Starting phenix.real_space_refine on Sat Jul 4 15:41:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ui9_42289/07_2026/8ui9_42289.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ui9_42289/07_2026/8ui9_42289.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ui9_42289/07_2026/8ui9_42289.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ui9_42289/07_2026/8ui9_42289.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ui9_42289/07_2026/8ui9_42289.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ui9_42289/07_2026/8ui9_42289.map" } resolution = 3.5 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= 0.001 sd= 0.036 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 146 5.16 5 C 13746 2.51 5 N 3709 2.21 5 O 4217 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 85 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: 21836 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 643, 5134 Classifications: {'peptide': 643} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 621} 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: 2697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2697 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 13, 'TRANS': 325} 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: 4.84, per 1000 atoms: 0.22 Number of scatterers: 21836 At special positions: 0 Unit cell: (123.372, 129.168, 141.588, 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 146 16.00 P 14 15.00 Mg 4 11.99 O 4217 8.00 N 3709 7.00 C 13746 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: 1.95 Conformation dependent library (CDL) restraints added in 817.6 milliseconds 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5252 Finding SS restraints... Secondary structure from input PDB file: 113 helices and 15 sheets defined 49.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 890 through 895 removed outlier: 3.645A pdb=" N THR A 894 " --> pdb=" O CYS A 890 " (cutoff:3.500A) 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 1062 through 1066 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: 6.309A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 3.955A 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 Processing helix chain 'A' and resid 1358 through 1373 Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 4.348A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1405 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.585A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1481 removed outlier: 3.585A pdb=" N HIS A1481 " --> pdb=" O SER A1477 " (cutoff:3.500A) 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 1662 Processing helix chain 'A' and resid 1699 through 1729 removed outlier: 4.010A pdb=" N GLN A1703 " --> pdb=" O GLY A1699 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER A1705 " --> pdb=" O THR A1701 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1738 removed outlier: 3.665A 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 removed outlier: 3.524A pdb=" N ALA A1768 " --> pdb=" O ASN A1764 " (cutoff:3.500A) Processing helix chain 'A' and resid 1780 through 1781 No H-bonds generated for 'chain 'A' and resid 1780 through 1781' Processing helix chain 'A' and resid 1782 through 1787 removed outlier: 3.634A pdb=" N LEU A1785 " --> pdb=" O ARG A1782 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N VAL A1787 " --> pdb=" O LEU A1784 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1782 through 1787' Processing helix chain 'A' and resid 1789 through 1814 Proline residue: A1799 - end of helix removed outlier: 3.530A pdb=" N GLY A1814 " --> pdb=" O LEU A1810 " (cutoff:3.500A) Processing helix chain 'A' and resid 1817 through 1822 removed outlier: 3.513A pdb=" N PHE A1820 " --> pdb=" O LYS A1817 " (cutoff:3.500A) 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: 4.241A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.445A 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 160 removed outlier: 4.970A pdb=" N ARG B 156 " --> pdb=" O GLN B 152 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR B 157 " --> pdb=" O ALA B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.543A pdb=" N GLN B 182 " --> pdb=" O ILE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 210 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 255 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: 3.977A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 removed outlier: 3.565A pdb=" N GLY B 330 " --> pdb=" O LYS B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 350 removed outlier: 3.545A pdb=" N MET B 337 " --> pdb=" O SER B 333 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N THR B 348 " --> pdb=" O LEU B 344 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 349 " --> pdb=" O CYS B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 removed outlier: 4.289A pdb=" N LYS C 7 " --> pdb=" O THR C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 26 removed outlier: 3.904A pdb=" N TYR C 26 " --> pdb=" O TRP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 50 Processing helix chain 'C' and resid 66 through 78 Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.641A pdb=" N PHE C 83 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 3.903A pdb=" N ARG C 102 " --> pdb=" O ILE C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 110 Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.077A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 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: 3.835A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 257 removed outlier: 3.547A pdb=" N GLN C 257 " --> pdb=" O TRP C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 276 through 289 removed outlier: 3.596A pdb=" N ILE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 339 removed outlier: 3.737A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 97 through 102 removed outlier: 4.399A pdb=" N ARG D 102 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 removed outlier: 4.477A pdb=" N VAL D 119 " --> pdb=" O GLY D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 182 through 186 removed outlier: 3.718A pdb=" N ARG D 185 " --> pdb=" O TYR D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 193 Processing helix chain 'D' and resid 203 through 218 Processing helix chain 'D' and resid 223 through 235 Processing helix chain 'D' and resid 237 through 252 Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.744A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.687A 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 Processing