LYS A 150 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ALA A 65 " --> pdb=" O GLY A 148 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY A 148 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N PHE A 67 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N CYS A 146 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 9.582A pdb=" N ARG S 596 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N CYS A 109 " --> pdb=" O ARG S 596 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 96 through 97 Processing sheet with id=AA4, first strand: chain 'A' and resid 114 through 117 Processing sheet with id=AA5, first strand: chain 'B' and resid 14 through 24 removed outlier: 6.570A pdb=" N ARG B 31 " --> pdb=" O VAL B 18 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER B 20 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N TYR B 29 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ARG B 22 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 27 " --> pdb=" O ARG B 22 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N GLU B 197 " --> pdb=" O PRO B 36 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU B 194 " --> pdb=" O ASN B 191 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N SER B 188 " --> pdb=" O GLU R 159 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 3.706A pdb=" N ARG B 64 " --> pdb=" O LYS B 150 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLU B 152 " --> pdb=" O ILE B 62 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N ILE B 62 " --> pdb=" O GLU B 152 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ASN B 154 " --> pdb=" O THR B 60 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N THR B 60 " --> pdb=" O ASN B 154 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 97 Processing sheet with id=AA8, first strand: chain 'B' and resid 114 through 117 Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 3.672A pdb=" N GLY C 102 " --> pdb=" O LEU C 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AB2, first strand: chain 'C' and resid 312 through 315 removed outlier: 6.808A pdb=" N ASN C 124 " --> pdb=" O SER C 394 " (cutoff:3.500A) removed outlier: 9.788A pdb=" N ILE C 435 " --> pdb=" O ILE C 424 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N ILE C 424 " --> pdb=" O ILE C 435 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N SER C 437 " --> pdb=" O CYS C 422 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 443 through 444 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 468 through 471 current: chain 'C' and resid 498 through 503 Processing sheet with id=AB4, first strand: chain 'C' and resid 565 through 566 Processing sheet with id=AB5, first strand: chain 'C' and resid 581 through 582 removed outlier: 6.388A pdb=" N ALA C 581 " --> pdb=" O LEU C 640 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 605 through 609 removed outlier: 3.589A pdb=" N TYR C 591 " --> pdb=" O ILE C 598 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER C 600 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ILE C 589 " --> pdb=" O SER C 600 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 614 through 615 Processing sheet with id=AB8, first strand: chain 'C' and resid 646 through 647 Processing sheet with id=AB9, first strand: chain 'C' and resid 655 through 656 removed outlier: 7.587A pdb=" N ILE C 675 " --> pdb=" O SER C 833 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ILE C 835 " --> pdb=" O ILE C 675 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ALA C 660 " --> pdb=" O PHE C 854 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ILE C 943 " --> pdb=" O TYR C 661 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 687 through 693 removed outlier: 6.818A pdb=" N TYR C 809 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY C 785 " --> pdb=" O VAL C 734 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 1067 through 1069 removed outlier: 4.101A pdb=" N HIS D 7 " --> pdb=" O VAL C1060 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 105 through 114 removed outlier: 10.141A pdb=" N LEU D 109 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 10.137A pdb=" N CYS D 111 " --> pdb=" O LEU D 268 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N LEU D 268 " --> pdb=" O CYS D 111 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 162 through 164 removed outlier: 3.721A pdb=" N GLY D 162 " --> pdb=" O ALA D 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 384 through 386 Processing sheet with id=AC6, first strand: chain 'D' and resid 394 through 397 Processing sheet with id=AC7, first strand: chain 'D' and resid 580 through 581 removed outlier: 7.435A pdb=" N PHE D 581 " --> pdb=" O ARG D 605 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE D 650 " --> pdb=" O TRP D 606 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ASN D 629 " --> pdb=" O GLU D 625 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU M 266 " --> pdb=" O ILE M 293 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N HIS M 295 " --> pdb=" O LEU M 266 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL J 188 " --> pdb=" O VAL M 267 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 215 through 217 Processing sheet with id=AC9, first strand: chain 'E' and resid 226 through 228 removed outlier: 4.310A pdb=" N VAL E 250 " --> pdb=" O ARG E 288 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 255 through 257 removed outlier: 6.887A pdb=" N ILE E 255 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 352 through 355 Processing sheet with id=AD3, first strand: chain 'E' and resid 397 through 402 Processing sheet with id=AD4, first strand: chain 'E' and resid 438 through 443 removed outlier: 3.579A pdb=" N VAL E1130 " --> pdb=" O ILE E 442 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LEU E1129 " --> pdb=" O HIS E1116 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 448 through 451 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 474 through 480 current: chain 'E' and resid 1030 through 1033 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1030 through 1033 current: chain 'E' and resid 1089 through 1094 removed outlier: 6.553A pdb=" N VAL E1100 " --> pdb=" O LEU E1092 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 1099 through 1109 current: chain 'H' and resid 290 through 294 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 301 through 304 current: chain 'H' and resid 340 through 346 Processing sheet with id=AD6, first strand: chain 'E' and resid 499 through 500 removed outlier: 6.949A pdb=" N GLN E 499 " --> pdb=" O HIS H 364 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'E' and resid 571 through 573 removed outlier: 9.272A pdb=" N VAL H 463 " --> pdb=" O ALA E 857 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N PHE E 859 " --> pdb=" O VAL H 463 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N LEU H 465 " --> pdb=" O PHE E 859 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N GLU E 861 " --> pdb=" O LEU H 465 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 600 through 601 removed outlier: 3.898A pdb=" N SER E 600 " --> pdb=" O PHE E 617 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE E 617 " --> pdb=" O SER E 600 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'E' and resid 613 through 614 Processing sheet with id=AE1, first strand: chain 'E' and resid 924 through 926 Processing sheet with id=AE2, first strand: chain 'E' and resid 997 through 998 Processing sheet with id=AE3, first strand: chain 'E' and resid 1039 through 1042 removed outlier: 3.696A pdb=" N ASN E1047 " --> pdb=" O ASN E1042 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 1248 through 1250 removed outlier: 4.747A pdb=" N LYS E1231 " --> pdb=" O VAL E1270 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 702 through 704 removed outlier: 6.359A pdb=" N TRP G 709 " --> pdb=" O VAL G 747 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL G 749 " --> pdb=" O TRP G 709 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL G 711 " --> pdb=" O VAL G 749 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 187 through 194 removed outlier: 3.683A pdb=" N ARG I 187 " --> pdb=" O LYS I 182 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N GLY I 175 " --> pdb=" O ASP I 211 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASP I 211 " --> pdb=" O GLY I 175 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL I 177 " --> pdb=" O ASN I 209 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ASN I 209 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU I 179 " --> pdb=" O ILE I 207 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 213 through 214 Processing sheet with id=AE8, first strand: chain 'K' and resid 183 through 186 removed outlier: 6.441A pdb=" N LYS K 184 " --> pdb=" O PHE K 156 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N GLY K 158 " --> pdb=" O LYS K 184 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N ASP K 186 " --> pdb=" O GLY K 158 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL K 160 " --> pdb=" O ASP K 186 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N VAL K 93 " --> pdb=" O ALA K 155 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET K 157 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N CYS K 95 " --> pdb=" O MET K 157 " (cutoff:3.500A) removed outlier: 8.504A pdb=" N LYS K 159 " --> pdb=" O