Starting phenix.real_space_refine on Sat Jul 4 15:04:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uii_42295/07_2026/8uii_42295.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uii_42295/07_2026/8uii_42295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uii_42295/07_2026/8uii_42295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uii_42295/07_2026/8uii_42295.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uii_42295/07_2026/8uii_42295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uii_42295/07_2026/8uii_42295.map" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 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 P 14 5.49 5 Mg 4 5.21 5 S 145 5.16 5 C 13664 2.51 5 N 3687 2.21 5 O 4190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21704 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5117 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 619} Chain breaks: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2582 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2536 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.54, per 1000 atoms: 0.21 Number of scatterers: 21704 At special positions: 0 Unit cell: (127.512, 123.372, 144.9, 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) S 145 16.00 P 14 15.00 Mg 4 11.99 O 4190 8.00 N 3687 7.00 C 13664 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=0, symmetry=0 Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.1 seconds 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 51.1% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.659A pdb=" N CYS A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1069 through 1098 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 6.193A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1327 Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 3.722A pdb=" N MET A1344 " --> pdb=" O THR A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1373 removed outlier: 3.594A pdb=" N VAL A1362 " --> pdb=" O SER A1358 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1373 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 3.715A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1406 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.818A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1481 Processing helix chain 'A' and resid 1485 through 1501 Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1633 through 1663 removed outlier: 3.805A pdb=" N LEU A1641 " --> pdb=" O LYS A1637 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A1642 " --> pdb=" O CYS A1638 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1663 " --> pdb=" O LEU A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1729 removed outlier: 3.580A pdb=" N SER A1702 " --> pdb=" O ASP A1698 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A1706 " --> pdb=" O SER A1702 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 3.817A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1746 Processing helix chain 'A' and resid 1764 through 1779 Processing helix chain 'A' and resid 1783 through 1787 removed outlier: 4.314A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1814 removed outlier: 4.727A pdb=" N LEU A1798 " --> pdb=" O ILE A1794 " (cutoff:3.500A) Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1817 through 1821 Processing helix chain 'A' and resid 1822 through 1827 Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.833A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.901A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.620A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.719A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.919A pdb=" N LEU C 34 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.505A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.098A pdb=" N ILE C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.055A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.638A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.939A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.565A pdb=" N LEU C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.606A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.643A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.732A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.597A pdb=" N ILE D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.792A pdb=" N GLY D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.696A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.563A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.514A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.517A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 removed outlier: 3.819A pdb=" N VAL E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.095A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.500A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.920A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.667A pdb=" N LYS E 202 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.625A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 