helix chain 'D' and resid 320 through 341 Processing helix chain 'D' and resid 343 through 362 removed outlier: 4.369A pdb=" N ASN D 362 " --> pdb=" O GLN D 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.667A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.505A pdb=" N CYS E 32 " --> pdb=" O ASN E 28 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.093A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.916A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 103 through 122 removed outlier: 4.413A pdb=" N VAL E 107 " --> pdb=" O SER E 103 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 removed outlier: 3.598A pdb=" N ARG E 176 " --> pdb=" O ILE E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 203 Processing helix chain 'E' and resid 208 through 219 removed outlier: 3.547A pdb=" N ALA E 212 " --> pdb=" O PRO E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.641A 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 300 removed outlier: 3.664A pdb=" N ILE E 291 " --> pdb=" O PRO E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 325 removed outlier: 4.591A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.349A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 19 Processing helix chain 'F' and resid 55 through 57 No H-bonds generated for 'chain 'F' and resid 55 through 57' Processing helix chain 'F' and resid 72 through 79 removed outlier: 3.844A pdb=" N LEU F 79 " --> pdb=" O MET F 75 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 155 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'G' and resid 9 through 18 Processing helix chain 'G' and resid 72 through 80 removed outlier: 3.764A pdb=" N LEU G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 155 Processing helix chain 'G' and resid 209 through 216 Processing helix chain 'G' and resid 217 through 222 Proline residue: G 220 - end of helix No H-bonds generated for 'chain 'G' and resid 217 through 222' Processing helix chain 'H' and resid 9 through 17 removed outlier: 4.020A pdb=" N LYS H 13 " --> pdb=" O GLY H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 21 removed outlier: 4.155A pdb=" N ASP H 21 " --> pdb=" O ALA H 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 18 through 21' Processing helix chain 'H' and resid 72 through 80 removed outlier: 4.031A pdb=" N SER H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS H 77 " --> pdb=" O THR H 73 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE H 78 " --> pdb=" O SER H 74 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS H 80 " --> pdb=" O SER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 153 removed outlier: 4.226A pdb=" N HIS H 153 " --> pdb=" O ARG H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 217 removed outlier: 3.880A pdb=" N LYS H 217 " --> pdb=" O ASN H 213 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.762A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 1152 through 1156 removed outlier: 5.787A pdb=" N LYS A1152 " --> pdb=" O LEU A1301 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A1303 " --> pdb=" O LYS A1152 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N PHE A1154 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N GLU A1305 " --> pdb=" O PHE A1154 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL A1156 " --> pdb=" O GLU A1305 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR A1127 " --> pdb=" O GLU A1350 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N ILE A1352 " --> pdb=" O THR A1127 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU A1129 " --> pdb=" O ILE A1352 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1519 through 1521 removed outlier: 3.711A pdb=" N VAL A1749 " --> pdb=" O ASP A1520 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.166A pdb=" N LYS B 136 " --> pdb=" O ARG B 166 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ALA B 168 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE B 138 " --> pdb=" O ALA B 168 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ALA B 170 " --> pdb=" O ILE B 138 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU B 140 " --> pdb=" O ALA B 170 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.279A pdb=" N LEU C 88 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ASP C 125 " --> pdb=" O LEU C 88 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LEU C 90 " --> pdb=" O ASP C 125 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU C 57 " --> pdb=" O PHE C 172 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.732A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 105 through 109 removed outlier: 6.174A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL D 147 " --> pdb=" O ARG D 175 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 68 through 75 removed outlier: 6.616A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 60 through 61 removed outlier: 4.679A pdb=" N ILE F 87 " --> pdb=" O GLU F 104 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU F 104 " --> pdb=" O ILE F 87 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 66 through 71 removed outlier: 5.251A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 166 through 171 removed outlier: 3.756A pdb=" N SER F 170 " --> pdb=" O VAL F 159 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU F 205 " --> pdb=" O ILE F 160 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 61 removed outlier: 4.082A pdb=" N THR G 59 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG G 61 " --> pdb=" O GLU G 3 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU G 3 " --> pdb=" O ARG G 61 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N TYR G 114 " --> pdb=" O LEU G 101 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 67 through 71 removed outlier: 6.525A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 60 through 61 removed outlier: 3.600A pdb=" N GLU H 3 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N SER H 112 " --> pdb=" O PHE H 103 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 6.329A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 249 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL H 237 " --> pdb=" O TYR H 249 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU H 251 " --> pdb=" O LEU H 235 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU H 235 " --> pdb=" O LEU H 251 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 178 through 183 1102 hydrogen bonds defined for protein. 3201 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: 4.14 Time building geometry restraints manager: 2.