CYS K 95 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ILE K 233 " --> pdb=" O LEU K 92 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ASN K 237 " --> pdb=" O PHE K 96 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N PHE K 234 " --> pdb=" O PHE K 265 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP K 267 " --> pdb=" O PHE K 234 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE K 236 " --> pdb=" O ASP K 267 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ILE K 295 " --> pdb=" O VAL K 355 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N THR K 357 " --> pdb=" O ILE K 295 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL K 297 " --> pdb=" O THR K 357 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 206 through 211 removed outlier: 6.715A pdb=" N ARG K 195 " --> pdb=" O VAL K 210 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR O 153 " --> pdb=" O PHE O 103 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE O 100 " --> pdb=" O VAL O 132 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL O 134 " --> pdb=" O ILE O 100 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP O 102 " --> pdb=" O VAL O 134 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG O 80 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N ASP O 135 " --> pdb=" O ARG O 80 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'L' and resid 73 through 74 Processing sheet with id=AF2, first strand: chain 'L' and resid 89 through 90 removed outlier: 3.595A pdb=" N ARG L 117 " --> pdb=" O SER L 308 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL L 306 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU L 121 " --> pdb=" O LEU L 304 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU L 304 " --> pdb=" O GLU L 121 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 138 through 139 removed outlier: 3.566A pdb=" N THR L 129 " --> pdb=" O PHE L 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 286 through 287 removed outlier: 6.042A pdb=" N ASN L 286 " --> pdb=" O ILE L 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'L' and resid 357 through 358 removed outlier: 6.323A pdb=" N ILE L 357 " --> pdb=" O TRP L 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF5 Processing sheet with id=AF6, first strand: chain 'L' and resid 368 through 369 Processing sheet with id=AF7, first strand: chain 'L' and resid 448 through 449 Processing sheet with id=AF8, first strand: chain 'M' and resid 141 through 145 removed outlier: 6.921A pdb=" N GLU M 168 " --> pdb=" O ARG M 154 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N ARG M 194 " --> pdb=" O LYS M 231 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N LYS M 231 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ALA M 196 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N LEU M 229 " --> pdb=" O ALA M 196 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER M 198 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N VAL M 227 " --> pdb=" O SER M 198 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N TYR M 200 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 14.002A pdb=" N GLU M 223 " --> pdb=" O ASP M 254 " (cutoff:3.500A) removed outlier: 11.889A pdb=" N ASP M 254 " --> pdb=" O GLU M 223 " (cutoff:3.500A) removed outlier: 11.196A pdb=" N SER M 225 " --> pdb=" O VAL M 252 " (cutoff:3.500A) removed outlier: 9.727A pdb=" N VAL M 252 " --> pdb=" O SER M 225 " (cutoff:3.500A) removed outlier: 10.396A pdb=" N VAL M 227 " --> pdb=" O ILE M 250 " (cutoff:3.500A) removed outlier: 9.445A pdb=" N ILE M 250 " --> pdb=" O VAL M 227 " (cutoff:3.500A) removed outlier: 10.900A pdb=" N LEU M 229 " --> pdb=" O GLU M 248 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N GLU M 248 " --> pdb=" O LEU M 229 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS M 231 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG M 183 " --> pdb=" O ILE M 260 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N ARG M 262 " --> pdb=" O ARG M 183 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'N' and resid 199 through 206 removed outlier: 3.566A pdb=" N LYS N 199 " --> pdb=" O LYS N 179 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY N 172 " --> pdb=" O ASP N 223 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ASP N 223 " --> pdb=" O GLY N 172 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N THR N 174 " --> pdb=" O THR N 221 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N THR N 221 " --> pdb=" O THR N 174 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU N 176 " --> pdb=" O LEU N 219 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'P' and resid 80 through 81 removed outlier: 6.354A pdb=" N ARG P 80 " --> pdb=" O LYS P 133 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASP P 135 " --> pdb=" O ARG P 80 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N ILE P 100 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N VAL P 134 " --> pdb=" O ILE P 100 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASP P 102 " --> pdb=" O VAL P 134 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR P 153 " --> pdb=" O PHE P 103 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR S 305 " --> pdb=" O VAL S 319 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'Q' and resid 578 through 579 removed outlier: 6.661A pdb=" N GLY Q 587 " --> pdb=" O VAL Q 714 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N VAL Q 716 " --> pdb=" O GLY Q 587 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ILE Q 589 " --> pdb=" O VAL Q 716 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE Q 615 " --> pdb=" O VAL Q 715 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE Q 614 " --> pdb=" O VAL Q 642 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N MET Q 644 " --> pdb=" O ILE Q 614 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR Q 616 " --> pdb=" O MET Q 644 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N THR Q 646 " --> pdb=" O THR Q 616 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ILE Q 618 " --> pdb=" O THR Q 646 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N ASP Q 648 " --> pdb=" O ILE Q 618 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS Q 620 " --> pdb=" O ASP Q 648 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N THR Q 643 " --> pdb=" O PHE Q 692 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Q' and resid 724 through 727 Processing sheet with id=AG4, first strand: chain 'S' and resid 293 through 296 removed outlier: 6.488A pdb=" N LYS S 294 " --> pdb=" O PHE S 266 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N GLY S 268 " --> pdb=" O LYS S 294 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N ASP S 296 " --> pdb=" O GLY S 268 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU S 270 " --> pdb=" O ASP S 296 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU S 202 " --> pdb=" O MET S 342 " (cutoff:3.500A) removed outlier: 8.240A pdb=" N TYR S 344 " --> pdb=" O LEU S 202 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N CYS S 204 " --> pdb=" O TYR S 344 " (cutoff:3.500A) removed outlier: 8.514A pdb=" N THR S 346 " --> pdb=" O CYS S 204 " (cutoff:3.500A) removed outlier: 8.171A pdb=" N PHE S 206 " --> pdb=" O THR S 346 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N PHE S 343 " --> pdb=" O PHE S 374 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP S 376 " --> pdb=" O PHE S 343 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N PHE S 345 " --> pdb=" O ASP S 376 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE S 404 " --> pdb=" O PHE S 453 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N THR S 455 " --> pdb=" O ILE S 404 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL S 406 " --> pdb=" O THR S 455 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 218 through 219 Processing sheet with id=AG6, first strand: chain 'T' and resid 48 through 49 removed outlier: 3.602A pdb=" N LYS T 48 " --> pdb=" O ARG T 113 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N SER T 129 " --> pdb=" O GLU T 89 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER T 67 " --> pdb=" O TYR T 132 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'T' and resid 74 through 79 2452 hydrogen bonds defined for protein. 6792 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: 24.42 Time building geometry restraints manager: 12.