287 through 302 Processing helix chain 'E' and resid 306 through 325 removed outlier: 4.183A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.230A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.467A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.645A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 17 removed outlier: 3.815A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 removed outlier: 4.238A pdb=" N LEU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.923A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.646A pdb=" N SER G 222 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 4.398A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 79 Processing helix chain 'H' and resid 141 through 153 Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.681A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.218A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 8.603A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1519 through 1521 Processing sheet with id=AA4, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 4.034A pdb=" N LYS A1683 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 4.034A pdb=" N LYS A1683 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.390A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.256A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.883A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.853A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.142A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.624A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE H 87 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.920A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.150A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 5.627A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7218 1.36 - 1.51: 5553 1.51 - 1.66: 9066 1.66 - 1.80: 120 1.80 - 1.95: 95 Bond restraints: 22052 Sorted by residual: bond pdb=" O3B AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.575 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.583 0.090 2.00e-02 2.50e+03 2.00e+01 bond pdb=" O3B AGS A2002 " pdb=" PB AGS A2002 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" O3A AGS B 402 " pdb=" PA AGS B 402 " ideal model delta sigma weight residual 1.664 1.587 0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 22047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 29279 2.56 - 5.13: 414 5.13 - 7.69: 75 7.69 - 10.26: 38 10.26 - 12.82: 6 Bond angle restraints: 29812 Sorted by residual: angle pdb=" C MET H 244 " pdb=" N GLY H 245 " pdb=" CA GLY H 245 " ideal model delta sigma weight residual 120.72 114.16 6.56 1.33e+00 5.65e-01 2.43e+01 angle pdb=" N LEU F 90 " pdb=" CA LEU F 90 " pdb=" C LEU F 90 " ideal model delta sigma weight residual 109.59 101.71 7.88 1.61e+00 3.86e-01 2.39e+01 angle pdb=" CB MET G 199 " pdb=" CG MET G 199 " pdb=" SD MET G 199 " ideal model delta sigma weight residual 112.70 125.52 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CA GLN F 204 " pdb=" CB GLN F 204 " pdb=" CG GLN F 204 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA TYR A1508 " pdb=" CB TYR A1508 " pdb=" CG TYR A1508 " ideal model delta sigma weight residual 113.90 121.44 -7.54 1.80e+00 3.09e-01 1.76e+01 ... (remaining 29807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.47: 13129 33.47 - 66.94: 496 66.94 - 100.41: 24 100.41 - 133.88: 7 133.88 - 167.35: 5 Dihedral angle restraints: 13661 sinusoidal: 5647 harmonic: 8014 Sorted by residual: dihedral pdb=" CA LEU G 247 " pdb=" C LEU G 247 " pdb=" N LYS G 248 " pdb=" CA LYS G 248 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" O1A AGS C 402 " pdb=" O3A AGS C 402 " pdb=" PA AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sinusoidal sigma weight residual 82.37 -84.98 167.35 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O1A AGS B 402 " pdb=" O3A AGS B 402 " pdb=" PA AGS B 402 " pdb=" PB AGS B 402 " ideal model delta sinusoidal sigma weight residual 82.37 -113.49 -164.14 1 3.00e+01 1.11e-03 2.09e+01 ... (remaining 13658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2951 0.064 - 0.129: 446 0.129 - 0.193: 41 0.193 - 0.258: 9 0.258 - 0.322: 6 Chirality restraints: 3453 Sorted by residual: chirality pdb=" CB ILE F 147 " pdb=" CA ILE F 147 " pdb=" CG1 ILE F 147 " pdb=" CG2 ILE F 147 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA LEU F 90 " pdb=" N LEU F 90 " pdb=" C LEU F 90 " pdb=" CB LEU F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" C3' AGS C 402 " pdb=" C2' AGS C 402 " pdb=" C4' AGS C 402 " pdb=" O3' AGS C 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.65 0.28 2.00e-01 2.50e+01 1.95e+00 ... (remaining 3450 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 113 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C LYS E 113 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS E 113 " -0.018 2.00e-02 2.50e+03 pdb=" N THR E 114 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 138 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS F 138 