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 7249 1.36 - 1.50: 5539 1.50 - 1.65: 9181 1.65 - 1.80: 122 1.80 - 1.95: 95 Bond restraints: 22186 Sorted by residual: bond pdb=" C THR H 219 " pdb=" N PRO H 220 " ideal model delta sigma weight residual 1.334 1.376 -0.042 8.40e-03 1.42e+04 2.50e+01 bond pdb=" O3B AGS A2002 " pdb=" PB AGS A2002 " 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 B 402 " pdb=" PB AGS B 402 " ideal model delta sigma weight residual 1.673 1.577 0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" O3B AGS C 402 " pdb=" PB AGS C 402 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.13e+01 bond pdb=" O3B AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.09e+01 ... (remaining 22181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 29161 2.41 - 4.82: 656 4.82 - 7.23: 111 7.23 - 9.64: 47 9.64 - 12.05: 16 Bond angle restraints: 29991 Sorted by residual: angle pdb=" CA LYS E 327 " pdb=" CB LYS E 327 " pdb=" CG LYS E 327 " ideal model delta sigma weight residual 114.10 124.26 -10.16 2.00e+00 2.50e-01 2.58e+01 angle pdb=" CA GLN G 204 " pdb=" CB GLN G 204 " pdb=" CG GLN G 204 " ideal model delta sigma weight residual 114.10 123.88 -9.78 2.00e+00 2.50e-01 2.39e+01 angle pdb=" CB GLU E 333 " pdb=" CG GLU E 333 " pdb=" CD GLU E 333 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.70e+00 3.46e-01 1.94e+01 angle pdb=" CA TRP A1679 " pdb=" CB TRP A1679 " pdb=" CG TRP A1679 " ideal model delta sigma weight residual 113.60 121.69 -8.09 1.90e+00 2.77e-01 1.81e+01 angle pdb=" CB GLN G 204 " pdb=" CG GLN G 204 " pdb=" CD GLN G 204 " ideal model delta sigma weight residual 112.60 119.71 -7.11 1.70e+00 3.46e-01 1.75e+01 ... (remaining 29986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.91: 13191 33.91 - 67.83: 498 67.83 - 101.74: 47 101.74 - 135.65: 5 135.65 - 169.57: 7 Dihedral angle restraints: 13748 sinusoidal: 5683 harmonic: 8065 Sorted by residual: dihedral pdb=" O2A ADP E2000 " pdb=" O3A ADP E2000 " pdb=" PA ADP E2000 " pdb=" PB ADP E2000 " ideal model delta sinusoidal sigma weight residual 300.00 140.78 159.22 1 2.00e+01 2.50e-03 4.64e+01 dihedral pdb=" CA GLU H 198 " pdb=" C GLU H 198 " pdb=" N MET H 199 " pdb=" CA MET H 199 " ideal model delta harmonic sigma weight residual -180.00 -150.72 -29.28 0 5.00e+00 4.00e-02 3.43e+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 -87.20 169.57 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 13745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 3237 0.099 - 0.198: 220 0.198 - 0.296: 14 0.296 - 0.395: 1 0.395 - 0.494: 1 Chirality restraints: 3473 Sorted by residual: chirality pdb=" CB ILE B 73 " pdb=" CA ILE B 73 " pdb=" CG1 ILE B 73 " pdb=" CG2 ILE B 73 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.10e+00 chirality pdb=" CB ILE G 11 " pdb=" CA ILE G 11 " pdb=" CG1 ILE G 11 " pdb=" CG2 ILE G 11 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C3' AGS B 402 " pdb=" C2' AGS B 402 " pdb=" C4' AGS B 402 " pdb=" O3' AGS B 402 " both_signs ideal model delta sigma weight residual False -2.37 -2.66 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 3470 not shown) Planarity restraints: 3815 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS A1189 " -0.072 5.00e-02 4.00e+02 1.10e-01 1.94e+01 pdb=" N PRO A1190 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A1190 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO A1190 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA H 252 " -0.066 5.00e-02 4.00e+02 9.80e-02 1.54e+01 pdb=" N PRO H 253 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO H 253 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO H 253 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 138 " 0.019 2.00e-02 2.50e+03 3.89e-02 1.51e+01 pdb=" C LYS H 138 " -0.067 2.00e-02 2.50e+03 pdb=" O LYS H 138 " 0.026 2.00e-02 2.50e+03 pdb=" N MET H 139 " 0.023 2.00e-02 2.50e+03 ... (remaining 3812 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 201 2.57 - 3.16: 16877 3.16 - 3.74: 35380 3.74 - 4.32: 46634 4.32 - 4.90: 78102 Nonbonded interactions: 177194 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 1.992 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 1.994 2.170 nonbonded pdb="MG MG C 401 " pdb=" O2G AGS C 402 " model vdw 2.029 2.170 nonbonded pdb=" OG1 THR B 83 " pdb="MG MG B 401 " model vdw 2.039 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.053 2.170 ... (remaining 177189 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.290 Find NCS groups from input model: 0.260 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: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 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 : 0.005 0.098 22186 Z= 0.259 Angle : 0.937 12.050 29991 Z= 0.481 Chirality : 0.052 0.494 3473 Planarity : 0.006 0.110 3815 Dihedral : 18.017 169.565 8496 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.78 % Rotamer: Outliers : 0.78 % Allowed : 24.77 % 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: -1.22 (0.15), residues: 2734 helix: -0.44 (0.13), residues: 1243 sheet: -0.52 (0.23), residues: 493 loop : -1.24 (0.17), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 91 TYR 0.030 0.002 TYR G 249 PHE 0.056 0.002 PHE E 335 TRP 0.042 0.003 TRP A1403 HIS 0.023 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.26 (22186) covalent geometry : angle 0.93684 / 0.48 (29991) hydrogen bonds : bond 0.12692 / 8.22 ( 1102) hydrogen bonds : angle 6.02134 / 4.17 ( 3201) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 288 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1344 MET cc_start: 0.8071 (mmm) cc_final: 0.7766 (mmt) REVERT: A 1784 LEU cc_start: 0.7889 (mt) cc_final: 0.7237 (pp) REVERT: D 194 CYS cc_start: 0.8257 (m) cc_final: 0.7656 (m) REVERT: E 83 GLU cc_start: 0.7216 (pp20) cc_final: 0.6866 (pm20) REVERT: F 64 ARG cc_start: 0.8136 (tmt170) cc_final: 0.7898 (tmt170) REVERT: H 71 ASN cc_start: 0.7069 (m-40) cc_final: 0.6861 (p0) outliers start: 19 outliers final: 10 residues processed: 299 average time/residue: 0.1492 time to fit residues: 70.6913 Evaluate side-chains 276 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 266 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 1.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 872 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1094 ASN ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 300 HIS ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.174864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.134962 restraints weight = 42986.