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 17821 1.34 - 1.46: 11233 1.46 - 1.58: 25934 1.58 - 1.70: 1 1.70 - 1.81: 443 Bond restraints: 55432 Sorted by residual: bond pdb=" C2 SAH L8001 " pdb=" N3 SAH L8001 " ideal model delta sigma weight residual 1.322 1.378 -0.056 2.00e-02 2.50e+03 7.75e+00 bond pdb=" C8 SAH L8001 " pdb=" N7 SAH L8001 " ideal model delta sigma weight residual 1.299 1.348 -0.049 2.00e-02 2.50e+03 5.96e+00 bond pdb=" C2 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.330 1.377 -0.047 2.00e-02 2.50e+03 5.53e+00 bond pdb=" C6 SAH L8001 " pdb=" N1 SAH L8001 " ideal model delta sigma weight residual 1.338 1.376 -0.038 2.00e-02 2.50e+03 3.62e+00 bond pdb=" CB PRO E1183 " pdb=" CG PRO E1183 " ideal model delta sigma weight residual 1.492 1.586 -0.094 5.00e-02 4.00e+02 3.54e+00 ... (remaining 55427 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 74341 1.99 - 3.98: 531 3.98 - 5.97: 49 5.97 - 7.96: 4 7.96 - 9.95: 4 Bond angle restraints: 74929 Sorted by residual: angle pdb=" C PHE B 226 " pdb=" N ILE B 227 " pdb=" CA ILE B 227 " ideal model delta sigma weight residual 120.24 122.95 -2.71 6.30e-01 2.52e+00 1.84e+01 angle pdb=" N PRO E1183 " pdb=" CA PRO E1183 " pdb=" C PRO E1183 " ideal model delta sigma weight residual 112.47 119.60 -7.13 2.06e+00 2.36e-01 1.20e+01 angle pdb=" CA PRO E1183 " pdb=" N PRO E1183 " pdb=" CD PRO E1183 " ideal model delta sigma weight residual 112.00 107.23 4.77 1.40e+00 5.10e-01 1.16e+01 angle pdb=" CG SAH L8001 " pdb=" SD SAH L8001 " pdb=" C5' SAH L8001 " ideal model delta sigma weight residual 101.77 91.82 9.95 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C LEU A 250 " pdb=" N PHE A 251 " pdb=" CA PHE A 251 " ideal model delta sigma weight residual 120.09 124.03 -3.94 1.25e+00 6.40e-01 9.96e+00 ... (remaining 74924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 31423 17.97 - 35.93: 1555 35.93 - 53.90: 324 53.90 - 71.86: 86 71.86 - 89.83: 31 Dihedral angle restraints: 33419 sinusoidal: 14009 harmonic: 19410 Sorted by residual: dihedral pdb=" CA GLU F 418 " pdb=" C GLU F 418 " pdb=" N PRO F 419 " pdb=" CA PRO F 419 " ideal model delta harmonic sigma weight residual 180.00 129.23 50.77 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA ILE F 417 " pdb=" C ILE F 417 " pdb=" N GLU F 418 " pdb=" CA GLU F 418 " ideal model delta harmonic sigma weight residual -180.00 -155.00 -25.00 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" CA TRP I 178 " pdb=" C TRP I 178 " pdb=" N LEU I 179 " pdb=" CA LEU I 179 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 33416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 6716 0.053 - 0.106: 1201 0.106 - 0.158: 194 0.158 - 0.211: 2 0.211 - 0.264: 1 Chirality restraints: 8114 Sorted by residual: chirality pdb=" CA PRO E1183 " pdb=" N PRO E1183 " pdb=" C PRO E1183 " pdb=" CB PRO E1183 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA PRO B 125 " pdb=" N PRO B 125 " pdb=" C PRO B 125 " pdb=" CB PRO B 125 " both_signs ideal model delta sigma weight residual False 2.72 2.55 0.17 2.00e-01 2.50e+01 6.87e-01 chirality pdb=" CA ILE H 305 " pdb=" N ILE H 305 " pdb=" C ILE H 305 " pdb=" CB ILE H 305 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.42e-01 ... (remaining 8111 not shown) Planarity restraints: 9663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E1182 " -0.076 5.00e-02 4.00e+02 1.14e-01 2.09e+01 pdb=" N PRO E1183 " 0.197 5.00e-02 4.00e+02 pdb=" CA PRO E1183 " -0.061 5.00e-02 4.00e+02 pdb=" CD PRO E1183 " -0.061 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU F 418 " 0.040 5.00e-02 4.00e+02 6.00e-02 5.76e+00 pdb=" N PRO F 419 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO F 419 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO F 419 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY O 109 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO O 110 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO O 110 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 110 " -0.025 5.00e-02 4.00e+02 ... (remaining 9660 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 492 2.61 - 3.19: 46145 3.19 - 3.76: 86322 3.76 - 4.33: 127698 4.33 - 4.90: 202190 Nonbonded interactions: 462847 Sorted by model distance: nonbonded pdb=" NE2 HIS N 227 " pdb="FE FE N8001 " model vdw 2.042 2.340 nonbonded pdb=" OD2 ASP N 223 " pdb="FE FE N8001 " model vdw 2.058 2.260 nonbonded pdb=" NE2 HIS I 127 " pdb="FE FE I8001 " model vdw 2.080 2.340 nonbonded pdb="FE FE I8001 " pdb=" O HOH I8104 " model vdw 2.116 2.260 nonbonded pdb=" OD2 ASP C 851 " pdb=" O HOH C1101 " model vdw 2.182 3.040 ... (remaining 462842 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 'O' and resid 78 through 185) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 7.890 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: 0.090 Extract box with map and model: 2.260 Check model and map are aligned: 0.300 Set scattering table: 0.380 Process input model: 108.420 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.210 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:14.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.010 Internal consistency checks: 0.000 Total: 134.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.002 0.094 55432 Z= 0.152 Angle : 0.455 9.946 74929 Z= 0.240 Chirality : 0.041 0.264 8114 Planarity : 0.004 0.114 9663 Dihedral : 11.765 89.831 20873 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.44 % Allowed : 4.49 % Favored : 95.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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 (0.10), residues: 6525 helix: 0.47 (0.10), residues: 2769 sheet: 0.40 (0.17), residues: 877 loop : 0.13 (0.12), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 127 HIS 0.005 0.001 HIS M 142 PHE 0.012 0.001 PHE E1284 TYR 0.013 0.001 TYR C 681 ARG 0.003 0.000 ARG S 244 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 823 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 797 time to evaluate : 4.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 21 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7324 (tp30) REVERT: C 366 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7805 (mp0) REVERT: C 595 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7141 (mt-10) REVERT: D 298 ARG cc_start: 0.7520 (ttm-80) cc_final: 0.7267 (mtt-85) REVERT: D 345 MET cc_start: 0.4521 (mtp) cc_final: 0.4309 (mtt) REVERT: E 330 GLU cc_start: 0.7588 (tt0) cc_final: 0.7265 (tm-30) REVERT: E 579 ILE cc_start: 0.8430 (mt) cc_final: 0.8145 (mp) REVERT: E 610 ARG cc_start: 0.6653 (ptt-90) cc_final: 0.6392 (ptt-90) REVERT: E 861 GLU cc_start: 0.7486 (tt0) cc_final: 0.7186 (tm-30) REVERT: G 445 TYR cc_start: 0.7231 (t80) cc_final: 0.6960 (t80) REVERT: G 541 PHE cc_start: 0.7491 (m-80) cc_final: 0.7059 (t80) REVERT: G 586 MET cc_start: 0.6851 (mtt) cc_final: 0.6537 (mtp) REVERT: G 596 MET cc_start: 0.7565 (mtm) cc_final: 0.6809 (mtm) REVERT: G 620 GLU cc_start: 0.6729 (tt0) cc_final: 0.6356 (tp30) REVERT: G 624 ASN cc_start: 0.1998 (OUTLIER) cc_final: 0.1479 (m-40) REVERT: H 416 MET cc_start: 0.7881 (ptp) cc_final: 0.7648 (ptm) REVERT: J 287 ARG cc_start: 0.9214 (OUTLIER) cc_final: 0.7996 (mtm110) REVERT: K 280 GLU cc_start: 0.7244 (pp20) cc_final: 0.7034 (pp20) REVERT: L 87 ARG cc_start: 0.8080 (OUTLIER) cc_final: 0.7759 (tmt-80) REVERT: N 70 ASP cc_start: 0.8101 (m-30) cc_final: 0.7682 (m-30) REVERT: P 174 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8359 (tp) REVERT: P 184 ASP cc_start: 0.7671 (p0) cc_final: 0.7432 (p0) REVERT: R 37 GLN cc_start: 0.7476 (tm-30) cc_final: 0.7101 (tm-30) REVERT: S 355 MET cc_start: 0.8392 (tpt) cc_final: 0.7968 (tpt) REVERT: T 48 LYS cc_start: 0.8375 (tttt) cc_final: 0.8127 (tmmt) outliers start: 26 outliers final: 10 residues processed: 817 average time/residue: 1.6880 time to fit residues: 1673.2210 Evaluate side-chains 662 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 648 time to evaluate : 4.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain G residue 624 ASN Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain J residue 287 ARG Chi-restraints excluded: chain L residue 87 ARG Chi-restraints excluded: chain O residue 128 ASN Chi-restraints excluded: chain P residue 174 LEU Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain S residue 562 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 556 optimal weight: 0.9980 chunk 499 optimal weight: 0.9980 chunk 277 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 336 optimal weight: 20.0000 chunk 266 optimal weight: 8.9990 chunk 516 optimal weight: 0.7980 chunk 199 optimal weight: 7.9990 chunk 314 optimal weight: 20.0000 chunk 384 optimal weight: 9.9990 chunk 598 optimal weight: 1.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 76 ASN A 105 ASN A 196 GLN B 132 ASN B 196 GLN B 216 HIS C 19 GLN C 322 GLN C 465 GLN C 623 HIS D 324 GLN D 417 GLN D 518 ASN E 370 HIS E 398 HIS E 863 ASN E1027 ASN E1032 ASN E1212 GLN E1282 GLN E1291 GLN F 123 GLN F 495 GLN F 838 HIS G 529 ASN G 624 ASN G 754 GLN G 777 HIS H 142 GLN H 308 ASN ** H 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 111 ASN J 329 GLN K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 438 GLN N 242 ASN O 85 GLN O 183 ASN P 88 GLN Q 751 HIS R 114 ASN S 361 GLN T 81 GLN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.076049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058888 restraints weight = 129795.963| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.72 r_work: 0.2812 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2680 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 55432 Z= 0.191 Angle : 0.536 13.334 74929 Z= 0.286 Chirality : 0.043 0.314 8114 Planarity : 0.005 0.150 9663 Dihedral : 4.910 56.695 7355 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.80 % Favored : 97.15 % Rotamer: Outliers : 1.46 % Allowed : 7.98 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.95 (0.10), residues: 6525 helix: 1.25 (0.10), residues: 2812 sheet: 0.52 (0.17), residues: 841 loop : 0.17 (0.12), residues: 2872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 127 HIS 0.007 0.001 HIS M 142 PHE 0.017 0.001 PHE L 150 TYR 0.021 0.001 TYR G 458 ARG 0.008 0.000 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 795 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 709 time to evaluate : 4.