Starting phenix.real_space_refine on Wed Jun 18 20:14:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uii_42295/06_2025/8uii_42295.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uii_42295/06_2025/8uii_42295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8uii_42295/06_2025/8uii_42295.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uii_42295/06_2025/8uii_42295.map" model { file = "/net/cci-nas-00/data/ceres_data/8uii_42295/06_2025/8uii_42295.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uii_42295/06_2025/8uii_42295.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 14 5.49 5 Mg 4 5.21 5 S 145 5.16 5 C 13664 2.51 5 N 3687 2.21 5 O 4190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21704 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 5117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 641, 5117 Classifications: {'peptide': 641} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 619} Chain breaks: 5 Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2514 Classifications: {'peptide': 319} Link IDs: {'PTRANS': 13, 'TRANS': 305} Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2582 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 311} Chain: "D" Number of atoms: 2536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 328, 2536 Classifications: {'peptide': 328} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 314} Chain: "E" Number of atoms: 2773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2773 Classifications: {'peptide': 348} Link IDs: {'PTRANS': 15, 'TRANS': 332} Chain: "F" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "H" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2009 Classifications: {'peptide': 261} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 253} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 12.51, per 1000 atoms: 0.58 Number of scatterers: 21704 At special positions: 0 Unit cell: (127.512, 123.372, 144.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 145 16.00 P 14 15.00 Mg 4 11.99 O 4190 8.00 N 3687 7.00 C 13664 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.00 Conformation dependent library (CDL) restraints added in 2.9 seconds 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5218 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 14 sheets defined 51.1% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 877 through 881 removed outlier: 3.659A pdb=" N CYS A 881 " --> pdb=" O ASP A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 895 Processing helix chain 'A' and resid 940 through 955 Processing helix chain 'A' and resid 963 through 972 Processing helix chain 'A' and resid 1053 through 1058 Processing helix chain 'A' and resid 1069 through 1098 Processing helix chain 'A' and resid 1137 through 1149 Processing helix chain 'A' and resid 1163 through 1177 removed outlier: 6.193A pdb=" N GLU A1173 " --> pdb=" O SER A1169 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA A1174 " --> pdb=" O GLN A1170 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N THR A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1327 Processing helix chain 'A' and resid 1340 through 1345 removed outlier: 3.722A pdb=" N MET A1344 " --> pdb=" O THR A1340 " (cutoff:3.500A) Processing helix chain 'A' and resid 1358 through 1373 removed outlier: 3.594A pdb=" N VAL A1362 " --> pdb=" O SER A1358 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU A1373 " --> pdb=" O ILE A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1389 removed outlier: 3.715A pdb=" N PHE A1382 " --> pdb=" O ASP A1378 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1406 Processing helix chain 'A' and resid 1457 through 1463 removed outlier: 3.818A pdb=" N THR A1461 " --> pdb=" O GLY A1457 " (cutoff:3.500A) Processing helix chain 'A' and resid 1474 through 1481 Processing helix chain 'A' and resid 1485 through 1501 Processing helix chain 'A' and resid 1505 through 1510 Processing helix chain 'A' and resid 1510 through 1515 Processing helix chain 'A' and resid 1633 through 1663 removed outlier: 3.805A pdb=" N LEU A1641 " --> pdb=" O LYS A1637 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N VAL A1642 " --> pdb=" O CYS A1638 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A1663 " --> pdb=" O LEU A1659 " (cutoff:3.500A) Processing helix chain 'A' and resid 1698 through 1729 removed outlier: 3.580A pdb=" N SER A1702 " --> pdb=" O ASP A1698 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY A1706 " --> pdb=" O SER A1702 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLU A1707 " --> pdb=" O GLN A1703 " (cutoff:3.500A) Processing helix chain 'A' and resid 1730 through 1737 removed outlier: 3.817A pdb=" N CYS A1734 " --> pdb=" O THR A1730 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1746 Processing helix chain 'A' and resid 1764 through 1779 Processing helix chain 'A' and resid 1783 through 1787 removed outlier: 4.314A pdb=" N TYR A1786 " --> pdb=" O SER A1783 " (cutoff:3.500A) Processing helix chain 'A' and resid 1790 through 1814 removed outlier: 4.727A pdb=" N LEU A1798 " --> pdb=" O ILE A1794 " (cutoff:3.500A) Proline residue: A1799 - end of helix Processing helix chain 'A' and resid 1817 through 1821 Processing helix chain 'A' and resid 1822 through 1827 Processing helix chain 'A' and resid 1832 through 1840 Processing helix chain 'B' and resid 37 through 42 Processing helix chain 'B' and resid 53 through 67 Processing helix chain 'B' and resid 81 through 95 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.833A pdb=" N ILE B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LYS B 121 " --> pdb=" O ARG B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 146 Processing helix chain 'B' and resid 147 through 154 Processing helix chain 'B' and resid 156 through 161 removed outlier: 