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.137192 restraints weight = 28469.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.137186 restraints weight = 21626.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.137407 restraints weight = 18419.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.137350 restraints weight = 17939.431| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22186 Z= 0.144 Angle : 0.575 7.574 29991 Z= 0.294 Chirality : 0.041 0.171 3473 Planarity : 0.004 0.071 3815 Dihedral : 11.822 179.100 3126 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.63 % Allowed : 22.64 % Favored : 74.73 % 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: -0.34 (0.16), residues: 2734 helix: 0.50 (0.14), residues: 1255 sheet: -0.42 (0.22), residues: 511 loop : -0.92 (0.19), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 210 TYR 0.018 0.002 TYR G 249 PHE 0.034 0.001 PHE H 214 TRP 0.022 0.001 TRP A1679 HIS 0.011 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (22186) covalent geometry : angle 0.57500 / 0.29 (29991) hydrogen bonds : bond 0.03761 / 2.50 ( 1102) hydrogen bonds : angle 4.70258 / 3.25 ( 3201) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 283 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 ARG cc_start: 0.7906 (mmt-90) cc_final: 0.7559 (mpt-90) REVERT: D 194 CYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7299 (m) REVERT: D 347 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.6456 (mp-120) REVERT: E 156 MET cc_start: 0.5786 (OUTLIER) cc_final: 0.5512 (ppp) REVERT: E 275 ARG cc_start: 0.8588 (tmt90) cc_final: 0.8381 (ttt90) REVERT: F 139 MET cc_start: 0.6200 (ttt) cc_final: 0.5949 (ttt) REVERT: G 49 GLN cc_start: 0.6585 (tp40) cc_final: 0.6177 (tm-30) REVERT: H 254 LYS cc_start: 0.6392 (mttt) cc_final: 0.5896 (mtmm) outliers start: 64 outliers final: 37 residues processed: 329 average time/residue: 0.1497 time to fit residues: 78.4606 Evaluate side-chains 300 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 260 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 156 MET Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 42 SER Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 214 PHE Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 241 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 232 optimal weight: 9.9990 chunk 97 optimal weight: 0.0070 chunk 104 optimal weight: 2.9990 chunk 188 optimal weight: 7.9990 chunk 158 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 229 optimal weight: 30.0000 chunk 6 optimal weight: 20.0000 chunk 4 optimal weight: 4.9990 chunk 262 optimal weight: 20.0000 chunk 118 optimal weight: 0.9990 overall best weight: 2.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 872 HIS A1077 HIS ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1481 HIS A1503 ASN B 287 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN F 71 ASN F 179 ASN H 71 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.172913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132695 restraints weight = 42894.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.132966 restraints weight = 30178.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.133894 restraints weight = 24812.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.134061 restraints weight = 20343.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.134229 restraints weight = 19523.526| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 22186 Z= 0.169 Angle : 0.590 8.215 29991 Z= 0.300 Chirality : 0.042 0.141 3473 Planarity : 0.004 0.065 3815 Dihedral : 11.263 177.346 3114 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 3.94 % Allowed : 22.56 % Favored : 73.50 % 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: -0.10 (0.16), residues: 2734 helix: 0.82 (0.15), residues: 1243 sheet: -0.50 (0.22), residues: 502 loop : -0.84 (0.19), residues: 989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 210 TYR 0.015 0.002 TYR F 239 PHE 0.019 0.002 PHE G 214 TRP 0.018 0.002 TRP A1403 HIS 0.013 0.001 HIS B 287 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 (22186) covalent geometry : angle 0.58966 / 0.30 (29991) hydrogen bonds : bond 0.03663 / 2.43 ( 1102) hydrogen bonds : angle 4.60290 / 3.19 ( 3201) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1784 LEU cc_start: 0.7961 (mt) cc_final: 0.7432 (pp) REVERT: C 213 MET cc_start: 0.7473 (tpp) cc_final: 0.7243 (mpp) REVERT: C 288 VAL cc_start: 0.7959 (OUTLIER) cc_final: 0.7581 (t) REVERT: D 347 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6495 (mp-120) REVERT: E 71 HIS cc_start: 0.6786 (m90) cc_final: 0.6415 (m-70) REVERT: E 156 MET cc_start: 0.5881 (ppp) cc_final: 0.5580 (ppp) REVERT: F 116 MET cc_start: 0.8059 (OUTLIER) cc_final: 0.7778 (mtp) REVERT: G 49 GLN cc_start: 0.6709 (tp40) cc_final: 0.6230 (tm-30) REVERT: G 154 ILE cc_start: 0.7578 (OUTLIER) cc_final: 0.7348 (mt) REVERT: H 40 MET cc_start: 0.6264 (tmm) cc_final: 0.5764 (tpt) REVERT: H 164 LYS cc_start: 0.5366 (OUTLIER) cc_final: 0.5064 (mmmt) REVERT: H 229 MET cc_start: 0.5446 (tpt) cc_final: 0.5206 (tpp) REVERT: H 254 LYS cc_start: 0.6402 (mttt) cc_final: 0.5880 (mtmm) outliers start: 96 outliers final: 55 residues processed: 351 average time/residue: 0.1503 time to fit residues: 84.0476 Evaluate side-chains 318 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 258 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1148 GLU Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 116 MET Chi-restraints excluded: chain F residue 219 THR Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 217 optimal weight: 6.9990 chunk 192 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 5 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 242 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 258 optimal weight: 30.0000 chunk 127 optimal weight: 0.5980 overall best weight: 2.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 48 ASN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 ASN B 324 HIS C 37 HIS ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.176812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.136432 restraints weight = 42744.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.137455 restraints weight = 29075.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137793 restraints weight = 23051.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.137940 restraints weight = 19924.