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7930 (OUTLIER) cc_final: 0.7654 (ptpp) REVERT: C 25 ARG cc_start: 0.8495 (ttp80) cc_final: 0.8148 (tmm160) REVERT: C 79 GLU cc_start: 0.7250 (mp0) cc_final: 0.6869 (mp0) REVERT: C 108 ASN cc_start: 0.7292 (t0) cc_final: 0.7010 (t0) REVERT: C 366 GLU cc_start: 0.8348 (mm-30) cc_final: 0.8074 (mp0) REVERT: C 622 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7547 (mtp) REVERT: C 923 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8766 (p90) REVERT: D 221 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7941 (tm-30) REVERT: D 236 LYS cc_start: 0.7942 (tptp) cc_final: 0.7705 (tppt) REVERT: D 330 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7640 (tm-30) REVERT: E 330 GLU cc_start: 0.8076 (tt0) cc_final: 0.7721 (tt0) REVERT: E 579 ILE cc_start: 0.8328 (mt) cc_final: 0.8023 (mp) REVERT: E 610 ARG cc_start: 0.6625 (ptt-90) cc_final: 0.6360 (ptt-90) REVERT: E 861 GLU cc_start: 0.7910 (tt0) cc_final: 0.7085 (tm-30) REVERT: E 868 ILE cc_start: 0.8118 (mm) cc_final: 0.7805 (mm) REVERT: E 1123 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8589 (mp) REVERT: F 844 PHE cc_start: 0.7610 (m-10) cc_final: 0.7338 (m-10) REVERT: G 445 TYR cc_start: 0.6797 (t80) cc_final: 0.6589 (t80) REVERT: G 596 MET cc_start: 0.7097 (mtm) cc_final: 0.6695 (mtm) REVERT: G 620 GLU cc_start: 0.6761 (tt0) cc_final: 0.6393 (tp30) REVERT: G 691 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7241 (mm-30) REVERT: G 721 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8182 (ttp) REVERT: K 280 GLU cc_start: 0.7346 (pp20) cc_final: 0.6983 (pp20) REVERT: L 87 ARG cc_start: 0.8334 (tpt90) cc_final: 0.8037 (tmt-80) REVERT: N 49 GLU cc_start: 0.7114 (OUTLIER) cc_final: 0.6789 (pp20) REVERT: N 66 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7518 (ttt90) REVERT: P 184 ASP cc_start: 0.7707 (p0) cc_final: 0.7428 (p0) REVERT: R 37 GLN cc_start: 0.7602 (tm-30) cc_final: 0.7116 (tm-30) REVERT: R 94 ASP cc_start: 0.8318 (m-30) cc_final: 0.8072 (p0) REVERT: S 355 MET cc_start: 0.8406 (tpt) cc_final: 0.8034 (tpt) REVERT: T 48 LYS cc_start: 0.8774 (tttt) cc_final: 0.8301 (tmmt) outliers start: 86 outliers final: 33 residues processed: 754 average time/residue: 1.7100 time to fit residues: 1566.7503 Evaluate side-chains 674 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 634 time to evaluate : 4.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 32 ILE Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 622 MET Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 56 SER Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1123 LEU Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain N residue 49 GLU Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 224 THR Chi-restraints excluded: chain N residue 260 SER Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 638 GLU Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain S residue 194 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 278 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 284 optimal weight: 7.9990 chunk 398 optimal weight: 2.9990 chunk 238 optimal weight: 3.9990 chunk 455 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 294 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 630 optimal weight: 0.7980 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN B 132 ASN D 324 GLN E 398 HIS E1038 ASN E1282 GLN F 123 GLN G 777 HIS H 308 ASN I 111 ASN J 184 ASN J 244 GLN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN O 183 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.075022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.057745 restraints weight = 129863.001| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 1.73 r_work: 0.2770 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 55432 Z= 0.304 Angle : 0.591 11.319 74929 Z= 0.315 Chirality : 0.046 0.291 8114 Planarity : 0.005 0.124 9663 Dihedral : 5.009 58.660 7339 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.26 % Favored : 96.70 % Rotamer: Outliers : 1.66 % Allowed : 9.31 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.96 (0.10), residues: 6525 helix: 1.39 (0.10), residues: 2812 sheet: 0.42 (0.17), residues: 848 loop : 0.06 (0.12), residues: 2865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 127 HIS 0.008 0.001 HIS I 127 PHE 0.025 0.002 PHE K 103 TYR 0.018 0.002 TYR M 251 ARG 0.007 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 679 time to evaluate : 4.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7907 (OUTLIER) cc_final: 0.7608 (ptpp) REVERT: C 21 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7746 (tp30) REVERT: C 25 ARG cc_start: 0.8469 (ttp80) cc_final: 0.8132 (ttm-80) REVERT: C 79 GLU cc_start: 0.7207 (mp0) cc_final: 0.6823 (mp0) REVERT: C 323 ASP cc_start: 0.8111 (t0) cc_final: 0.7782 (t0) REVERT: C 366 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8086 (mp0) REVERT: C 622 MET cc_start: 0.7976 (mtt) cc_final: 0.7563 (mtp) REVERT: C 923 TYR cc_start: 0.9096 (OUTLIER) cc_final: 0.8823 (p90) REVERT: D 12 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (pp) REVERT: D 221 GLN cc_start: 0.8494 (tm-30) cc_final: 0.7979 (tm-30) REVERT: D 236 LYS cc_start: 0.7942 (tptp) cc_final: 0.7709 (tppt) REVERT: D 330 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7611 (tm-30) REVERT: E 579 ILE cc_start: 0.8290 (mt) cc_final: 0.7991 (mp) REVERT: E 610 ARG cc_start: 0.6658 (ptt-90) cc_final: 0.6362 (ptt-90) REVERT: E 861 GLU cc_start: 0.7931 (tt0) cc_final: 0.7022 (tm-30) REVERT: F 392 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7494 (ttm-80) REVERT: F 442 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8647 (mt) REVERT: G 620 GLU cc_start: 0.6684 (tt0) cc_final: 0.6270 (tp30) REVERT: G 691 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7207 (mm-30) REVERT: G 721 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.8194 (ttp) REVERT: G 793 MET cc_start: 0.8211 (tmm) cc_final: 0.7896 (tmm) REVERT: L 87 ARG cc_start: 0.8420 (tpt90) cc_final: 0.8197 (tmt-80) REVERT: L 159 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7699 (tp30) REVERT: L 440 GLN cc_start: 0.8081 (tp40) cc_final: 0.7207 (tm-30) REVERT: N 66 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7670 (ttt90) REVERT: N 267 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7867 (tm-30) REVERT: O 169 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: P 184 ASP cc_start: 0.7637 (p0) cc_final: 0.7326 (p0) REVERT: R 37 GLN cc_start: 0.7577 (tm-30) cc_final: 0.7318 (tm-30) REVERT: R 112 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7585 (mp0) REVERT: S 353 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7710 (mmmt) REVERT: T 48 LYS cc_start: 0.8813 (tttt) cc_final: 0.8350 (tmmt) REVERT: T 121 ASP cc_start: 0.8312 (m-30) cc_final: 0.8085 (m-30) outliers start: 98 outliers final: 40 residues processed: 738 average time/residue: 1.7209 time to fit residues: 1541.3086 Evaluate side-chains 689 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 638 time to evaluate : 4.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 205 ASP Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 318 GLU Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 159 GLU Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 214 TRP Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 126 GLU Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 353 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 103 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 561 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 chunk 454 optimal weight: 0.0980 chunk 605 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 584 optimal weight: 9.9990 chunk 420 optimal weight: 9.9990 chunk 251 optimal weight: 1.9990 overall best weight: 6.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 303 GLN B 132 ASN E 398 HIS F 495 GLN G 777 HIS H 308 ASN I 111 ASN ** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.074343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.057105 restraints weight = 129680.509| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.72 r_work: 0.2749 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 55432 Z= 0.463 Angle : 0.688 12.518 74929 Z= 0.367 Chirality : 0.051 0.285 8114 Planarity : 0.006 0.118 9663 Dihedral : 5.356 63.602 7339 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.33 % Favored : 96.64 % Rotamer: Outliers : 1.98 % Allowed : 10.00 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.70 (0.10), residues: 6525 helix: 1.19 (0.10), residues: 2817 sheet: 0.32 (0.17), residues: 825 loop : -0.11 (0.11), residues: 2883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 127 HIS 0.009 0.002 HIS I 127 PHE 0.031 0.003 PHE K 103 TYR 0.021 0.003 TYR M 251 ARG 0.007 0.001 ARG J 247 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 783 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 666 time to evaluate : 4.834 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.6518 (OUTLIER) cc_final: 0.6288 (mp) REVERT: A 319 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7650 (ptpp) REVERT: B 110 VAL cc_start: 0.8469 (t) cc_final: 0.8142 (m) REVERT: C 21 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7791 (tp30) REVERT: C 25 ARG cc_start: 0.8465 (ttp80) cc_final: 0.8132 (tmm160) REVERT: C 79 GLU cc_start: 0.7192 (mp0) cc_final: 0.6777 (mp0) REVERT: C 323 ASP cc_start: 0.8139 (t0) cc_final: 0.7789 (t0) REVERT: C 366 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7966 (mp0) REVERT: C 599 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7799 (tp) REVERT: C 923 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.8868 (p90) REVERT: D 12 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8697 (pp) REVERT: D 221 GLN cc_start: 0.8506 (tm-30) cc_final: 0.8032 (tm-30) REVERT: D 330 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7591 (tm-30) REVERT: E 579 ILE cc_start: 0.8307 (mt) cc_final: 0.8013 (mp) REVERT: E 861 GLU cc_start: 0.7958 (tt0) cc_final: 0.7033 (tm-30) REVERT: E 1135 GLU cc_start: 0.6116 (tm-30) cc_final: 0.4988 (tt0) REVERT: F 392 ARG cc_start: 0.7968 (OUTLIER) cc_final: 0.7470 (ttm-80) REVERT: F 442 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8672 (mt) REVERT: G 620 GLU cc_start: 0.6662 (tt0) cc_final: 0.6293 (tp30) REVERT: G 691 GLU cc_start: 0.7647 (mm-30) cc_final: 0.7342 (mm-30) REVERT: G 721 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8288 (ttp) REVERT: G 793 MET cc_start: 0.8145 (tmm) cc_final: 0.7868 (tmm) REVERT: K 412 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7983 (pt0) REVERT: L 440 GLN cc_start: 0.8092 (tp40) cc_final: 0.7238 (tm-30) REVERT: N 66 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7719 (ttt90) REVERT: N 267 GLN cc_start: 0.8069 (tm-30) cc_final: 0.7790 (tm-30) REVERT: O 169 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: P 184 ASP cc_start: 0.7552 (p0) cc_final: 0.7266 (p0) REVERT: R 37 GLN cc_start: 0.7537 (tm-30) cc_final: 0.7305 (tm-30) REVERT: R 112 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: S 353 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7742 (mmmt) REVERT: S 355 MET cc_start: 0.8549 (tpt) cc_final: 0.8139 (tpt) REVERT: S 587 MET cc_start: 0.6164 (OUTLIER) cc_final: 0.5737 (mtm) REVERT: T 48 LYS cc_start: 0.8859 (tttt) cc_final: 0.8408 (tmmt) REVERT: T 75 LYS cc_start: 0.8999 (tttm) cc_final: 0.8765 (tttm) outliers start: 117 outliers final: 57 residues processed: 740 average time/residue: 1.7122 time to fit residues: 1537.4313 Evaluate side-chains 710 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 639 time to evaluate : 4.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 105 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 471 LEU Chi-restraints excluded: chain C residue 508 LEU Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 646 THR Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 175 ILE Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 808 ILE Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain E residue 1266 CYS Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 392 ARG Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain F residue 836 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain H residue 378 CYS Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain J residue 427 ILE Chi-restraints excluded: chain K residue 248 SER Chi-restraints excluded: chain K residue 277 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain K residue 412 GLU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 139 ASP Chi-restraints excluded: chain M residue 244 VAL Chi-restraints excluded: chain M residue 256 LYS Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 214 TRP Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 120 MET Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 98 GLU Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 353 LYS Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 566 optimal weight: 4.9990 chunk 453 optimal weight: 10.0000 chunk 521 optimal weight: 0.0040 chunk 263 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 154 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 320 optimal weight: 5.9990 chunk 120 optimal weight: 0.8980 chunk 603 optimal weight: 0.7980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 180 GLN B 132 ASN C1056 ASN D 553 ASN E 398 HIS E1282 GLN G 777 HIS H 308 ASN I 68 GLN I 111 ASN I 159 ASN J 297 GLN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN S 277 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.076185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058841 restraints weight = 129870.074| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.75 r_work: 0.2818 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 55432 Z= 0.147 Angle : 0.493 9.552 74929 Z= 0.264 Chirality : 0.042 0.258 8114 Planarity : 0.004 0.116 9663 Dihedral : 4.762 59.017 7339 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.54 % Favored : 97.41 % Rotamer: Outliers : 1.32 % Allowed : 11.12 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.14 (0.10), residues: 6525 helix: 1.63 (0.10), residues: 2805 sheet: 0.35 (0.17), residues: 835 loop : 0.11 (0.12), residues: 2885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP K 127 HIS 0.006 0.001 HIS F 344 PHE 0.017 0.001 PHE L 150 TYR 0.017 0.001 TYR E 998 ARG 0.008 0.000 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 674 time to evaluate : 4.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7944 (ptpp) cc_final: 0.7704 (ptpt) REVERT: C 21 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7703 (tp30) REVERT: C 25 ARG cc_start: 0.8462 (ttp80) cc_final: 0.8165 (tmm160) REVERT: C 79 GLU cc_start: 0.7177 (mp0) cc_final: 0.6700 (mp0) REVERT: C 323 ASP cc_start: 0.8141 (t0) cc_final: 0.7886 (t0) REVERT: C 366 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7978 (mp0) REVERT: C 622 MET cc_start: 0.7896 (mtt) cc_final: 0.7505 (mtp) REVERT: D 12 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8471 (pp) REVERT: D 221 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8034 (tm-30) REVERT: D 330 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7536 (tm-30) REVERT: D 354 LYS cc_start: 0.6960 (mttt) cc_final: 0.6207 (ptmm) REVERT: E 191 ASP cc_start: 0.7068 (m-30) cc_final: 0.6588 (m-30) REVERT: E 579 ILE cc_start: 0.8300 (mt) cc_final: 0.8019 (mp) REVERT: E 861 GLU cc_start: 0.7931 (tt0) cc_final: 0.7017 (tm-30) REVERT: F 442 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8611 (mt) REVERT: G 620 GLU cc_start: 0.6722 (tt0) cc_final: 0.6381 (tp30) REVERT: G 691 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7270 (mm-30) REVERT: G 721 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: G 763 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6823 (mp0) REVERT: G 793 MET cc_start: 0.8215 (tmm) cc_final: 0.7820 (tmm) REVERT: H 148 ASP cc_start: 0.8225 (m-30) cc_final: 0.7758 (m-30) REVERT: K 167 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: L 212 GLN cc_start: 0.8439 (mp10) cc_final: 0.8120 (mt0) REVERT: L 410 ILE cc_start: 0.8191 (mm) cc_final: 0.7946 (tp) REVERT: L 440 GLN cc_start: 0.8034 (tp40) cc_final: 0.7045 (tm130) REVERT: N 264 ARG cc_start: 0.8346 (OUTLIER) cc_final: 0.8085 (tmt170) REVERT: N 267 GLN cc_start: 0.8100 (tm-30) cc_final: 0.7828 (tm-30) REVERT: N 269 GLU cc_start: 0.7243 (mt-10) cc_final: 0.7029 (mt-10) REVERT: P 184 ASP cc_start: 0.7600 (p0) cc_final: 0.7285 (p0) REVERT: Q 766 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6903 (pm20) REVERT: R 37 GLN cc_start: 0.7474 (tm-30) cc_final: 0.7248 (tm-30) REVERT: R 112 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: S 353 LYS cc_start: 0.8044 (mmmt) cc_final: 0.7837 (tptp) REVERT: S 587 MET cc_start: 0.6112 (OUTLIER) cc_final: 0.5651 (mtm) REVERT: T 48 LYS cc_start: 0.8810 (tttt) cc_final: 0.8329 (tmmt) REVERT: T 75 LYS cc_start: 0.8929 (tttm) cc_final: 0.8681 (tttm) REVERT: T 121 ASP cc_start: 0.8294 (m-30) cc_final: 0.8013 (t70) outliers start: 78 outliers final: 24 residues processed: 725 average time/residue: 1.7573 time to fit residues: 1541.0697 Evaluate side-chains 659 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 626 time to evaluate : 4.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 763 GLU Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 139 ASP Chi-restraints excluded: chain N residue 69 LEU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain Q residue 766 GLU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 180 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 493 optimal weight: 3.9990 chunk 296 optimal weight: 10.0000 chunk 348 optimal weight: 7.9990 chunk 597 optimal weight: 10.0000 chunk 190 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 310 optimal weight: 5.9990 chunk 359 optimal weight: 7.9990 chunk 223 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 111 GLN B 132 ASN C 505 GLN E1151 GLN E1282 GLN F 123 GLN G 777 HIS G 801 GLN H 308 ASN I 111 ASN J 244 GLN ** J 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN T 105 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.074804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.057581 restraints weight = 129554.325| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.73 r_work: 0.2763 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2628 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 55432 Z= 0.340 Angle : 0.607 11.340 74929 Z= 0.324 Chirality : 0.047 0.276 8114 Planarity : 0.005 0.117 9663 Dihedral : 5.088 60.983 7338 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 1.64 % Allowed : 11.07 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.99 (0.10), residues: 6525 helix: 1.49 (0.10), residues: 2813 sheet: 0.35 (0.17), residues: 835 loop : 0.01 (0.11), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 127 HIS 0.008 0.001 HIS C 689 PHE 0.028 0.002 PHE B 