3.901A pdb=" N TYR B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 177 Processing helix chain 'B' and resid 178 through 184 removed outlier: 3.620A pdb=" N ARG B 184 " --> pdb=" O PRO B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 208 Processing helix chain 'B' and resid 214 through 225 Processing helix chain 'B' and resid 228 through 243 Processing helix chain 'B' and resid 247 through 256 Processing helix chain 'B' and resid 259 through 272 Processing helix chain 'B' and resid 274 through 288 Processing helix chain 'B' and resid 291 through 305 removed outlier: 3.719A pdb=" N THR B 305 " --> pdb=" O ARG B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 330 Processing helix chain 'B' and resid 333 through 350 Processing helix chain 'C' and resid 21 through 26 Processing helix chain 'C' and resid 30 through 34 removed outlier: 3.919A pdb=" N LEU C 34 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 removed outlier: 3.505A pdb=" N GLU C 50 " --> pdb=" O LYS C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 82 through 86 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.098A pdb=" N ILE C 101 " --> pdb=" O GLY C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 111 Processing helix chain 'C' and resid 127 through 130 Processing helix chain 'C' and resid 131 through 145 removed outlier: 4.055A pdb=" N ARG C 140 " --> pdb=" O ASN C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 161 Processing helix chain 'C' and resid 162 through 169 removed outlier: 3.638A pdb=" N ARG C 168 " --> pdb=" O ALA C 164 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS C 169 " --> pdb=" O LEU C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 194 Proline residue: C 184 - end of helix Processing helix chain 'C' and resid 198 through 210 removed outlier: 3.939A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 227 Processing helix chain 'C' and resid 231 through 239 Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 258 through 274 Processing helix chain 'C' and resid 277 through 291 removed outlier: 3.565A pdb=" N LEU C 286 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS C 289 " --> pdb=" O HIS C 285 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 Processing helix chain 'C' and resid 317 through 340 removed outlier: 3.606A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N THR C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP C 334 " --> pdb=" O GLN C 330 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU C 335 " --> pdb=" O VAL C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 44 Processing helix chain 'D' and resid 56 through 68 Processing helix chain 'D' and resid 83 through 96 Processing helix chain 'D' and resid 116 through 129 Processing helix chain 'D' and resid 152 through 155 Processing helix chain 'D' and resid 156 through 170 removed outlier: 3.643A pdb=" N ARG D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N THR D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 187 through 194 removed outlier: 3.732A pdb=" N ARG D 193 " --> pdb=" O PRO D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 219 Processing helix chain 'D' and resid 223 through 235 removed outlier: 3.597A pdb=" N ILE D 227 " --> pdb=" O SER D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 253 removed outlier: 3.792A pdb=" N GLY D 253 " --> pdb=" O THR D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 266 removed outlier: 3.696A pdb=" N ILE D 262 " --> pdb=" O THR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 284 removed outlier: 3.563A pdb=" N ILE D 274 " --> pdb=" O PRO D 270 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY D 284 " --> pdb=" O ALA D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 299 Processing helix chain 'D' and resid 302 through 315 removed outlier: 3.514A pdb=" N LEU D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 320 through 340 Processing helix chain 'D' and resid 343 through 361 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.517A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 30 removed outlier: 3.819A pdb=" N VAL E 30 " --> pdb=" O LEU E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 60 Processing helix chain 'E' and resid 61 through 65 removed outlier: 4.095A pdb=" N VAL E 64 " --> pdb=" O GLY E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 102 removed outlier: 3.500A pdb=" N ALA E 100 " --> pdb=" O PRO E 97 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY E 101 " --> pdb=" O SER E 98 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ASN E 102 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 122 removed outlier: 3.920A pdb=" N MET E 111 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 140 Processing helix chain 'E' and resid 141 through 155 Processing helix chain 'E' and resid 172 through 177 Processing helix chain 'E' and resid 188 through 202 removed outlier: 3.667A pdb=" N LYS E 202 " --> pdb=" O THR E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 222 through 237 Processing helix chain 'E' and resid 249 through 265 removed outlier: 3.625A pdb=" N GLN E 265 " --> pdb=" O ALA E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 283 Processing helix chain 'E' and resid 287 through 302 Processing helix chain 'E' and resid 306 through 325 removed outlier: 4.183A pdb=" N GLU E 310 " --> pdb=" O GLN E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 327 through 348 removed outlier: 4.230A pdb=" N HIS E 331 " --> pdb=" O LYS E 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 19 removed outlier: 4.467A pdb=" N LEU F 12 " --> pdb=" O GLN F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 72 through 80 Processing helix chain 'F' and resid 141 through 153 removed outlier: 3.645A pdb=" N HIS F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 