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.138676 restraints weight = 19332.721| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 22186 Z= 0.203 Angle : 0.624 8.797 29991 Z= 0.318 Chirality : 0.043 0.210 3473 Planarity : 0.005 0.104 3815 Dihedral : 11.032 173.648 3114 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.01 % Allowed : 22.80 % Favored : 72.19 % 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: -0.09 (0.16), residues: 2734 helix: 0.83 (0.15), residues: 1248 sheet: -0.48 (0.23), residues: 495 loop : -0.86 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 105 TYR 0.017 0.002 TYR F 239 PHE 0.036 0.002 PHE H 215 TRP 0.018 0.002 TRP A1403 HIS 0.011 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00472 / 0.20 (22186) covalent geometry : angle 0.62429 / 0.32 (29991) hydrogen bonds : bond 0.03759 / 2.49 ( 1102) hydrogen bonds : angle 4.64174 / 3.21 ( 3201) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 273 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 LYS cc_start: 0.7579 (OUTLIER) cc_final: 0.7313 (tptm) REVERT: A 1784 LEU cc_start: 0.8163 (mt) cc_final: 0.7664 (pp) REVERT: C 288 VAL cc_start: 0.8078 (OUTLIER) cc_final: 0.7704 (t) REVERT: D 264 ASP cc_start: 0.6314 (OUTLIER) cc_final: 0.5999 (t0) REVERT: D 347 GLN cc_start: 0.7818 (OUTLIER) cc_final: 0.6486 (mp-120) REVERT: D 356 MET cc_start: 0.8239 (tmm) cc_final: 0.7965 (tmm) REVERT: E 71 HIS cc_start: 0.7168 (m90) cc_final: 0.6835 (m-70) REVERT: E 79 LYS cc_start: 0.6844 (mmtt) cc_final: 0.6585 (mmtt) REVERT: E 231 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: E 256 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6443 (tmm-80) REVERT: F 211 TYR cc_start: 0.7841 (m-80) cc_final: 0.7635 (m-10) REVERT: G 139 MET cc_start: 0.7559 (tpp) cc_final: 0.7303 (ttm) REVERT: G 154 ILE cc_start: 0.7764 (OUTLIER) cc_final: 0.7488 (mt) REVERT: G 177 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7408 (p0) REVERT: H 254 LYS cc_start: 0.6323 (mttt) cc_final: 0.5786 (mtmm) outliers start: 122 outliers final: 76 residues processed: 361 average time/residue: 0.1470 time to fit residues: 84.5255 Evaluate side-chains 343 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 259 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1368 MET Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 315 GLU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 95 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 139 optimal weight: 20.0000 chunk 237 optimal weight: 4.9990 chunk 62 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 157 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 90 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.171285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130226 restraints weight = 42655.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.130949 restraints weight = 30257.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.131589 restraints weight = 24950.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.131757 restraints weight = 20467.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.131883 restraints weight = 19795.691| |-----------------------------------------------------------------------------| r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22186 Z= 0.194 Angle : 0.616 9.825 29991 Z= 0.312 Chirality : 0.043 0.249 3473 Planarity : 0.004 0.084 3815 Dihedral : 10.879 175.038 3112 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.93 % Allowed : 23.91 % Favored : 71.16 % 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: -0.15 (0.16), residues: 2734 helix: 0.79 (0.15), residues: 1260 sheet: -0.54 (0.22), residues: 496 loop : -0.92 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 210 TYR 0.016 0.002 TYR G 250 PHE 0.034 0.002 PHE H 215 TRP 0.021 0.002 TRP A1403 HIS 0.012 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.19 (22186) covalent geometry : angle 0.61622 / 0.31 (29991) hydrogen bonds : bond 0.03699 / 2.45 ( 1102) hydrogen bonds : angle 4.58041 / 3.18 ( 3201) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 277 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7331 (tptm) REVERT: A 1325 MET cc_start: 0.6797 (mmt) cc_final: 0.6573 (mmm) REVERT: A 1823 TYR cc_start: 0.6410 (t80) cc_final: 0.6196 (t80) REVERT: C 98 ILE cc_start: 0.6540 (OUTLIER) cc_final: 0.6151 (pt) REVERT: C 288 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7652 (t) REVERT: D 264 ASP cc_start: 0.6305 (t0) cc_final: 0.6013 (t0) REVERT: D 347 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.6422 (mp-120) REVERT: E 71 HIS cc_start: 0.7209 (m90) cc_final: 0.6957 (m-70) REVERT: E 79 LYS cc_start: 0.6852 (mmtt) cc_final: 0.6617 (mmtt) REVERT: E 231 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: E 256 ARG cc_start: 0.6946 (OUTLIER) cc_final: 0.6540 (tmm-80) REVERT: E 333 GLU cc_start: 0.6576 (tm-30) cc_final: 0.6274 (tm-30) REVERT: E 338 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8434 (mtmt) REVERT: G 139 MET cc_start: 0.7552 (tpp) cc_final: 0.7292 (ttm) REVERT: G 154 ILE cc_start: 0.7748 (OUTLIER) cc_final: 0.7468 (mt) REVERT: G 210 ARG cc_start: 0.6857 (tpm170) cc_final: 0.6595 (tpm170) REVERT: H 40 MET cc_start: 0.6166 (tmm) cc_final: 0.5903 (tmm) REVERT: H 133 TYR cc_start: 0.3132 (m-80) cc_final: 0.2853 (m-80) outliers start: 120 outliers final: 73 residues processed: 373 average time/residue: 0.1508 time to fit residues: 90.2705 Evaluate side-chains 349 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 268 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1180 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 287 PHE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 231 GLU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 338 LYS Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 107 optimal weight: 5.9990 chunk 166 optimal weight: 8.9990 chunk 251 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 198 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 59 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 GLN B 272 ASN ** C 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN E 126 GLN ** E 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.170268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.130093 restraints weight = 43068.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.130541 restraints weight = 31121.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.131387 restraints weight = 24828.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.131524 restraints weight = 20767.