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS F 138 " -0.017 2.00e-02 2.50e+03 pdb=" N MET F 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO E 174 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.037 5.00e-02 4.00e+02 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 240 2.63 - 3.20: 17921 3.20 - 3.76: 34305 3.76 - 4.33: 46471 4.33 - 4.90: 77944 Nonbonded interactions: 176881 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 2.061 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.071 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A1139 " pdb="MG MG A2001 " model vdw 2.102 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G AGS D 402 " model vdw 2.112 2.170 ... (remaining 176876 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 'F' selection = chain 'G' selection = chain 'H' } 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: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 20.550 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 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 : 0.004 0.098 22052 Z= 0.203 Angle : 0.819 12.821 29812 Z= 0.406 Chirality : 0.048 0.322 3453 Planarity : 0.005 0.066 3792 Dihedral : 17.307 167.347 8443 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 23.48 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 2717 helix: -0.30 (0.13), residues: 1275 sheet: -0.42 (0.22), residues: 524 loop : -1.22 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 149 TYR 0.024 0.002 TYR G 249 PHE 0.027 0.002 PHE D 96 TRP 0.009 0.001 TRP F 28 HIS 0.006 0.001 HIS A1178 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.20 (22052) covalent geometry : angle 0.81897 / 0.41 (29812) hydrogen bonds : bond 0.12126 / 7.83 ( 1151) hydrogen bonds : angle 5.80972 / 3.94 ( 3318) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1166 GLN cc_start: 0.7145 (mt0) cc_final: 0.6928 (mt0) REVERT: D 93 ARG cc_start: 0.6854 (mtp85) cc_final: 0.6595 (mtp180) REVERT: G 16 LEU cc_start: 0.6994 (pp) cc_final: 0.5862 (mp) REVERT: G 249 TYR cc_start: 0.6687 (m-80) cc_final: 0.6461 (m-80) outliers start: 17 outliers final: 9 residues processed: 337 average time/residue: 0.1652 time to fit residues: 85.1579 Evaluate side-chains 311 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 302 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 246 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.4980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 0.2980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 945 ASN A1361 ASN A1481 HIS A1789 ASN B 269 HIS B 332 ASN E 301 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 GLN G 179 ASN H 200 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.195448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151666 restraints weight = 27742.134| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.40 r_work: 0.3619 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.0919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22052 Z= 0.164 Angle : 0.564 9.159 29812 Z= 0.285 Chirality : 0.042 0.162 3453 Planarity : 0.004 0.052 3792 Dihedral : 11.172 171.135 3112 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.10 % Allowed : 20.67 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2717 helix: 0.60 (0.14), residues: 1266 sheet: -0.39 (0.22), residues: 519 loop : -0.92 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 214 TYR 0.034 0.002 TYR G 249 PHE 0.020 0.001 PHE D 126 TRP 0.008 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.16 (22052) covalent geometry : angle 0.56399 / 0.28 (29812) hydrogen bonds : bond 0.03814 / 2.52 ( 1151) hydrogen bonds : angle 4.63842 / 3.18 ( 3318) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 327 time to evaluate : 0.852 Fit side-chains REVERT: A 1181 ASP cc_start: 0.7147 (t0) cc_final: 0.6783 (t0) REVERT: B 89 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7153 (tp) REVERT: D 93 ARG cc_start: 0.6915 (mtp85) cc_final: 0.6631 (mtp180) REVERT: D 94 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7328 (mm-30) REVERT: E 112 LEU cc_start: 0.7533 (OUTLIER) cc_final: 0.6978 (mt) REVERT: E 340 MET cc_start: 0.7246 (OUTLIER) cc_final: 0.7036 (mtt) REVERT: G 91 ARG cc_start: 0.7296 (tmm160) cc_final: 0.7076 (tmm160) REVERT: H 5 ARG cc_start: 0.7135 (tpp80) cc_final: 0.6858 (tpp80) REVERT: H 139 MET cc_start: 0.7828 (tpt) cc_final: 0.7592 (tpt) REVERT: H 209 LEU cc_start: 0.6634 (OUTLIER) cc_final: 0.6387 (tm) outliers start: 75 outliers final: 46 residues processed: 375 average time/residue: 0.1644 time to fit residues: 95.1198 Evaluate side-chains 339 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 289 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 106 LEU Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 177 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 194 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 143 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 116 optimal weight: 0.0470 overall best weight: 0.6880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1500 GLN B 332 ASN E 301 HIS G 179 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.198065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.154945 restraints weight = 27886.081| |-----------------------------------------------------------------------------| r_work (start): 0.3848 rms_B_bonded: 2.41 r_work: 0.3642 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22052 Z= 0.101 Angle : 0.502 7.806 29812 Z= 0.253 Chirality : 0.040 0.193 3453 Planarity : 0.003 0.044 3792 Dihedral : 10.576 179.170 3099 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.56 % Allowed : 21.37 % Favored : 76.