217 through 222 Proline residue: F 220 - end of helix No H-bonds generated for 'chain 'F' and resid 217 through 222' Processing helix chain 'G' and resid 9 through 17 removed outlier: 3.815A pdb=" N LEU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 removed outlier: 4.238A pdb=" N LEU G 22 " --> pdb=" O ALA G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 80 Processing helix chain 'G' and resid 141 through 155 removed outlier: 3.923A pdb=" N HIS G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE G 154 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 217 Processing helix chain 'G' and resid 218 through 222 removed outlier: 3.646A pdb=" N SER G 222 " --> pdb=" O THR G 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 19 removed outlier: 4.398A pdb=" N LEU H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 72 through 79 Processing helix chain 'H' and resid 141 through 153 Processing helix chain 'H' and resid 209 through 217 Processing helix chain 'H' and resid 218 through 222 removed outlier: 3.681A pdb=" N SER H 222 " --> pdb=" O THR H 219 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 872 through 873 removed outlier: 6.218A pdb=" N LEU D 75 " --> pdb=" O PHE D 197 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LEU D 74 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N CYS D 180 " --> pdb=" O LEU D 74 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N PHE D 76 " --> pdb=" O CYS D 180 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL D 147 " --> pdb=" O CYS D 177 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ILE D 179 " --> pdb=" O VAL D 147 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU D 149 " --> pdb=" O ILE D 179 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N LEU D 106 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ASP D 150 " --> pdb=" O LEU D 106 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU D 108 " --> pdb=" O ASP D 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1151 through 1156 removed outlier: 8.603A pdb=" N ILE A1333 " --> pdb=" O SER A1300 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE A1302 " --> pdb=" O ILE A1333 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR A1335 " --> pdb=" O ILE A1302 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N PHE A1304 " --> pdb=" O THR A1335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1519 through 1521 Processing sheet with id=AA4, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 4.034A pdb=" N LYS A1683 " --> pdb=" O GLU E 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1683 through 1685 removed outlier: 4.034A pdb=" N LYS A1683 " --> pdb=" O GLU E 83 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU E 38 " --> pdb=" O LEU E 163 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N CYS E 165 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N VAL E 40 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU E 39 " --> pdb=" O VAL E 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.390A pdb=" N ILE B 72 " --> pdb=" O LEU B 169 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N CYS B 171 " --> pdb=" O ILE B 72 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ILE B 74 " --> pdb=" O CYS B 171 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 73 " --> pdb=" O LEU B 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 87 through 91 removed outlier: 6.256A pdb=" N LYS C 120 " --> pdb=" O ARG C 150 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N CYS C 152 " --> pdb=" O LYS C 120 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 122 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE C 154 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 124 " --> pdb=" O ILE C 154 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 56 " --> pdb=" O LEU C 153 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N CYS C 155 " --> pdb=" O LEU C 56 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU C 58 " --> pdb=" O CYS C 155 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 196 through 197 removed outlier: 6.883A pdb=" N ASP C 196 " --> pdb=" O VAL C 230 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 59 through 62 removed outlier: 3.853A pdb=" N THR F 59 " --> pdb=" O ARG F 5 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 66 through 71 removed outlier: 6.142A pdb=" N GLU F 25 " --> pdb=" O MET F 40 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N MET F 40 " --> pdb=" O GLU F 25 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS F 27 " --> pdb=" O GLN F 38 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN F 38 " --> pdb=" O CYS F 27 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N LYS F 240 " --> pdb=" O THR F 224 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N THR F 224 " --> pdb=" O LYS F 240 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 196 " --> pdb=" O LYS F 138 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 203 through 208 removed outlier: 3.624A pdb=" N LYS F 181 " --> pdb=" O VAL H 111 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N VAL H 111 " --> pdb=" O LYS F 181 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE H 87 " --> pdb=" O GLU H 104 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 59 through 62 removed outlier: 3.920A pdb=" N VAL H 167 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL H 203 " --> pdb=" O CYS H 162 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 71 removed outlier: 6.150A pdb=" N GLU G 25 " --> pdb=" O MET G 40 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N MET G 40 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS G 27 " --> pdb=" O GLN G 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN G 38 " --> pdb=" O CYS G 27 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY G 245 " --> pdb=" O ILE G 241 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LYS G 240 " --> pdb=" O THR G 224 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N THR G 224 " --> pdb=" O LYS G 240 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 66 through 71 removed outlier: 5.627A pdb=" N GLU H 25 " --> pdb=" O MET H 40 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N MET H 40 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N CYS H 27 " --> pdb=" O GLN H 38 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN H 38 " --> pdb=" O CYS H 27 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS H 240 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N THR H 224 " --> pdb=" O LYS H 240 " (cutoff:3.500A) 1154 hydrogen bonds defined for protein. 