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.131702 restraints weight = 19746.893| |-----------------------------------------------------------------------------| r_work (final): 0.3874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 22186 Z= 0.175 Angle : 0.613 10.299 29991 Z= 0.311 Chirality : 0.043 0.255 3473 Planarity : 0.004 0.074 3815 Dihedral : 10.735 177.816 3112 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.64 % Allowed : 24.53 % Favored : 70.83 % 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: -0.12 (0.16), residues: 2734 helix: 0.84 (0.15), residues: 1267 sheet: -0.58 (0.22), residues: 496 loop : -0.91 (0.19), residues: 971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 91 TYR 0.026 0.002 TYR E 330 PHE 0.029 0.001 PHE H 215 TRP 0.029 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (22186) covalent geometry : angle 0.61256 / 0.31 (29991) hydrogen bonds : bond 0.03643 / 2.41 ( 1102) hydrogen bonds : angle 4.55922 / 3.17 ( 3201) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 280 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1172 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7364 (tptm) REVERT: C 98 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6342 (pp) REVERT: C 288 VAL cc_start: 0.8057 (OUTLIER) cc_final: 0.7687 (t) REVERT: D 264 ASP cc_start: 0.6249 (OUTLIER) cc_final: 0.6044 (t0) REVERT: D 347 GLN cc_start: 0.7802 (OUTLIER) cc_final: 0.6441 (mp-120) REVERT: E 79 LYS cc_start: 0.6914 (mmtt) cc_final: 0.6653 (mmtt) REVERT: E 256 ARG cc_start: 0.6839 (OUTLIER) cc_final: 0.6477 (tmm-80) REVERT: E 333 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6449 (tm-30) REVERT: G 139 MET cc_start: 0.7521 (tpp) cc_final: 0.7277 (ttm) REVERT: G 154 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7415 (mt) REVERT: G 251 LEU cc_start: 0.8891 (tp) cc_final: 0.8656 (tp) REVERT: H 237 VAL cc_start: 0.7645 (t) cc_final: 0.7225 (p) outliers start: 113 outliers final: 79 residues processed: 366 average time/residue: 0.1480 time to fit residues: 86.4529 Evaluate side-chains 352 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 266 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1172 LYS Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 99 ASP Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 103 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 230 optimal weight: 20.0000 chunk 177 optimal weight: 0.0570 chunk 37 optimal weight: 0.0970 chunk 70 optimal weight: 6.9990 chunk 117 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 9.9990 chunk 168 optimal weight: 9.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.171185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.127955 restraints weight = 43024.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.127752 restraints weight = 31554.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129130 restraints weight = 22971.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.129576 restraints weight = 21207.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.129850 restraints weight = 19493.060| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22186 Z= 0.139 Angle : 0.596 10.577 29991 Z= 0.303 Chirality : 0.042 0.234 3473 Planarity : 0.004 0.075 3815 Dihedral : 10.513 179.087 3112 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.94 % Allowed : 25.39 % Favored : 70.67 % 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: 0.05 (0.16), residues: 2734 helix: 1.04 (0.15), residues: 1252 sheet: -0.60 (0.22), residues: 496 loop : -0.82 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 210 TYR 0.031 0.002 TYR E 330 PHE 0.025 0.001 PHE H 215 TRP 0.027 0.002 TRP A1403 HIS 0.013 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22186) covalent geometry : angle 0.59585 / 0.30 (29991) hydrogen bonds : bond 0.03438 / 2.28 ( 1102) hydrogen bonds : angle 4.46136 / 3.09 ( 3201) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1818 ARG cc_start: 0.3823 (OUTLIER) cc_final: 0.2803 (mmp-170) REVERT: C 288 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.6688 (m) REVERT: D 194 CYS cc_start: 0.8136 (m) cc_final: 0.7685 (m) REVERT: D 264 ASP cc_start: 0.6316 (t0) cc_final: 0.5979 (t0) REVERT: D 347 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.6391 (mp-120) REVERT: E 71 HIS cc_start: 0.7171 (m90) cc_final: 0.6841 (m-70) REVERT: E 79 LYS cc_start: 0.6644 (mmtt) cc_final: 0.6416 (mmtt) REVERT: E 256 ARG cc_start: 0.6883 (OUTLIER) cc_final: 0.6517 (tmm-80) REVERT: F 40 MET cc_start: 0.7019 (tpp) cc_final: 0.6499 (tpp) REVERT: F 97 ASP cc_start: 0.7406 (m-30) cc_final: 0.7131 (t0) REVERT: G 139 MET cc_start: 0.7479 (tpp) cc_final: 0.7257 (ttm) REVERT: G 251 LEU cc_start: 0.8773 (tp) cc_final: 0.8482 (tp) REVERT: H 40 MET cc_start: 0.6569 (tmm) cc_final: 0.6167 (tmm) REVERT: H 237 VAL cc_start: 0.7837 (t) cc_final: 0.7400 (p) REVERT: H 254 LYS cc_start: 0.5909 (mttm) cc_final: 0.5529 (mtmm) outliers start: 96 outliers final: 73 residues processed: 356 average time/residue: 0.1513 time to fit residues: 85.1295 Evaluate side-chains 342 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 265 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1461 THR Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 85 SER Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 225 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 225 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 260 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 161 optimal weight: 7.9990 chunk 42 optimal weight: 20.0000 chunk 120 optimal weight: 4.9990 chunk 242 optimal weight: 1.9990 chunk 248 optimal weight: 30.0000 chunk 79 optimal weight: 3.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** D 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.168040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127551 restraints weight = 43086.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.127401 restraints weight = 31380.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.128265 restraints weight = 27370.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.128570 restraints weight = 21809.