226 TYR 0.019 0.002 TYR M 251 ARG 0.007 0.001 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 647 time to evaluate : 4.887 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 ILE cc_start: 0.6474 (OUTLIER) cc_final: 0.6273 (mp) REVERT: A 319 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7659 (ptpp) REVERT: C 21 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7721 (tp30) REVERT: C 79 GLU cc_start: 0.7181 (mp0) cc_final: 0.6747 (mp0) REVERT: C 323 ASP cc_start: 0.8141 (t0) cc_final: 0.7864 (t0) REVERT: C 366 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7960 (mp0) REVERT: C 599 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7818 (tp) REVERT: C 923 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8864 (p90) REVERT: D 12 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8634 (pp) REVERT: D 221 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8064 (tm-30) REVERT: D 330 GLU cc_start: 0.7876 (tm-30) cc_final: 0.7584 (tm-30) REVERT: D 354 LYS cc_start: 0.6934 (mttt) cc_final: 0.6355 (mtpp) REVERT: E 436 GLU cc_start: 0.3637 (pm20) cc_final: 0.3211 (pm20) REVERT: E 579 ILE cc_start: 0.8298 (mt) cc_final: 0.8015 (mp) REVERT: E 861 GLU cc_start: 0.7948 (tt0) cc_final: 0.7024 (tm-30) REVERT: E 1029 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8123 (mtm-85) REVERT: F 206 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8683 (mtp) REVERT: F 442 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8647 (mt) REVERT: G 620 GLU cc_start: 0.6730 (tt0) cc_final: 0.6359 (tp30) REVERT: G 691 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7296 (mm-30) REVERT: G 721 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8278 (ttp) REVERT: G 763 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: G 793 MET cc_start: 0.8188 (tmm) cc_final: 0.7819 (tmm) REVERT: H 366 ASP cc_start: 0.7875 (p0) cc_final: 0.7572 (t70) REVERT: K 280 GLU cc_start: 0.7293 (pp20) cc_final: 0.7010 (pp20) REVERT: L 440 GLN cc_start: 0.8064 (tp40) cc_final: 0.7860 (tp-100) REVERT: N 66 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.7680 (ttt90) REVERT: N 267 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7842 (tm-30) REVERT: N 269 GLU cc_start: 0.7288 (mt-10) cc_final: 0.7001 (mt-10) REVERT: O 169 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7715 (mt-10) REVERT: P 184 ASP cc_start: 0.7570 (p0) cc_final: 0.7248 (p0) REVERT: Q 766 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6895 (pm20) REVERT: R 37 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7138 (tm-30) REVERT: R 112 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7518 (mp0) REVERT: S 353 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7751 (mmmt) REVERT: S 587 MET cc_start: 0.6106 (OUTLIER) cc_final: 0.5668 (mtm) REVERT: T 48 LYS cc_start: 0.8837 (tttt) cc_final: 0.8366 (tmmt) REVERT: T 121 ASP cc_start: 0.8336 (m-30) cc_final: 0.8084 (m-30) outliers start: 97 outliers final: 40 residues processed: 702 average time/residue: 1.7356 time to fit residues: 1481.2354 Evaluate side-chains 692 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 636 time to evaluate : 4.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 137 LEU Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain E residue 1236 GLU Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 763 GLU Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 139 ASP Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain Q residue 766 GLU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 353 LYS Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 495 optimal weight: 6.9990 chunk 651 optimal weight: 8.9990 chunk 12 optimal weight: 0.1980 chunk 409 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 612 optimal weight: 3.9990 chunk 160 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 chunk 437 optimal weight: 0.9990 chunk 196 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 111 GLN B 132 ASN D 324 GLN E1151 GLN E1282 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.075375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.058145 restraints weight = 129215.183| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.72 r_work: 0.2782 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 55432 Z= 0.219 Angle : 0.541 11.166 74929 Z= 0.289 Chirality : 0.044 0.268 8114 Planarity : 0.004 0.116 9663 Dihedral : 4.924 59.476 7338 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.94 % Favored : 97.01 % Rotamer: Outliers : 1.34 % Allowed : 11.71 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.08 (0.10), residues: 6525 helix: 1.59 (0.10), residues: 2825 sheet: 0.34 (0.17), residues: 857 loop : 0.05 (0.12), residues: 2843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP K 127 HIS 0.007 0.001 HIS F 344 PHE 0.021 0.001 PHE L 150 TYR 0.016 0.001 TYR D 649 ARG 0.010 0.000 ARG T 56 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 646 time to evaluate : 4.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7718 (ptpt) REVERT: C 21 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7683 (tp30) REVERT: C 25 ARG cc_start: 0.8451 (ttp80) cc_final: 0.8156 (tmm160) REVERT: C 79 GLU cc_start: 0.7163 (mp0) cc_final: 0.6718 (mp0) REVERT: C 323 ASP cc_start: 0.8131 (t0) cc_final: 0.7869 (t0) REVERT: C 366 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7977 (mp0) REVERT: C 599 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7797 (tp) REVERT: D 12 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8553 (pp) REVERT: D 221 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8030 (tm-30) REVERT: D 330 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 354 LYS cc_start: 0.6931 (mttt) cc_final: 0.6175 (ptmm) REVERT: E 191 ASP cc_start: 0.7013 (m-30) cc_final: 0.6598 (m-30) REVERT: E 436 GLU cc_start: 0.3609 (pm20) cc_final: 0.3223 (pm20) REVERT: E 579 ILE cc_start: 0.8297 (mt) cc_final: 0.8027 (mp) REVERT: E 861 GLU cc_start: 0.7919 (tt0) cc_final: 0.7044 (tm-30) REVERT: E 1029 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.8078 (mtm-85) REVERT: F 206 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8664 (mtp) REVERT: F 442 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8630 (mt) REVERT: G 441 LYS cc_start: 0.6800 (mmtt) cc_final: 0.6577 (mmmt) REVERT: G 458 TYR cc_start: 0.7544 (m-80) cc_final: 0.7305 (m-80) REVERT: G 617 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6635 (tt) REVERT: G 620 GLU cc_start: 0.6789 (tt0) cc_final: 0.6450 (tp30) REVERT: G 691 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7276 (mm-30) REVERT: G 721 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8264 (ttp) REVERT: G 763 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: G 793 MET cc_start: 0.8206 (tmm) cc_final: 0.7855 (tmm) REVERT: H 366 ASP cc_start: 0.7869 (p0) cc_final: 0.7549 (t0) REVERT: L 87 ARG cc_start: 0.8392 (tmt-80) cc_final: 0.8154 (tmt-80) REVERT: L 440 GLN cc_start: 0.8094 (tp40) cc_final: 0.7203 (tm-30) REVERT: N 66 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7618 (ttt90) REVERT: N 103 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8640 (tp) REVERT: N 267 GLN cc_start: 0.8123 (tm-30) cc_final: 0.7860 (tm-30) REVERT: O 169 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7691 (mt-10) REVERT: P 184 ASP cc_start: 0.7588 (p0) cc_final: 0.7265 (p0) REVERT: Q 766 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: R 37 GLN cc_start: 0.7499 (tm-30) cc_final: 0.7284 (tm-30) REVERT: R 112 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7533 (mp0) REVERT: S 587 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5655 (mtm) REVERT: T 48 LYS cc_start: 0.8803 (tttt) cc_final: 0.8365 (tmmt) REVERT: T 56 ARG cc_start: 0.7930 (ttp80) cc_final: 0.7723 (tmm-80) REVERT: T 75 LYS cc_start: 0.8937 (tttm) cc_final: 0.8619 (tttm) REVERT: T 121 ASP cc_start: 0.8290 (m-30) cc_final: 0.8037 (t0) outliers start: 79 outliers final: 38 residues processed: 697 average time/residue: 1.6999 time to fit residues: 1438.4456 Evaluate side-chains 684 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 631 time to evaluate : 4.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 619 GLU Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 763 GLU Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain Q residue 766 GLU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 623 optimal weight: 5.9990 chunk 297 optimal weight: 7.9990 chunk 180 optimal weight: 0.9980 chunk 460 optimal weight: 7.9990 chunk 154 optimal weight: 8.9990 chunk 347 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 308 optimal weight: 10.0000 chunk 116 optimal weight: 2.9990 chunk 644 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 111 GLN B 132 ASN ** E 398 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN E1282 GLN F 123 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN M 190 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN O 183 ASN T 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.074557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.057425 restraints weight = 129645.150| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 1.72 r_work: 0.2747 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 55432 Z= 0.396 Angle : 0.645 12.592 74929 Z= 0.343 Chirality : 0.049 0.277 8114 Planarity : 0.006 0.117 9663 Dihedral : 5.208 61.248 7338 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.51 % Allowed : 11.58 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.86 (0.10), residues: 6525 helix: 1.38 (0.10), residues: 2820 sheet: 0.30 (0.17), residues: 827 loop : -0.06 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 127 HIS 0.008 0.002 HIS E 92 PHE 0.029 0.002 PHE B 226 TYR 0.022 0.002 TYR D 649 ARG 0.008 0.001 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 650 time to evaluate : 4.