3318 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.75 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.36: 7218 1.36 - 1.51: 5553 1.51 - 1.66: 9066 1.66 - 1.80: 120 1.80 - 1.95: 95 Bond restraints: 22052 Sorted by residual: bond pdb=" N LEU B 154 " pdb=" CA LEU B 154 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.35e+00 bond pdb=" N MET H 229 " pdb=" CA MET H 229 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.26e-02 6.30e+03 6.07e+00 bond pdb=" C GLU B 257 " pdb=" N PRO B 258 " ideal model delta sigma weight residual 1.333 1.361 -0.029 1.17e-02 7.31e+03 5.99e+00 bond pdb=" C MET F 139 " pdb=" N PRO F 140 " ideal model delta sigma weight residual 1.330 1.360 -0.030 1.22e-02 6.72e+03 5.97e+00 bond pdb=" N MET F 139 " pdb=" CA MET F 139 " ideal model delta sigma weight residual 1.455 1.485 -0.030 1.25e-02 6.40e+03 5.62e+00 ... (remaining 22047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.56: 29356 2.56 - 5.13: 368 5.13 - 7.69: 67 7.69 - 10.26: 18 10.26 - 12.82: 3 Bond angle restraints: 29812 Sorted by residual: angle pdb=" C MET H 244 " pdb=" N GLY H 245 " pdb=" CA GLY H 245 " ideal model delta sigma weight residual 120.72 114.16 6.56 1.33e+00 5.65e-01 2.43e+01 angle pdb=" N LEU F 90 " pdb=" CA LEU F 90 " pdb=" C LEU F 90 " ideal model delta sigma weight residual 109.59 101.71 7.88 1.61e+00 3.86e-01 2.39e+01 angle pdb=" CB MET G 199 " pdb=" CG MET G 199 " pdb=" SD MET G 199 " ideal model delta sigma weight residual 112.70 125.52 -12.82 3.00e+00 1.11e-01 1.83e+01 angle pdb=" CA GLN F 204 " pdb=" CB GLN F 204 " pdb=" CG GLN F 204 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA TYR A1508 " pdb=" CB TYR A1508 " pdb=" CG TYR A1508 " ideal model delta sigma weight residual 113.90 121.44 -7.54 1.80e+00 3.09e-01 1.76e+01 ... (remaining 29807 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 11732 17.95 - 35.90: 1430 35.90 - 53.85: 347 53.85 - 71.80: 64 71.80 - 89.74: 16 Dihedral angle restraints: 13589 sinusoidal: 5575 harmonic: 8014 Sorted by residual: dihedral pdb=" CA LEU G 247 " pdb=" C LEU G 247 " pdb=" N LYS G 248 " pdb=" CA LYS G 248 " ideal model delta harmonic sigma weight residual -180.00 -155.42 -24.58 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA LEU G 79 " pdb=" C LEU G 79 " pdb=" N LYS G 80 " pdb=" CA LYS G 80 " ideal model delta harmonic sigma weight residual 180.00 159.52 20.48 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA PRO G 140 " pdb=" C PRO G 140 " pdb=" N SER G 141 " pdb=" CA SER G 141 " ideal model delta harmonic sigma weight residual -180.00 -159.57 -20.43 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 13586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2966 0.064 - 0.129: 443 0.129 - 0.193: 41 0.193 - 0.258: 9 0.258 - 0.322: 2 Chirality restraints: 3461 Sorted by residual: chirality pdb=" CB ILE F 147 " pdb=" CA ILE F 147 " pdb=" CG1 ILE F 147 " pdb=" CG2 ILE F 147 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA LEU F 90 " pdb=" N LEU F 90 " pdb=" C LEU F 90 " pdb=" CB LEU F 90 " both_signs ideal model delta sigma weight residual False 2.51 2.80 -0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB VAL E 107 " pdb=" CA VAL E 107 " pdb=" CG1 VAL E 107 " pdb=" CG2 VAL E 107 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.64e+00 ... (remaining 3458 not shown) Planarity restraints: 3792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E 113 " -0.014 2.00e-02 2.50e+03 2.77e-02 7.69e+00 pdb=" C LYS E 113 " 0.048 2.00e-02 2.50e+03 pdb=" O LYS E 113 " -0.018 2.00e-02 2.50e+03 pdb=" N THR E 114 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 138 " -0.013 2.00e-02 2.50e+03 2.70e-02 7.27e+00 pdb=" C LYS F 138 " 0.047 2.00e-02 2.50e+03 pdb=" O LYS F 138 " -0.017 2.00e-02 2.50e+03 pdb=" N MET F 139 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO E 173 " -0.044 5.00e-02 4.00e+02 6.57e-02 6.91e+00 pdb=" N PRO E 174 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.037 5.00e-02 4.00e+02 ... (remaining 3789 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 240 2.63 - 3.20: 17921 3.20 - 3.76: 34305 3.76 - 4.33: 46471 4.33 - 4.90: 77944 Nonbonded interactions: 176881 Sorted by model distance: nonbonded pdb=" OE2 GLU A1305 " pdb="MG MG A2001 " model vdw 2.061 2.170 nonbonded pdb="MG MG A2001 " pdb=" O1B AGS A2002 " model vdw 2.071 2.170 nonbonded pdb="MG MG A2001 " pdb=" O3G AGS A2002 " model vdw 2.076 2.170 nonbonded pdb=" OG1 THR A1139 " pdb="MG MG A2001 " model vdw 2.102 2.170 nonbonded pdb="MG MG D 401 " pdb=" O3G AGS D 402 " model vdw 2.112 2.170 ... (remaining 176876 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 48.180 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.090 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 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 : 0.003 0.063 22052 Z= 0.169 Angle : 0.758 12.821 29812 Z= 0.393 Chirality : 0.047 0.322 3461 Planarity : 0.005 0.066 3792 Dihedral : 16.545 89.744 8371 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.70 % Allowed : 23.48 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.15), residues: 2717 helix: -0.30 (0.13), residues: 1275 sheet: -0.42 (0.22), residues: 524 loop : -1.22 (0.18), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 28 HIS 0.006 0.001 HIS A1178 PHE 0.027 0.002 PHE D 96 TYR 0.024 0.002 TYR G 249 ARG 0.013 0.001 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.12126 ( 1151) hydrogen bonds : angle 5.80972 ( 3318) covalent geometry : bond 0.00346 (22052) covalent geometry : angle 0.75782 (29812) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 328 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1166 GLN cc_start: 0.7145 (mt0) cc_final: 0.6928 (mt0) REVERT: D 93 ARG cc_start: 0.6854 (mtp85) cc_final: 0.6595 (mtp180) REVERT: G 16 LEU cc_start: 0.6994 (pp) cc_final: 0.5862 (mp) REVERT: G 249 TYR cc_start: 0.6687 (m-80) cc_final: 0.6461 (m-80) outliers start: 17 outliers final: 9 residues processed: 337 average time/residue: 0.4047 time to fit residues: 206.8647 Evaluate side-chains 311 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 302 time to evaluate : 2.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 177 ASN Chi-restraints excluded: chain G residue 246 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 228 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 109 optimal weight: 0.0980 chunk 212 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 chunk 246 optimal weight: 20.0000 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN A1094 ASN A1481 HIS A1789 ASN B 269 HIS B 332 ASN E 301 HIS ** F 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 179 ASN H 200 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.192751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.148596 restraints weight = 27570.906| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.40 r_work: 0.3578 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.1133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22052 Z= 0.237 Angle : 0.635 8.761 29812 Z= 0.323 Chirality : 0.044 0.149 3461 Planarity : 0.004 0.052 3792 Dihedral : 7.906 75.524 3040 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 3.93 % Allowed : 20.13 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2717 helix: 0.41 (0.14), residues: 1260 sheet: -0.46 (0.23), residues: 516 loop : -0.99 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1079 HIS 0.006 0.001 HIS E 92 PHE 0.022 0.002 PHE D 126 TYR 0.035 0.002 TYR G 249 ARG 0.005 0.001 ARG E 214 Details of bonding type rmsd hydrogen bonds : bond 0.04302 ( 1151) hydrogen bonds : angle 4.77828 ( 3318) covalent geometry : bond 0.00567 (22052) covalent geometry : angle 0.63480 (29812) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 313 time to evaluate : 2.349 Fit side-chains revert: symmetry clash REVERT: A 1157 ASN cc_start: 0.8012 (OUTLIER) cc_final: 0.7701 (m-40) REVERT: A 1181 ASP cc_start: 0.7436 (t0) cc_final: 0.7137 (t0) REVERT: B 89 LEU cc_start: 0.8012 (OUTLIER) cc_final: 0.7520 (tp) REVERT: C 182 MET cc_start: 0.7292 (ttt) cc_final: 0.6996 (ttt) REVERT: D 93 ARG cc_start: 0.7076 (mtp85) cc_final: 0.6770 (mtp180) REVERT: D 94 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7427 (mm-30) REVERT: E 83 GLU cc_start: 0.6992 (tm-30) cc_final: 0.6670 (tm-30) REVERT: E 112 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7160 (mt) REVERT: E 340 MET cc_start: 0.7433 (OUTLIER) cc_final: 0.7185 (mtt) REVERT: G 91 ARG cc_start: 0.7312 (tmm160) cc_final: 0.7087 (tmm160) REVERT: G 131 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7333 (mp10) REVERT: H 21 ASP cc_start: 0.7408 (t0) cc_final: 0.7183 (t0) REVERT: H 139 MET cc_start: 0.7836 (tpt) cc_final: 0.7602 (tpt) REVERT: H 209 LEU cc_start: 0.6660 (OUTLIER) cc_final: 0.6410 (tm) outliers start: 95 outliers final: 59 residues processed: 380 average time/residue: 0.3530 time to fit residues: 207.1051 Evaluate side-chains 346 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 281 time to evaluate : 2.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 142 GLU Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 190 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 198 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 131 GLN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 208 optimal weight: 10.0000 chunk 187 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 161 optimal weight: 3.9990 chunk 217 optimal weight: 8.9990 chunk 124 optimal weight: 0.7980 chunk 158 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN B 332 ASN E 301 HIS F 95 ASN G 131 GLN G 179 ASN H 200 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.195117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.151681 restraints weight = 27467.456| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.39 r_work: 0.3617 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22052 Z= 0.133 Angle : 0.534 7.745 29812 Z= 0.270 Chirality : 0.041 0.217 3461 Planarity : 0.003 0.045 3792 Dihedral : 7.553 77.019 3030 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.31 % Allowed : 21.33 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.16), residues: 2717 helix: 0.86 (0.15), residues: 1265 sheet: -0.43 (0.23), residues: 517 loop : -0.89 (0.19), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1403 HIS 0.004 0.001 HIS C 37 PHE 0.021 0.001 PHE D 126 TYR 0.015 0.001 TYR G 250 ARG 0.004 0.000 ARG D 93 Details of bonding type rmsd hydrogen bonds : bond 0.03524 ( 1151) hydrogen bonds : angle 4.51604 ( 3318) covalent geometry : bond 0.00309 (22052) covalent geometry : angle 0.53434 (29812) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 312 time to evaluate : 3.191 Fit side-chains REVERT: A 1181 ASP cc_start: 0.7451 (t0) cc_final: 0.7071 (t0) REVERT: B 54 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: B 89 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7285 (tp) REVERT: C 182 MET cc_start: 0.7081 (ttt) cc_final: 0.6832 (ttt) REVERT: D 93 ARG cc_start: 0.6966 (mtp85) cc_final: 0.6672 (mtp180) REVERT: D 94 GLU cc_start: 0.7763 (mm-30) cc_final: 0.7517 (mm-30) REVERT: D 109 ASN cc_start: 0.7827 (t0) cc_final: 0.7574 (t0) REVERT: D 151 GLU cc_start: 0.7741 (mp0) cc_final: 0.7301 (mp0) REVERT: D 317 ASN cc_start: 0.8283 (m-40) cc_final: 0.8011 (m-40) REVERT: E 105 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7467 (ttp80) REVERT: E 111 MET cc_start: 0.6765 (tpt) cc_final: 0.6537 (tpt) REVERT: E 112 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7136 (mt) REVERT: F 89 THR cc_start: 0.7917 (m) cc_final: 0.7703 (m) REVERT: G 250 TYR cc_start: 0.8645 (m-80) cc_final: 0.8439 (m-80) REVERT: H 21 ASP cc_start: 0.7556 (t0) cc_final: 0.7322 (t0) REVERT: H 162 CYS cc_start: 0.5146 (m) cc_final: 0.4012 (p) REVERT: H 209 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6385 (tm) REVERT: H 251 LEU cc_start: 0.8159 (tp) cc_final: 0.7873 (tt) outliers start: 80 outliers final: 42 residues processed: 372 average time/residue: 0.3667 time to fit residues: 211.4257 Evaluate side-chains 325 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 278 time to evaluate : 2.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1346 ASP Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 209 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 98 optimal weight: 0.3980 chunk 133 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 171 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 2 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 231 optimal weight: 0.4980 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 332 ASN E 301 HIS G 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.192995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.149041 restraints weight = 28210.313| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.42 r_work: 0.3585 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22052 Z= 0.188 Angle : 0.570 9.716 29812 Z= 0.288 Chirality : 0.042 0.150 3461 Planarity : 0.004 0.046 3792 Dihedral : 7.452 84.379 3025 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.05 % Allowed : 21.12 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.16), residues: 2717 helix: 0.92 (0.15), residues: 1258 sheet: -0.47 (0.22), residues: 518 loop : -0.89 (0.19), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1489 HIS 0.004 0.001 HIS E 92 PHE 0.016 0.001 PHE D 126 TYR 0.013 0.002 TYR G 249 ARG 0.003 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 1151) hydrogen bonds : angle 4.52268 ( 3318) covalent geometry : bond 0.00451 (22052) covalent geometry : angle 0.57017 (29812) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 318 time to evaluate : 2.640 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1157 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7709 (m-40) REVERT: A 1181 ASP cc_start: 0.7425 (t0) cc_final: 0.7064 (t0) REVERT: A 1385 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6971 (tp) REVERT: A 1790 ARG cc_start: 0.6560 (OUTLIER) cc_final: 0.6095 (mmt180) REVERT: B 54 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7609 (mp0) REVERT: B 89 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7346 (tp) REVERT: C 37 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7633 (m90) REVERT: D 93 ARG cc_start: 0.7062 (mtp85) cc_final: 0.6745 (mtp180) REVERT: D 94 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7463 (mm-30) REVERT: D 122 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.8017 (mttp) REVERT: D 151 GLU cc_start: 0.7764 (mp0) cc_final: 0.7425 (mp0) REVERT: D 317 ASN cc_start: 0.8343 (m-40) cc_final: 0.8009 (m-40) REVERT: E 83 GLU cc_start: 0.7033 (tm-30) cc_final: 0.6676 (tm-30) REVERT: E 105 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.7444 (ttp80) REVERT: E 112 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7141 (mt) REVERT: E 191 ASP cc_start: 0.7217 (m-30) cc_final: 0.6865 (m-30) REVERT: F 25 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7774 (pm20) REVERT: G 91 ARG cc_start: 0.7207 (tmm160) cc_final: 0.6957 (tmm160) REVERT: H 162 CYS cc_start: 0.5142 (m) cc_final: 0.3930 (p) REVERT: H 251 LEU cc_start: 0.8207 (tp) cc_final: 0.7895 (tt) outliers start: 98 outliers final: 68 residues processed: 389 average time/residue: 0.3847 time to fit residues: 231.0862 Evaluate side-chains 357 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 279 time to evaluate : 2.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1157 ASN Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1359 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1728 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 245 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 chunk 201 optimal weight: 0.0970 chunk 108 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 chunk 266 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 60 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 260 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN B 332 ASN E 301 HIS G 84 ASN ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.193653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.149145 restraints weight = 27592.392| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.46 r_work: 0.3572 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22052 Z= 0.158 Angle : 0.551 8.815 29812 Z= 0.277 Chirality : 0.042 0.169 3461 Planarity : 0.003 0.043 3792 Dihedral : 7.384 87.887 3025 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.63 % Allowed : 21.04 % Favored : 74.