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.128672 restraints weight = 21216.902| |-----------------------------------------------------------------------------| r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 22186 Z= 0.272 Angle : 0.725 11.651 29991 Z= 0.368 Chirality : 0.046 0.349 3473 Planarity : 0.005 0.075 3815 Dihedral : 10.518 177.334 3112 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.68 % Allowed : 24.77 % Favored : 70.54 % 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: 2734 helix: 0.53 (0.15), residues: 1269 sheet: -0.71 (0.22), residues: 490 loop : -1.07 (0.19), residues: 975 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 210 TYR 0.037 0.003 TYR E 330 PHE 0.024 0.002 PHE H 215 TRP 0.037 0.002 TRP A1403 HIS 0.015 0.002 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.27 (22186) covalent geometry : angle 0.72462 / 0.37 (29991) hydrogen bonds : bond 0.04302 / 2.84 ( 1102) hydrogen bonds : angle 4.80754 / 3.33 ( 3201) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 279 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1646 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 1818 ARG cc_start: 0.3979 (OUTLIER) cc_final: 0.2914 (mmp-170) REVERT: B 282 LEU cc_start: 0.8402 (OUTLIER) cc_final: 0.7981 (tt) REVERT: C 288 VAL cc_start: 0.8196 (OUTLIER) cc_final: 0.7831 (t) REVERT: D 264 ASP cc_start: 0.6304 (OUTLIER) cc_final: 0.5958 (t0) REVERT: D 347 GLN cc_start: 0.7843 (OUTLIER) cc_final: 0.6371 (mp-120) REVERT: E 79 LYS cc_start: 0.6924 (mmtt) cc_final: 0.6666 (mmtt) REVERT: E 256 ARG cc_start: 0.6785 (OUTLIER) cc_final: 0.6377 (tmm-80) REVERT: G 154 ILE cc_start: 0.7914 (OUTLIER) cc_final: 0.7599 (mt) REVERT: G 177 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.7498 (p0) REVERT: G 210 ARG cc_start: 0.6917 (tpm170) cc_final: 0.6696 (tpm170) REVERT: H 229 MET cc_start: 0.5613 (tpt) cc_final: 0.5032 (tpp) REVERT: H 237 VAL cc_start: 0.7718 (t) cc_final: 0.7270 (p) outliers start: 114 outliers final: 80 residues processed: 363 average time/residue: 0.1522 time to fit residues: 87.9329 Evaluate side-chains 359 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 270 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1340 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1387 THR Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1468 ILE Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 69 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 130 MET Chi-restraints excluded: chain C residue 162 ILE Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 280 ILE Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 288 VAL Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 157 SER Chi-restraints excluded: chain D residue 227 ILE Chi-restraints excluded: chain D residue 263 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 314 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 55 ILE Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 274 VAL Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 225 VAL Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 21 ASP Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 148 CYS Chi-restraints excluded: chain H residue 150 ASP Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 167 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 263 optimal weight: 40.0000 chunk 164 optimal weight: 0.8980 chunk 209 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 177 optimal weight: 0.6980 chunk 208 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 211 optimal weight: 20.0000 chunk 229 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1176 GLN A1186 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 GLN ** F 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.171675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.131337 restraints weight = 42835.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.131580 restraints weight = 28136.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.132138 restraints weight = 22239.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.132485 restraints weight = 19702.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.132621 restraints weight = 19038.446| |-----------------------------------------------------------------------------| r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22186 Z= 0.122 Angle : 0.617 12.329 29991 Z= 0.310 Chirality : 0.042 0.253 3473 Planarity : 0.004 0.093 3815 Dihedral : 10.195 177.886 3112 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.16 % Allowed : 26.25 % Favored : 70.58 % 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: 0.02 (0.16), residues: 2734 helix: 1.03 (0.15), residues: 1265 sheet: -0.61 (0.23), residues: 490 loop : -0.87 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 146 TYR 0.027 0.002 TYR E 330 PHE 0.022 0.001 PHE H 215 TRP 0.021 0.002 TRP A1403 HIS 0.014 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 (22186) covalent geometry : angle 0.61717 / 0.31 (29991) hydrogen bonds : bond 0.03416 / 2.26 ( 1102) hydrogen bonds : angle 4.47921 / 3.11 ( 3201) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 291 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1646 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8174 (tt) REVERT: A 1707 GLU cc_start: 0.7035 (mm-30) cc_final: 0.6720 (mm-30) REVERT: A 1818 ARG cc_start: 0.3801 (OUTLIER) cc_final: 0.2885 (mmp-170) REVERT: B 62 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8331 (t) REVERT: D 264 ASP cc_start: 0.6293 (t0) cc_final: 0.6030 (t0) REVERT: D 347 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6302 (mp-120) REVERT: E 79 LYS cc_start: 0.6692 (mmtt) cc_final: 0.6457 (mmtt) REVERT: E 256 ARG cc_start: 0.6836 (OUTLIER) cc_final: 0.6445 (tmm-80) REVERT: E 275 ARG cc_start: 0.8775 (ttt90) cc_final: 0.8537 (ttt90) REVERT: F 40 MET cc_start: 0.6812 (tpp) cc_final: 0.6072 (tpp) REVERT: G 122 ASP cc_start: 0.6167 (p0) cc_final: 0.5718 (p0) REVERT: G 139 MET cc_start: 0.7434 (tpp) cc_final: 0.7211 (ttm) REVERT: G 251 LEU cc_start: 0.8721 (tp) cc_final: 0.8357 (tp) REVERT: H 40 MET cc_start: 0.6330 (tmm) cc_final: 0.5814 (tpt) REVERT: H 237 VAL cc_start: 0.7812 (t) cc_final: 0.7364 (p) REVERT: H 254 LYS cc_start: 0.5814 (mttm) cc_final: 0.5535 (mtmm) outliers start: 77 outliers final: 58 residues processed: 347 average time/residue: 0.1571 time to fit residues: 85.9058 Evaluate side-chains 344 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 281 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1343 LEU Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1787 VAL Chi-restraints excluded: chain A residue 1793 SER Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 113 ASP Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 225 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 240 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 chunk 248 optimal weight: 5.9990 chunk 83 optimal weight: 0.0060 chunk 95 optimal weight: 20.0000 chunk 229 optimal weight: 1.9990 chunk 153 optimal weight: 0.8980 chunk 158 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1147 GLN A1179 GLN A1186 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 ASN ** F 71 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 = 0.4430 r_free = 0.4430 target = 0.172452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.132062 restraints weight = 43171.