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.16), residues: 2717 helix: 1.13 (0.15), residues: 1266 sheet: -0.32 (0.23), residues: 518 loop : -0.81 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 149 TYR 0.014 0.001 TYR G 250 PHE 0.016 0.001 PHE H 169 TRP 0.008 0.001 TRP A1403 HIS 0.003 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (22052) covalent geometry : angle 0.50198 / 0.25 (29812) hydrogen bonds : bond 0.03167 / 2.10 ( 1151) hydrogen bonds : angle 4.33894 / 2.99 ( 3318) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 331 time to evaluate : 0.867 Fit side-chains REVERT: A 945 ASN cc_start: 0.5812 (m110) cc_final: 0.5555 (t0) REVERT: A 1181 ASP cc_start: 0.7170 (t0) cc_final: 0.6836 (t0) REVERT: A 1501 MET cc_start: 0.6927 (mmp) cc_final: 0.6613 (mmm) REVERT: B 89 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.6998 (tp) REVERT: C 182 MET cc_start: 0.7017 (ttt) cc_final: 0.6778 (ttt) REVERT: D 93 ARG cc_start: 0.6780 (mtp85) cc_final: 0.6401 (mtp180) REVERT: D 151 GLU cc_start: 0.7575 (mp0) cc_final: 0.7190 (mp0) REVERT: E 102 ASN cc_start: 0.7987 (t0) cc_final: 0.7777 (m-40) REVERT: E 105 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.7290 (ttp80) REVERT: E 112 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7002 (mt) REVERT: F 143 GLU cc_start: 0.6144 (tp30) cc_final: 0.5897 (tp30) REVERT: G 60 TYR cc_start: 0.5651 (t80) cc_final: 0.5449 (t80) REVERT: G 124 GLU cc_start: 0.5446 (mt-10) cc_final: 0.4562 (pm20) REVERT: H 139 MET cc_start: 0.7819 (tpt) cc_final: 0.7530 (tpt) REVERT: H 162 CYS cc_start: 0.5051 (m) cc_final: 0.3993 (p) REVERT: H 209 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6392 (tm) outliers start: 62 outliers final: 36 residues processed: 377 average time/residue: 0.1606 time to fit residues: 93.7162 Evaluate side-chains 329 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 289 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 30 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 151 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 24 optimal weight: 0.1980 chunk 99 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 167 optimal weight: 8.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1789 ASN B 332 ASN E 301 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.194681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150941 restraints weight = 27912.414| |-----------------------------------------------------------------------------| r_work (start): 0.3803 rms_B_bonded: 2.41 r_work: 0.3595 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22052 Z= 0.164 Angle : 0.550 11.163 29812 Z= 0.275 Chirality : 0.042 0.169 3453 Planarity : 0.003 0.043 3792 Dihedral : 10.547 172.516 3095 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.60 % Allowed : 20.88 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2717 helix: 1.10 (0.15), residues: 1266 sheet: -0.30 (0.23), residues: 514 loop : -0.82 (0.19), residues: 937 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 149 TYR 0.013 0.001 TYR B 279 PHE 0.013 0.001 PHE A1717 TRP 0.008 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (22052) covalent geometry : angle 0.55000 / 0.27 (29812) hydrogen bonds : bond 0.03513 / 2.32 ( 1151) hydrogen bonds : angle 4.37526 / 3.01 ( 3318) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 318 time to evaluate : 0.874 Fit side-chains revert: symmetry clash REVERT: A 945 ASN cc_start: 0.5901 (m110) cc_final: 0.5662 (t0) REVERT: A 1181 ASP cc_start: 0.7174 (t0) cc_final: 0.6818 (t0) REVERT: A 1344 MET cc_start: 0.7807 (mmp) cc_final: 0.6808 (ptp) REVERT: A 1501 MET cc_start: 0.7037 (mmp) cc_final: 0.6684 (mmm) REVERT: B 54 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7375 (mp0) REVERT: B 89 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7113 (tp) REVERT: D 151 GLU cc_start: 0.7559 (mp0) cc_final: 0.7154 (mp0) REVERT: E 102 ASN cc_start: 0.7990 (t0) cc_final: 0.7745 (m-40) REVERT: E 105 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7274 (ttp80) REVERT: E 112 LEU cc_start: 0.7573 (OUTLIER) cc_final: 0.7046 (mt) REVERT: E 191 ASP cc_start: 0.7008 (m-30) cc_final: 0.6751 (m-30) REVERT: H 139 MET cc_start: 0.7760 (tpt) cc_final: 0.7493 (tpt) REVERT: H 162 CYS cc_start: 0.5050 (m) cc_final: 0.3971 (p) REVERT: H 209 LEU cc_start: 0.6503 (OUTLIER) cc_final: 0.6258 (tm) outliers start: 87 outliers final: 64 residues processed: 378 average time/residue: 0.1546 time to fit residues: 