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.16), residues: 2717 helix: 1.02 (0.15), residues: 1261 sheet: -0.46 (0.22), residues: 512 loop : -0.87 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1489 HIS 0.003 0.001 HIS E 92 PHE 0.015 0.001 PHE A1717 TYR 0.013 0.001 TYR A1399 ARG 0.003 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1151) hydrogen bonds : angle 4.45131 ( 3318) covalent geometry : bond 0.00376 (22052) covalent geometry : angle 0.55142 (29812) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 311 time to evaluate : 2.462 Fit side-chains revert: symmetry clash REVERT: A 1181 ASP cc_start: 0.7243 (t0) cc_final: 0.6842 (t0) REVERT: A 1729 GLU cc_start: 0.8002 (pm20) cc_final: 0.7784 (pm20) REVERT: A 1790 ARG cc_start: 0.6309 (OUTLIER) cc_final: 0.5811 (mmt180) REVERT: B 54 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7354 (mp0) REVERT: B 89 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7066 (tp) REVERT: C 37 HIS cc_start: 0.7914 (OUTLIER) cc_final: 0.7537 (m90) REVERT: D 93 ARG cc_start: 0.7045 (mtp85) cc_final: 0.6739 (mtp180) REVERT: D 94 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7368 (mm-30) REVERT: D 122 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.8002 (mttp) REVERT: D 151 GLU cc_start: 0.7620 (mp0) cc_final: 0.7277 (mp0) REVERT: D 232 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8433 (tttp) REVERT: D 317 ASN cc_start: 0.8109 (m-40) cc_final: 0.7750 (m-40) REVERT: E 83 GLU cc_start: 0.6841 (tm-30) cc_final: 0.6528 (tm-30) REVERT: E 105 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.7232 (ttp80) REVERT: E 112 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7027 (mt) REVERT: E 275 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.8053 (ttt90) REVERT: E 279 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7487 (m-80) REVERT: E 340 MET cc_start: 0.7359 (OUTLIER) cc_final: 0.7145 (mtt) REVERT: F 25 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: F 28 TRP cc_start: 0.8058 (m100) cc_final: 0.7610 (m100) REVERT: G 58 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7348 (m-30) REVERT: G 124 GLU cc_start: 0.5437 (mt-10) cc_final: 0.4755 (pm20) REVERT: H 75 MET cc_start: 0.7693 (tpp) cc_final: 0.7484 (mpp) REVERT: H 162 CYS cc_start: 0.5129 (m) cc_final: 0.3994 (p) outliers start: 112 outliers final: 73 residues processed: 397 average time/residue: 0.3494 time to fit residues: 213.6032 Evaluate side-chains 372 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 286 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1495 LEU Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 279 TYR Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 79 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 220 optimal weight: 7.9990 chunk 213 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1789 ASN B 332 ASN E 301 HIS G 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.191056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.146099 restraints weight = 27849.489| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.49 r_work: 0.3530 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 22052 Z= 0.243 Angle : 0.628 10.331 29812 Z= 0.316 Chirality : 0.045 0.163 3461 Planarity : 0.004 0.045 3792 Dihedral : 7.456 93.377 3025 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.17 % Allowed : 21.12 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.16), residues: 2717 helix: 0.80 (0.15), residues: 1251 sheet: -0.57 (0.22), residues: 512 loop : -0.92 (0.19), residues: 954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1489 HIS 0.006 0.001 HIS E 92 PHE 0.018 0.002 PHE A1779 TYR 0.016 0.002 TYR G 249 ARG 0.004 0.000 ARG A1414 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 1151) hydrogen bonds : angle 4.62978 ( 3318) covalent geometry : bond 0.00588 (22052) covalent geometry : angle 0.62804 (29812) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 290 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5804 (mp) REVERT: A 1729 GLU cc_start: 0.8020 (pm20) cc_final: 0.7765 (pm20) REVERT: A 1790 ARG cc_start: 0.6472 (OUTLIER) cc_final: 0.5986 (mmt180) REVERT: B 54 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 89 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7154 (tp) REVERT: C 37 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.7542 (m90) REVERT: D 93 ARG cc_start: 0.7140 (mtp85) cc_final: 0.6685 (mtp180) REVERT: D 94 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7407 (mm-30) REVERT: D 101 PHE cc_start: 0.6855 (OUTLIER) cc_final: 0.5784 (t80) REVERT: D 151 GLU cc_start: 0.7680 (mp0) cc_final: 0.7347 (mp0) REVERT: D 232 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8467 (tttp) REVERT: D 317 ASN cc_start: 0.8130 (m-40) cc_final: 0.7748 (m-40) REVERT: E 15 ARG cc_start: 0.7564 (OUTLIER) cc_final: 0.6640 (mtt-85) REVERT: E 105 ARG cc_start: 0.7642 (OUTLIER) cc_final: 0.6751 (ttp80) REVERT: E 112 LEU cc_start: 0.7612 (OUTLIER) cc_final: 0.7054 (mt) REVERT: E 340 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.7131 (mtt) REVERT: F 25 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7180 (pp20) REVERT: F 28 TRP cc_start: 0.8079 (m100) cc_final: 0.7683 (m100) REVERT: F 199 MET cc_start: 0.7448 (tmm) cc_final: 0.7111 (tmm) REVERT: G 124 GLU cc_start: 0.5610 (mt-10) cc_final: 0.4535 (pm20) REVERT: H 162 CYS cc_start: 0.5249 (m) cc_final: 0.4020 (p) REVERT: H 251 LEU cc_start: 0.8087 (tp) cc_final: 0.7723 (tt) outliers start: 125 outliers final: 89 residues processed: 380 average time/residue: 0.3458 time to fit residues: 201.6769 Evaluate side-chains 380 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 279 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1356 THR Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 24 GLU Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 340 MET Chi-restraints excluded: chain E residue 345 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 167 