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7972 (OUTLIER) cc_final: 0.7661 (ptpp) REVERT: C 21 GLU cc_start: 0.8227 (mm-30) cc_final: 0.7716 (tp30) REVERT: C 79 GLU cc_start: 0.7208 (mp0) cc_final: 0.6769 (mp0) REVERT: C 323 ASP cc_start: 0.8130 (t0) cc_final: 0.7852 (t0) REVERT: C 366 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7969 (mp0) REVERT: C 599 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7811 (tp) REVERT: C 953 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8344 (pp) REVERT: D 12 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8656 (pp) REVERT: D 221 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8096 (tm-30) REVERT: D 330 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7564 (tm-30) REVERT: D 354 LYS cc_start: 0.6918 (mttt) cc_final: 0.6439 (mtpt) REVERT: E 579 ILE cc_start: 0.8328 (mt) cc_final: 0.8058 (mp) REVERT: E 861 GLU cc_start: 0.7947 (tt0) cc_final: 0.7050 (tm-30) REVERT: E 1029 ARG cc_start: 0.8589 (OUTLIER) cc_final: 0.8104 (mtm-85) REVERT: F 206 MET cc_start: 0.8959 (OUTLIER) cc_final: 0.8693 (mtp) REVERT: F 442 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8655 (mt) REVERT: G 458 TYR cc_start: 0.7551 (m-80) cc_final: 0.7334 (m-80) REVERT: G 584 GLU cc_start: 0.6501 (pp20) cc_final: 0.6152 (mp0) REVERT: G 617 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6486 (tt) REVERT: G 620 GLU cc_start: 0.6719 (tt0) cc_final: 0.6342 (tp30) REVERT: G 691 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7360 (mm-30) REVERT: G 721 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8308 (ttp) REVERT: G 763 GLU cc_start: 0.7070 (OUTLIER) cc_final: 0.6830 (mp0) REVERT: G 793 MET cc_start: 0.8229 (tmm) cc_final: 0.7848 (tmm) REVERT: H 366 ASP cc_start: 0.7900 (p0) cc_final: 0.7558 (t0) REVERT: K 243 SER cc_start: 0.7945 (OUTLIER) cc_final: 0.7667 (t) REVERT: N 49 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7415 (tm-30) REVERT: N 66 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.7711 (ttt90) REVERT: N 103 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8671 (tp) REVERT: N 267 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7860 (tm-30) REVERT: N 269 GLU cc_start: 0.7293 (mt-10) cc_final: 0.7040 (mt-10) REVERT: O 169 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7740 (mt-10) REVERT: P 184 ASP cc_start: 0.7544 (p0) cc_final: 0.7251 (p0) REVERT: Q 766 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6860 (pm20) REVERT: R 37 GLN cc_start: 0.7543 (tm-30) cc_final: 0.7184 (tm-30) REVERT: R 112 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: S 353 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7781 (mmmt) REVERT: S 587 MET cc_start: 0.6123 (OUTLIER) cc_final: 0.5689 (mtm) REVERT: T 48 LYS cc_start: 0.8834 (tttt) cc_final: 0.8404 (tmmt) REVERT: T 121 ASP cc_start: 0.8320 (m-30) cc_final: 0.8097 (m-30) outliers start: 89 outliers final: 45 residues processed: 704 average time/residue: 1.7094 time to fit residues: 1461.6071 Evaluate side-chains 698 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 635 time to evaluate : 4.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain C residue 953 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 433 LEU Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 619 GLU Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 763 GLU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 243 SER Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain Q residue 766 GLU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 353 LYS Chi-restraints excluded: chain S residue 562 ASN Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 541 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 343 optimal weight: 2.9990 chunk 390 optimal weight: 9.9990 chunk 328 optimal weight: 9.9990 chunk 538 optimal weight: 8.9990 chunk 581 optimal weight: 0.9980 chunk 226 optimal weight: 7.9990 chunk 395 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 519 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN A 111 GLN B 132 ASN D 128 ASN E 398 HIS E1151 GLN E1282 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN L 440 GLN M 190 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN O 183 ASN R 114 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.057847 restraints weight = 129548.571| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 1.73 r_work: 0.2759 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2623 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 55432 Z= 0.293 Angle : 0.591 11.846 74929 Z= 0.315 Chirality : 0.046 0.277 8114 Planarity : 0.005 0.116 9663 Dihedral : 5.105 60.640 7338 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.10 % Favored : 96.87 % Rotamer: Outliers : 1.34 % Allowed : 11.76 % Favored : 86.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 0.93 (0.10), residues: 6525 helix: 1.46 (0.10), residues: 2817 sheet: 0.32 (0.17), residues: 841 loop : -0.03 (0.11), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP K 127 HIS 0.009 0.001 HIS E 398 PHE 0.024 0.002 PHE B 226 TYR 0.022 0.002 TYR D 649 ARG 0.008 0.001 ARG F 393 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 724 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 645 time to evaluate : 4.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7658 (ptpp) REVERT: C 21 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7706 (tp30) REVERT: C 25 ARG cc_start: 0.8487 (ttp80) cc_final: 0.8182 (tmm160) REVERT: C 79 GLU cc_start: 0.7220 (mp0) cc_final: 0.6778 (mp0) REVERT: C 323 ASP cc_start: 0.8115 (t0) cc_final: 0.7844 (t0) REVERT: C 599 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7832 (tp) REVERT: D 12 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8592 (pp) REVERT: D 221 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 330 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7598 (tm-30) REVERT: D 354 LYS cc_start: 0.6894 (mttt) cc_final: 0.6141 (ptmm) REVERT: E 436 GLU cc_start: 0.3715 (pm20) cc_final: 0.3332 (pm20) REVERT: E 579 ILE cc_start: 0.8345 (mt) cc_final: 0.8081 (mp) REVERT: E 861 GLU cc_start: 0.7968 (tt0) cc_final: 0.7037 (tm-30) REVERT: E 1029 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8142 (mtm-85) REVERT: E 1039 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8265 (mt) REVERT: F 206 MET cc_start: 0.8948 (OUTLIER) cc_final: 0.8686 (mtp) REVERT: F 442 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8645 (mt) REVERT: G 458 TYR cc_start: 0.7556 (m-80) cc_final: 0.7331 (m-80) REVERT: G 584 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: G 617 LEU cc_start: 0.6644 (OUTLIER) cc_final: 0.6391 (tt) REVERT: G 620 GLU cc_start: 0.6655 (tt0) cc_final: 0.6277 (tp30) REVERT: G 691 GLU cc_start: 0.7677 (mm-30) cc_final: 0.7403 (mm-30) REVERT: G 721 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8333 (ttp) REVERT: G 763 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6850 (mp0) REVERT: G 793 MET cc_start: 0.8245 (tmm) cc_final: 0.7891 (tmm) REVERT: H 366 ASP cc_start: 0.7931 (p0) cc_final: 0.7560 (t70) REVERT: L 440 GLN cc_start: 0.7954 (tp40) cc_final: 0.7262 (tm130) REVERT: N 49 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7417 (tm-30) REVERT: N 66 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7677 (ttt90) REVERT: N 103 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8649 (tp) REVERT: N 267 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7866 (tm-30) REVERT: N 269 GLU cc_start: 0.7310 (mt-10) cc_final: 0.7035 (mt-10) REVERT: O 169 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7713 (mt-10) REVERT: P 184 ASP cc_start: 0.7541 (p0) cc_final: 0.7192 (p0) REVERT: Q 766 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6886 (pm20) REVERT: R 37 GLN cc_start: 0.7529 (tm-30) cc_final: 0.7161 (tm-30) REVERT: R 112 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7522 (mp0) REVERT: S 353 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7765 (mmmt) REVERT: S 587 MET cc_start: 0.6113 (OUTLIER) cc_final: 0.5680 (mtm) REVERT: T 48 LYS cc_start: 0.8833 (tttt) cc_final: 0.8392 (tmmt) REVERT: T 75 LYS cc_start: 0.8938 (tttm) cc_final: 0.8735 (tttm) REVERT: T 121 ASP cc_start: 0.8310 (m-30) cc_final: 0.8016 (m-30) outliers start: 79 outliers final: 45 residues processed: 693 average time/residue: 1.7309 time to fit residues: 1454.1257 Evaluate side-chains 688 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 625 time to evaluate : 4.