90.7779 Evaluate side-chains 354 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1789 ASN Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 70 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 2 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 chunk 246 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1789 ASN B 332 ASN E 301 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.195619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.153229 restraints weight = 27673.187| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 2.48 r_work: 0.3608 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22052 Z= 0.127 Angle : 0.524 10.500 29812 Z= 0.261 Chirality : 0.040 0.154 3453 Planarity : 0.003 0.042 3792 Dihedral : 10.462 172.697 3095 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 3.47 % Allowed : 21.83 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.16), residues: 2717 helix: 1.22 (0.15), residues: 1266 sheet: -0.25 (0.23), residues: 510 loop : -0.78 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 149 TYR 0.013 0.001 TYR G 250 PHE 0.013 0.001 PHE A1717 TRP 0.008 0.001 TRP A1403 HIS 0.003 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (22052) covalent geometry : angle 0.52385 / 0.26 (29812) hydrogen bonds : bond 0.03258 / 2.16 ( 1151) hydrogen bonds : angle 4.29468 / 2.96 ( 3318) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 317 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 945 ASN cc_start: 0.5933 (m110) cc_final: 0.5711 (t0) REVERT: A 1181 ASP cc_start: 0.7193 (t0) cc_final: 0.6797 (t0) REVERT: A 1344 MET cc_start: 0.7813 (mmp) cc_final: 0.6768 (ptp) REVERT: A 1501 MET cc_start: 0.6973 (mmp) cc_final: 0.6639 (mmm) REVERT: A 1790 ARG cc_start: 0.6391 (OUTLIER) cc_final: 0.5780 (mtt180) REVERT: B 54 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7383 (mp0) REVERT: B 89 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7090 (tp) REVERT: C 37 HIS cc_start: 0.7890 (OUTLIER) cc_final: 0.7444 (m90) REVERT: D 122 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.7952 (mttm) REVERT: D 151 GLU cc_start: 0.7541 (mp0) cc_final: 0.7178 (mp0) REVERT: D 317 ASN cc_start: 0.8017 (m-40) cc_final: 0.7641 (m-40) REVERT: E 102 ASN cc_start: 0.8000 (t0) cc_final: 0.7744 (m-40) REVERT: E 105 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.7243 (ttp80) REVERT: E 112 LEU cc_start: 0.7570 (OUTLIER) cc_final: 0.7041 (mt) REVERT: E 191 ASP cc_start: 0.7010 (m-30) cc_final: 0.6752 (m-30) REVERT: F 25 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7144 (pp20) REVERT: G 75 MET cc_start: 0.8412 (ttt) cc_final: 0.7548 (tpt) REVERT: G 91 ARG cc_start: 0.7229 (tmm160) cc_final: 0.7010 (tmm160) REVERT: H 139 MET cc_start: 0.7724 (tpt) cc_final: 0.7461 (tpt) REVERT: H 162 CYS cc_start: 0.5040 (m) cc_final: 0.3987 (p) REVERT: H 209 LEU cc_start: 0.6566 (OUTLIER) cc_final: 0.6333 (tm) REVERT: H 251 LEU cc_start: 0.8028 (tp) cc_final: 0.7738 (tt) outliers start: 84 outliers final: 55 residues processed: 381 average time/residue: 0.1610 time to fit residues: 95.3233 Evaluate side-chains 354 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 290 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 331 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 166 optimal weight: 9.9990 chunk 266 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 57 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1094 ASN A1789 ASN B 332 ASN E 301 HIS ** F 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.191149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.146457 restraints weight = 27746.460| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.43 r_work: 0.3534 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 22052 Z= 0.248 Angle : 0.640 9.695 29812 Z= 0.320 Chirality : 0.045 0.169 3453 Planarity : 0.004 0.044 3792 Dihedral : 10.800 165.435 3095 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.63 % Allowed : 21.04 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.16), residues: 2717 helix: 0.83 (0.14), residues: 1251 sheet: -0.53 (0.22), residues: 513 loop : -0.88 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 149 TYR 0.015 0.002 TYR B 279 PHE 0.019 0.002 PHE A1154 TRP 0.013 0.001 TRP A1489 HIS 0.006 0.001 HIS E 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.25 (22052) covalent geometry : angle 0.64043 / 0.32 (29812) hydrogen bonds : bond 0.04141 / 2.73 ( 1151) hydrogen bonds : angle 4.61141 / 3.18 ( 3318) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 286 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.7162 (t0) cc_final: 0.6822 (t0) REVERT: A 1344 MET cc_start: 0.8061 (mmp) cc_final: 0.6867 (ptp) REVERT: B 54 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: B 89 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7175 (tp) REVERT: C 37 HIS cc_start: 0.7966 (OUTLIER) cc_final: 0.7528 (m90) REVERT: D 122 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7968 (mttm) REVERT: D 151 GLU cc_start: 0.7584 (mp0) cc_final: 0.7188 (mp0) REVERT: E 105 ARG cc_start: 