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.133210 restraints weight = 28523.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.133680 restraints weight = 21630.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.134007 restraints weight = 19309.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.134196 restraints weight = 18784.659| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22186 Z= 0.119 Angle : 0.634 12.944 29991 Z= 0.318 Chirality : 0.042 0.296 3473 Planarity : 0.004 0.113 3815 Dihedral : 10.018 177.894 3110 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.79 % Allowed : 26.71 % Favored : 70.50 % 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: 2734 helix: 1.08 (0.15), residues: 1275 sheet: -0.57 (0.23), residues: 491 loop : -0.83 (0.20), residues: 968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 91 TYR 0.026 0.002 TYR E 330 PHE 0.048 0.001 PHE H 215 TRP 0.033 0.002 TRP A1403 HIS 0.015 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (22186) covalent geometry : angle 0.63422 / 0.32 (29991) hydrogen bonds : bond 0.03371 / 2.22 ( 1102) hydrogen bonds : angle 4.45226 / 3.09 ( 3201) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5468 Ramachandran restraints generated. 2734 Oldfield, 0 Emsley, 2734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 286 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1344 MET cc_start: 0.7744 (mmm) cc_final: 0.7493 (mmt) REVERT: A 1386 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7208 (mm) REVERT: A 1646 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8171 (tt) REVERT: A 1707 GLU cc_start: 0.6972 (mm-30) cc_final: 0.6641 (mm-30) REVERT: A 1818 ARG cc_start: 0.3862 (OUTLIER) cc_final: 0.2958 (mmp-170) REVERT: B 62 VAL cc_start: 0.8555 (OUTLIER) cc_final: 0.8307 (t) REVERT: D 264 ASP cc_start: 0.6326 (t0) cc_final: 0.6093 (t0) REVERT: D 347 GLN cc_start: 0.7537 (OUTLIER) cc_final: 0.6174 (mp-120) REVERT: E 256 ARG cc_start: 0.6855 (OUTLIER) cc_final: 0.6491 (tmm-80) REVERT: E 275 ARG cc_start: 0.8746 (ttt90) cc_final: 0.8536 (ttt90) REVERT: G 122 ASP cc_start: 0.6034 (p0) cc_final: 0.5673 (p0) REVERT: G 251 LEU cc_start: 0.8699 (tp) cc_final: 0.8328 (tp) REVERT: H 40 MET cc_start: 0.6373 (tmm) cc_final: 0.5891 (tpt) REVERT: H 71 ASN cc_start: 0.6547 (m110) cc_final: 0.6166 (p0) REVERT: H 237 VAL cc_start: 0.7820 (t) cc_final: 0.7347 (p) REVERT: H 254 LYS cc_start: 0.5834 (mttm) cc_final: 0.5555 (mtmm) outliers start: 68 outliers final: 55 residues processed: 332 average time/residue: 0.1590 time to fit residues: 82.9164 Evaluate side-chains 326 residues out of total 2434 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 265 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1186 ASN Chi-restraints excluded: chain A residue 1188 GLN Chi-restraints excluded: chain A residue 1336 THR Chi-restraints excluded: chain A residue 1386 LEU Chi-restraints excluded: chain A residue 1394 ARG Chi-restraints excluded: chain A residue 1646 LEU Chi-restraints excluded: chain A residue 1779 PHE Chi-restraints excluded: chain A residue 1818 ARG Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 158 MET Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain C residue 3 THR Chi-restraints excluded: chain C residue 212 ASP Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 347 GLN Chi-restraints excluded: chain E residue 11 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 256 ARG Chi-restraints excluded: chain E residue 262 ILE Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 283 THR Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 7 VAL Chi-restraints excluded: chain F residue 11 ILE Chi-restraints excluded: chain F residue 29 ASP Chi-restraints excluded: chain F residue 41 ASP Chi-restraints excluded: chain F residue 43 SER Chi-restraints excluded: chain F residue 71 ASN Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 99 LEU Chi-restraints excluded: chain F residue 159 VAL Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 230 SER Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain G residue 2 PHE Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 SER Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 137 VAL Chi-restraints excluded: chain G residue 154 ILE Chi-restraints excluded: chain G residue 160 ILE Chi-restraints excluded: chain G residue 196 THR Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain H residue 28 TRP Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 241 ILE Chi-restraints excluded: chain H residue 244 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 97 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 185 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 134 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 chunk 146 optimal weight: 10.0000 chunk 192 optimal weight: 0.0970 chunk 249 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1186 ASN ** C 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.171747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.132074 restraints weight = 43053.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.133373 restraints weight = 30255.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.133910 restraints weight = 22845.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.134059 restraints weight = 20131.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.134212 restraints weight = 18901.811| |-----------------------------------------------------------------------------| r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22186 Z= 0.139 Angle : 0.647 12.717 29991 Z= 0.321 Chirality : 0.043 0.284 3473 Planarity : 0.004 0.114 3815 Dihedral : 9.973 176.996 3110 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.67 % Allowed : 26.75 % Favored : 70.58 % 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: 0.09 (0.16), residues: 2734 helix: 1.06 (0.15), residues: 1273 sheet: -0.55 (0.23), residues: 489 loop : -0.84 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 91 TYR 0.025 0.002 TYR E 330 PHE 0.049 0.001 PHE H 215 TRP 0.035 0.002 TRP A1403 HIS 0.016 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (22186) covalent geometry : angle 0.64699 / 0.32 (29991) hydrogen bonds : bond 0.03412 / 2.26 ( 1102) hydrogen bonds : angle 4.42439 / 3.07 ( 3201) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3629.76 seconds wall clock time: 64 minutes 8.24 seconds (3848.24 seconds total)