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain A residue 319 LYS Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 363 THR Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 401 THR Chi-restraints excluded: chain E residue 438 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1039 LEU Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 206 MET Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain F residue 443 THR Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 549 VAL Chi-restraints excluded: chain G residue 584 GLU Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 619 GLU Chi-restraints excluded: chain G residue 649 ILE Chi-restraints excluded: chain G residue 657 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 763 GLU Chi-restraints excluded: chain H residue 131 MET Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain L residue 365 VAL Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 66 ARG Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 214 TRP Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain O residue 169 GLU Chi-restraints excluded: chain P residue 112 ILE Chi-restraints excluded: chain P residue 153 THR Chi-restraints excluded: chain Q residue 669 THR Chi-restraints excluded: chain Q residue 766 GLU Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 194 SER Chi-restraints excluded: chain S residue 353 LYS Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 84 optimal weight: 20.0000 chunk 638 optimal weight: 7.9990 chunk 561 optimal weight: 7.9990 chunk 299 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 351 optimal weight: 0.9980 chunk 513 optimal weight: 10.0000 chunk 317 optimal weight: 5.9990 chunk 654 optimal weight: 0.9980 chunk 569 optimal weight: 0.9990 chunk 425 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN E 398 HIS ** E 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN E1282 GLN H 308 ASN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 190 GLN ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 88 GLN O 183 ASN T 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.076032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.058778 restraints weight = 129967.460| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.73 r_work: 0.2815 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.094 55432 Z= 0.157 Angle : 0.510 10.331 74929 Z= 0.273 Chirality : 0.042 0.257 8114 Planarity : 0.004 0.115 9663 Dihedral : 4.782 58.134 7338 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.88 % Favored : 97.07 % Rotamer: Outliers : 0.80 % Allowed : 12.44 % Favored : 86.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.20 (0.10), residues: 6525 helix: 1.71 (0.10), residues: 2809 sheet: 0.38 (0.17), residues: 828 loop : 0.11 (0.12), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP K 127 HIS 0.008 0.001 HIS E 398 PHE 0.017 0.001 PHE L 150 TYR 0.016 0.001 TYR E 998 ARG 0.016 0.000 ARG F 393 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13050 Ramachandran restraints generated. 6525 Oldfield, 0 Emsley, 6525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 700 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 653 time to evaluate : 4.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7738 (ptpt) REVERT: C 25 ARG cc_start: 0.8445 (ttp80) cc_final: 0.8165 (tmm160) REVERT: C 79 GLU cc_start: 0.7164 (mp0) cc_final: 0.6691 (mp0) REVERT: C 323 ASP cc_start: 0.8112 (t0) cc_final: 0.7845 (t0) REVERT: C 366 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7921 (mp0) REVERT: C 599 LEU cc_start: 0.8042 (OUTLIER) cc_final: 0.7802 (tp) REVERT: C 622 MET cc_start: 0.7896 (mtt) cc_final: 0.7484 (mtp) REVERT: D 12 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8488 (pp) REVERT: D 221 GLN cc_start: 0.8548 (tm-30) cc_final: 0.8031 (tm-30) REVERT: D 330 GLU cc_start: 0.7840 (tm-30) cc_final: 0.7511 (tm-30) REVERT: D 354 LYS cc_start: 0.6898 (mttt) cc_final: 0.6146 (ptmm) REVERT: E 191 ASP cc_start: 0.6945 (m-30) cc_final: 0.6507 (m-30) REVERT: E 436 GLU cc_start: 0.3546 (pm20) cc_final: 0.3168 (pm20) REVERT: E 579 ILE cc_start: 0.8252 (mt) cc_final: 0.7977 (mp) REVERT: E 861 GLU cc_start: 0.7910 (tt0) cc_final: 0.7159 (tm-30) REVERT: E 1029 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8110 (mtm-85) REVERT: E 1039 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8169 (mt) REVERT: F 442 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8593 (mt) REVERT: F 844 PHE cc_start: 0.7676 (m-10) cc_final: 0.7401 (m-10) REVERT: G 458 TYR cc_start: 0.7536 (m-80) cc_final: 0.7288 (m-80) REVERT: G 584 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.6188 (mp0) REVERT: G 617 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6444 (tt) REVERT: G 620 GLU cc_start: 0.6692 (tt0) cc_final: 0.6352 (tp30) REVERT: G 691 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7315 (mm-30) REVERT: G 721 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8267 (ttp) REVERT: G 763 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: G 793 MET cc_start: 0.8186 (tmm) cc_final: 0.7835 (tmm) REVERT: H 366 ASP cc_start: 0.7887 (p0) cc_final: 0.7509 (t70) REVERT: H 508 GLU cc_start: 0.7730 (tt0) cc_final: 0.7448 (tt0) REVERT: L 212 GLN cc_start: 0.8424 (mp10) cc_final: 0.8105 (mt0) REVERT: L 410 ILE cc_start: 0.8180 (mm) cc_final: 0.7960 (tp) REVERT: L 440 GLN cc_start: 0.7957 (tp40) cc_final: 0.7299 (tm130) REVERT: N 49 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7312 (tm-30) REVERT: N 103 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8566 (tp) REVERT: N 264 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8070 (tmt170) REVERT: N 267 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7862 (tm-30) REVERT: P 184 ASP cc_start: 0.7519 (p0) cc_final: 0.7221 (p0) REVERT: R 37 GLN cc_start: 0.7450 (tm-30) cc_final: 0.7228 (tm-30) REVERT: R 112 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7420 (mp0) REVERT: S 587 MET cc_start: 0.6109 (OUTLIER) cc_final: 0.5645 (mtm) REVERT: T 48 LYS cc_start: 0.8794 (tttt) cc_final: 0.8320 (tmmt) outliers start: 47 outliers final: 26 residues processed: 685 average time/residue: 1.7634 time to fit residues: 1464.0849 Evaluate side-chains 665 residues out of total 5900 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 626 time to evaluate : 4.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 129 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 305 ASP Chi-restraints excluded: chain B residue 109 CYS Chi-restraints excluded: chain C residue 476 ASP Chi-restraints excluded: chain C residue 599 LEU Chi-restraints excluded: chain C residue 943 ILE Chi-restraints excluded: chain D residue 12 ILE Chi-restraints excluded: chain D residue 514 PHE Chi-restraints excluded: chain D residue 517 MET Chi-restraints excluded: chain D residue 537 ILE Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain E residue 97 LEU Chi-restraints excluded: chain E residue 128 VAL Chi-restraints excluded: chain E residue 1029 ARG Chi-restraints excluded: chain E residue 1039 LEU Chi-restraints excluded: chain E residue 1099 VAL Chi-restraints excluded: chain E residue 1182 ILE Chi-restraints excluded: chain F residue 385 ILE Chi-restraints excluded: chain F residue 442 LEU Chi-restraints excluded: chain G residue 481 MET Chi-restraints excluded: chain G residue 584 GLU Chi-restraints excluded: chain G residue 617 LEU Chi-restraints excluded: chain G residue 721 MET Chi-restraints excluded: chain G residue 747 VAL Chi-restraints excluded: chain G residue 763 GLU Chi-restraints excluded: chain J residue 270 LYS Chi-restraints excluded: chain K residue 284 LEU Chi-restraints excluded: chain L residue 109 ASP Chi-restraints excluded: chain M residue 296 VAL Chi-restraints excluded: chain N residue 103 LEU Chi-restraints excluded: chain N residue 264 ARG Chi-restraints excluded: chain O residue 158 SER Chi-restraints excluded: chain P residue 160 ASP Chi-restraints excluded: chain R residue 36 ILE Chi-restraints excluded: chain R residue 50 THR Chi-restraints excluded: chain R residue 112 GLU Chi-restraints excluded: chain S residue 587 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 659 random chunks: chunk 411 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 chunk 377 optimal weight: 10.0000 chunk 412 optimal weight: 0.7980 chunk 363 optimal weight: 1.9990 chunk 585 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 570 optimal weight: 0.0170 chunk 201 optimal weight: 10.0000 chunk 279 optimal weight: 0.9990 chunk 639 optimal weight: 8.9990 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN E 398 HIS ** E 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1151 GLN E1282 GLN F 123 GLN G 777 HIS H 308 ASN I 111 ASN J 329 GLN ** K 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 255 GLN ** L 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 183 ASN T 105 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.076300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.058072 restraints weight = 130075.406| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.69 r_work: 0.2844 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.095 55432 Z= 0.153 Angle : 0.500 9.816 74929 Z= 0.267 Chirality : 0.042 0.253 8114 Planarity : 0.004 0.115 9663 Dihedral : 4.607 56.829 7336 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.93 % Favored : 97.03 % Rotamer: Outliers : 0.86 % Allowed : 12.73 % Favored : 86.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.50 % Cis-general : 0.00 % Twisted Proline : 0.30 % 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: 1.29 (0.10), residues: 6525 helix: 1.78 (0.10), residues: 2817 sheet: 0.42 (0.17), residues: 840 loop : 0.16 (0.12), residues: 2868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 127 HIS 0.008 0.001 HIS E 398 PHE 0.017 0.001 PHE L 150 TYR 0.018 0.001 TYR E 998 ARG 0.015 0.000 ARG F 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51265.13 seconds wall clock time: 873 minutes 18.77 seconds (52398.77 seconds total)