0.7675 (OUTLIER) cc_final: 0.7371 (ttp80) REVERT: E 112 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.6996 (mt) REVERT: F 25 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7796 (pp20) REVERT: H 75 MET cc_start: 0.7832 (tpp) cc_final: 0.7596 (mpp) REVERT: H 139 MET cc_start: 0.7752 (tpt) cc_final: 0.7480 (tpt) REVERT: H 162 CYS cc_start: 0.5235 (m) cc_final: 0.4071 (p) outliers start: 112 outliers final: 75 residues processed: 370 average time/residue: 0.1521 time to fit residues: 87.5364 Evaluate side-chains 357 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 275 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 280 GLU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 23 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 114 optimal weight: 0.8980 chunk 216 optimal weight: 0.8980 chunk 239 optimal weight: 5.9990 chunk 229 optimal weight: 7.9990 chunk 187 optimal weight: 0.4980 chunk 153 optimal weight: 0.9990 chunk 262 optimal weight: 8.9990 chunk 202 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 332 ASN E 301 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.195524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151551 restraints weight = 27743.201| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.60 r_work: 0.3592 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22052 Z= 0.118 Angle : 0.537 8.364 29812 Z= 0.268 Chirality : 0.041 0.192 3453 Planarity : 0.003 0.042 3792 Dihedral : 10.529 169.971 3095 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.06 % Allowed : 22.41 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.16), residues: 2717 helix: 1.16 (0.15), residues: 1262 sheet: -0.50 (0.22), residues: 514 loop : -0.77 (0.20), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 150 TYR 0.023 0.001 TYR G 249 PHE 0.014 0.001 PHE A1717 TRP 0.009 0.001 TRP A1403 HIS 0.006 0.001 HIS F 44 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.12 (22052) covalent geometry : angle 0.53655 / 0.27 (29812) hydrogen bonds : bond 0.03253 / 2.17 ( 1151) hydrogen bonds : angle 4.35690 / 3.02 ( 3318) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 307 time to evaluate : 0.899 Fit side-chains revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.7126 (t0) cc_final: 0.6788 (t0) REVERT: A 1344 MET cc_start: 0.8011 (mmp) cc_final: 0.6866 (ptp) REVERT: A 1490 HIS cc_start: 0.7725 (t-170) cc_final: 0.7497 (t-170) REVERT: A 1501 MET cc_start: 0.7000 (mmp) cc_final: 0.6650 (mmm) REVERT: B 54 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: B 89 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.6972 (tp) REVERT: C 37 HIS cc_start: 0.7849 (OUTLIER) cc_final: 0.7515 (m90) REVERT: D 122 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7911 (mttm) REVERT: D 151 GLU cc_start: 0.7546 (mp0) cc_final: 0.7154 (mp0) REVERT: D 317 ASN cc_start: 0.8174 (m-40) cc_final: 0.7892 (m-40) REVERT: E 105 ARG cc_start: 0.7561 (OUTLIER) cc_final: 0.6587 (ttp80) REVERT: E 112 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.6974 (mt) REVERT: E 275 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7844 (tpt-90) REVERT: E 340 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7118 (mtt) REVERT: F 25 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7624 (pm20) REVERT: F 28 TRP cc_start: 0.8013 (m100) cc_final: 0.7563 (m100) REVERT: F 89 THR cc_start: 0.7702 (m) cc_final: 0.7444 (m) REVERT: F 143 GLU cc_start: 0.6199 (tp30) cc_final: 0.5994 (tp30) REVERT: G 91 ARG cc_start: 0.7279 (tmm160) cc_final: 0.7057 (tmm160) REVERT: G 124 GLU cc_start: 0.5437 (mt-10) cc_final: 0.4767 (pm20) REVERT: H 139 MET cc_start: 0.7796 (tpt) cc_final: 0.7546 (tpt) REVERT: H 162 CYS cc_start: 0.5250 (m) cc_final: 0.4075 (p) REVERT: H 251 LEU cc_start: 0.8111 (tp) cc_final: 0.7891 (tp) outliers start: 74 outliers final: 57 residues processed: 363 average time/residue: 0.1496 time to fit residues: 84.6006 Evaluate side-chains 359 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 293 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 92 HIS Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 36 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 chunk 173 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 267 optimal weight: 4.9990 chunk 157 optimal weight: 0.9980 chunk 253 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 132 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1789 ASN B 332 ASN D 318 ASN E 301 HIS F 95 ASN G 84 ASN G 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.194053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.149484 restraints weight = 27508.195| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.46 r_work: 0.3570 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.1675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22052 Z= 0.152 Angle : 0.566 11.667 29812 Z= 0.280 Chirality : 0.042 0.199 3453 Planarity : 0.003 0.042 3792 Dihedral : 10.532 169.621 3095 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.64 % Allowed : 21.99 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.16), residues: 2717 helix: 1.16 (0.15), residues: 1261 sheet: -0.51 (0.22), residues: 514 loop : -0.74 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 149 TYR 0.031 0.002 TYR G 249 PHE 0.014 0.001 PHE A1717 TRP 0.009 0.001 TRP A1489 HIS 0.003 0.001 HIS E 37 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (22052) covalent geometry : angle 0.56634 / 0.28 (29812) hydrogen bonds : bond 0.03410 / 2.26 ( 1151) hydrogen bonds : angle 4.35963 / 3.02 ( 3318) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 297 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1344 MET cc_start: 0.8021 (mmp) cc_final: 0.6853 (ptp) REVERT: A 1501 MET cc_start: 0.7035 (mmp) cc_final: 0.6675 (mmm) REVERT: B 54 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: B 89 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7058 (tp) REVERT: C 37 HIS cc_start: 0.7896 (OUTLIER) cc_final: 0.7564 (m90) REVERT: D 151 GLU cc_start: 0.7583 (mp0) cc_final: 0.7180 (mp0) REVERT: D 317 ASN cc_start: 0.8106 (m-40) cc_final: 0.7804 (m-40) REVERT: E 105 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.7210 (ttp80) REVERT: E 112 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7011 (mt) REVERT: E 340 MET cc_start: 0.7395 (OUTLIER) cc_final: 0.7163 (mtt) REVERT: F 25 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7625 (pm20) REVERT: F 28 TRP cc_start: 0.8032 (m100) cc_final: 0.7587 (m100) REVERT: F 89 THR cc_start: 0.7712 (m) cc_final: 0.7465 (m) REVERT: F 143 GLU cc_start: 0.6239 (tp30) cc_final: 0.6033 (tp30) REVERT: G 75 MET cc_start: 0.8107 (ttp) cc_final: 0.7184 (tpt) REVERT: G 91 ARG cc_start: 0.7263 (tmm160) cc_final: 0.7053 (tmm160) REVERT: G 124 GLU cc_start: 0.5448 (mt-10) cc_final: 0.4766 (pm20) REVERT: H 139 MET cc_start: 0.7772 (tpt) cc_final: 0.7522 (tpt) REVERT: H 162 CYS cc_start: 0.5324 (m) cc_final: 0.4160 (p) outliers start: 88 outliers final: 67 residues processed: 362 average time/residue: 0.1568 time to fit residues: 87.7933 Evaluate side-chains 367 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 293 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1377 THR Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 112 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 132 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 239 optimal weight: 0.7980 chunk 173 optimal weight: 0.8980 chunk 71 optimal weight: 3.9990 chunk 137 optimal weight: 0.0370 chunk 11 optimal weight: 0.6980 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1094 ASN A1789 ASN B 332 ASN E 301 HIS G 179 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.197067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.154762 restraints weight = 27967.579| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 2.68 r_work: 0.3665 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22052 Z= 0.098 Angle : 0.541 12.650 29812 Z= 0.265 Chirality : 0.040 0.200 3453 Planarity : 0.003 0.041 3792 Dihedral : 10.360 175.320 3095 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.40 % Allowed : 23.15 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.16), residues: 2717 helix: 1.40 (0.15), residues: 1268 sheet: -0.37 (0.22), residues: 517 loop : -0.70 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 149 TYR 0.024 0.001 TYR G 239 PHE 0.011 0.001 PHE A1652 TRP 0.010 0.001 TRP A1403 HIS 0.003 0.001 HIS E 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 (22052) covalent geometry : angle 0.54112 / 0.26 (29812) hydrogen bonds : bond 0.02953 / 1.96 ( 1151) hydrogen bonds : angle 4.18509 / 2.91 ( 3318) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 323 time to evaluate : 0.746 Fit side-chains revert: symmetry clash REVERT: A 1310 ILE cc_start: 0.8690 (mm) cc_final: 0.8469 (mm) REVERT: A 1325 MET cc_start: 0.6833 (mmm) cc_final: 0.6214 (mmm) REVERT: A 1344 MET cc_start: 0.7967 (mmp) cc_final: 0.6806 (ptp) REVERT: A 1490 HIS cc_start: 0.7718 (t-170) cc_final: 0.7507 (t-170) REVERT: A 1501 MET cc_start: 0.6837 (mmp) cc_final: 0.6597 (mmm) REVERT: B 89 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.6988 (tp) REVERT: B 296 ILE cc_start: 0.8601 (tp) cc_final: 0.8327 (tp) REVERT: C 26 TYR cc_start: 0.7981 (m-80) cc_final: 0.7771 (m-80) REVERT: D 151 GLU cc_start: 0.7521 (mp0) cc_final: 0.7171 (mp0) REVERT: D 317 ASN cc_start: 0.7906 (m-40) cc_final: 0.7690 (m-40) REVERT: E 105 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7185 (ttp80) REVERT: E 275 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7924 (tpt-90) REVERT: F 28 TRP cc_start: 0.7996 (m100) cc_final: 0.7609 (m100) REVERT: F 89 THR cc_start: 0.7652 (m) cc_final: 0.7419 (m) REVERT: F 143 GLU cc_start: 0.6180 (tp30) cc_final: 0.5970 (tp30) REVERT: F 198 GLU cc_start: 0.6780 (mt-10) cc_final: 0.6261 (tm-30) REVERT: G 75 MET cc_start: 0.8097 (ttp) cc_final: 0.7026 (tpt) REVERT: G 124 GLU cc_start: 0.5431 (mt-10) cc_final: 0.4739 (pm20) REVERT: G 246 HIS cc_start: 0.6870 (OUTLIER) cc_final: 0.6641 (t-90) REVERT: H 116 MET cc_start: 0.7002 (OUTLIER) cc_final: 0.6578 (ptm) REVERT: H 139 MET cc_start: 0.7828 (tpt) cc_final: 0.7547 (tpt) REVERT: H 162 CYS cc_start: 0.5236 (m) cc_final: 0.4045 (p) REVERT: H 251 LEU cc_start: 0.8045 (tp) cc_final: 0.7742 (tt) outliers start: 58 outliers final: 47 residues processed: 363 average time/residue: 0.1508 time to fit residues: 84.4407 Evaluate side-chains 349 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 15 optimal weight: 6.9990 chunk 36 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 254 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 184 optimal weight: 0.9990 chunk 210 optimal weight: 10.0000 chunk 4 optimal weight: 0.0980 chunk 76 optimal weight: 3.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1500 GLN A1789 ASN B 332 ASN D 318 ASN E 301 HIS F 153 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.196503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.154260 restraints weight = 27942.792| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.67 r_work: 0.3643 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.115 22052 Z= 0.151 Angle : 0.697 59.128 29812 Z= 0.377 Chirality : 0.042 0.338 3453 Planarity : 0.003 0.066 3792 Dihedral : 10.375 175.012 3095 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.56 % Allowed : 23.48 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.16), residues: 2717 helix: 1.39 (0.15), residues: 1268 sheet: -0.35 (0.22), residues: 517 loop : -0.69 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 61 TYR 0.021 0.001 TYR G 239 PHE 0.015 0.001 PHE C 119 TRP 0.009 0.001 TRP A1403 HIS 0.016 0.001 HIS F 246 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (22052) covalent geometry : angle 0.69739 / 0.38 (29812) hydrogen bonds : bond 0.03005 / 2.00 ( 1151) hydrogen bonds : angle 4.18906 / 2.92 ( 3318) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 298 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 1310 ILE cc_start: 0.8696 (mm) cc_final: 0.8477 (mm) REVERT: A 1344 MET cc_start: 0.7963 (mmp) cc_final: 0.6803 (ptp) REVERT: A 1490 HIS cc_start: 0.7686 (t-170) cc_final: 0.7468 (t-170) REVERT: A 1501 MET cc_start: 0.6886 (mmp) cc_final: 0.6608 (mmm) REVERT: B 89 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.6993 (tp) REVERT: B 296 ILE cc_start: 0.8617 (tp) cc_final: 0.8324 (tp) REVERT: D 151 GLU cc_start: 0.7506 (mp0) cc_final: 0.7152 (mp0) REVERT: D 317 ASN cc_start: 0.7940 (m-40) cc_final: 0.7714 (m-40) REVERT: E 105 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7154 (ttp80) REVERT: E 112 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.7054 (mt) REVERT: E 275 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.6864 (tpt-90) REVERT: F 28 TRP cc_start: 0.8004 (m100) cc_final: 0.7600 (m100) REVERT: F 89 THR cc_start: 0.7652 (m) cc_final: 0.7413 (m) REVERT: F 198 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6242 (tm-30) REVERT: G 75 MET cc_start: 0.8102 (ttp) cc_final: 0.7031 (tpt) REVERT: G 124 GLU cc_start: 0.5435 (mt-10) cc_final: 0.4743 (pm20) REVERT: G 246 HIS cc_start: 0.6886 (OUTLIER) cc_final: 0.6640 (t-90) REVERT: H 116 MET cc_start: 0.7062 (OUTLIER) cc_final: 0.6827 (ptp) REVERT: H 139 MET cc_start: 0.7829 (tpt) cc_final: 0.7548 (tpt) REVERT: H 162 CYS cc_start: 0.5215 (m) cc_final: 0.4043 (p) REVERT: H 251 LEU cc_start: 0.8030 (tp) cc_final: 0.7737 (tt) outliers start: 62 outliers final: 50 residues processed: 336 average time/residue: 0.1537 time to fit residues: 80.0409 Evaluate side-chains 347 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 291 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 244 MET Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 185 optimal weight: 0.7980 chunk 128 optimal weight: 7.9990 chunk 236 optimal weight: 9.9990 chunk 91 optimal weight: 0.0050 chunk 122 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 243 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 187 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1789 ASN E 301 HIS G 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.196462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.154702 restraints weight = 27962.378| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.29 r_work: 0.3663 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22052 Z= 0.106 Angle : 0.548 12.406 29812 Z= 0.269 Chirality : 0.041 0.230 3453 Planarity : 0.003 0.050 3792 Dihedral : 10.341 175.908 3095 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.73 % Allowed : 23.07 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2717 helix: 1.43 (0.15), residues: 1270 sheet: -0.31 (0.22), residues: 519 loop : -0.68 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 150 TYR 0.023 0.001 TYR G 239 PHE 0.011 0.001 PHE D 96 TRP 0.010 0.001 TRP A1403 HIS 0.003 0.001 HIS E 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (22052) covalent geometry : angle 0.54798 / 0.27 (29812) hydrogen bonds : bond 0.03004 / 2.00 ( 1151) hydrogen bonds : angle 4.17757 / 2.90 ( 3318) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5473.87 seconds wall clock time: 94 minutes 43.24 seconds (5683.24 seconds total)