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 138 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 185 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 268 optimal weight: 40.0000 chunk 9 optimal weight: 0.0570 chunk 269 optimal weight: 7.9990 chunk 261 optimal weight: 8.9990 chunk 191 optimal weight: 0.9990 chunk 187 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 945 ASN B 332 ASN E 301 HIS F 153 HIS G 84 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.194047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.149923 restraints weight = 27634.759| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.47 r_work: 0.3581 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22052 Z= 0.130 Angle : 0.542 9.280 29812 Z= 0.272 Chirality : 0.041 0.189 3461 Planarity : 0.003 0.044 3792 Dihedral : 7.297 98.432 3025 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.97 % Allowed : 22.86 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.16), residues: 2717 helix: 1.09 (0.15), residues: 1266 sheet: -0.53 (0.22), residues: 512 loop : -0.84 (0.20), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1403 HIS 0.004 0.001 HIS F 153 PHE 0.015 0.001 PHE A1717 TYR 0.013 0.001 TYR G 249 ARG 0.006 0.000 ARG E 149 Details of bonding type rmsd hydrogen bonds : bond 0.03322 ( 1151) hydrogen bonds : angle 4.41125 ( 3318) covalent geometry : bond 0.00303 (22052) covalent geometry : angle 0.54195 (29812) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 308 time to evaluate : 2.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1318 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7928 (mm) REVERT: A 1490 HIS cc_start: 0.7751 (t-170) cc_final: 0.7520 (t-170) REVERT: A 1501 MET cc_start: 0.7033 (mmp) cc_final: 0.6686 (mmm) REVERT: A 1729 GLU cc_start: 0.7956 (pm20) cc_final: 0.7744 (pm20) REVERT: A 1790 ARG cc_start: 0.6366 (OUTLIER) cc_final: 0.5893 (mmt180) REVERT: B 54 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7340 (mp0) REVERT: B 89 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.6983 (tp) REVERT: C 37 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7454 (m90) REVERT: D 93 ARG cc_start: 0.7089 (mtp85) cc_final: 0.6655 (mtp180) REVERT: D 94 GLU cc_start: 0.7609 (mm-30) cc_final: 0.7401 (mm-30) REVERT: D 101 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5803 (t80) REVERT: D 151 GLU cc_start: 0.7664 (mp0) cc_final: 0.7257 (mp0) REVERT: D 317 ASN cc_start: 0.7983 (m-40) cc_final: 0.7579 (m-40) REVERT: E 105 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6624 (ttp80) REVERT: E 111 MET cc_start: 0.6589 (tpt) cc_final: 0.6382 (tpt) REVERT: E 112 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7042 (mt) REVERT: E 133 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8441 (tt) REVERT: F 25 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: F 28 TRP cc_start: 0.8040 (m100) cc_final: 0.7647 (m100) REVERT: F 89 THR cc_start: 0.7747 (m) cc_final: 0.7500 (m) REVERT: F 143 GLU cc_start: 0.6293 (tp30) cc_final: 0.6068 (tp30) REVERT: F 162 CYS cc_start: 0.6921 (OUTLIER) cc_final: 0.6693 (t) REVERT: F 198 GLU cc_start: 0.7035 (mt-10) cc_final: 0.6360 (tm-30) REVERT: F 199 MET cc_start: 0.7308 (tmm) cc_final: 0.7024 (tmm) REVERT: G 58 ASP cc_start: 0.7531 (OUTLIER) cc_final: 0.7327 (m-30) REVERT: G 91 ARG cc_start: 0.7240 (tmm160) cc_final: 0.7017 (tmm160) REVERT: G 124 GLU cc_start: 0.5444 (mt-10) cc_final: 0.4745 (pm20) REVERT: H 5 ARG cc_start: 0.7306 (tpp80) cc_final: 0.6934 (tpp80) REVERT: H 162 CYS cc_start: 0.5286 (m) cc_final: 0.4065 (p) REVERT: H 251 LEU cc_start: 0.8071 (tp) cc_final: 0.7740 (tt) outliers start: 96 outliers final: 71 residues processed: 378 average time/residue: 0.3398 time to fit residues: 199.6855 Evaluate side-chains 373 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 290 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1794 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 332 ASN Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 256 GLU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 133 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 162 CYS Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 193 optimal weight: 7.9990 chunk 240 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 236 optimal weight: 7.9990 chunk 230 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 226 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 145 optimal weight: 5.9990 chunk 227 optimal weight: 20.0000 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1069 ASN A1789 ASN B 332 ASN E 301 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 ASN H 177 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.189053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.143889 restraints weight = 27961.041| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 2.76 r_work: 0.3494 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 22052 Z= 0.323 Angle : 0.706 12.047 29812 Z= 0.355 Chirality : 0.048 0.206 3461 Planarity : 0.005 0.045 3792 Dihedral : 7.502 106.545 3023 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.84 % Allowed : 22.12 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.16), residues: 2717 helix: 0.56 (0.14), residues: 1257 sheet: -0.73 (0.22), residues: 521 loop : -1.01 (0.19), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1489 HIS 0.007 0.002 HIS E 92 PHE 0.022 0.002 PHE A1779 TYR 0.017 0.002 TYR G 249 ARG 0.006 0.001 ARG F 5 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 1151) hydrogen bonds : angle 4.78576 ( 3318) covalent geometry : bond 0.00785 (22052) covalent geometry : angle 0.70588 (29812) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 283 time to evaluate : 2.361 Fit side-chains revert: symmetry clash REVERT: A 1490 HIS cc_start: 0.7874 (t-170) cc_final: 0.7641 (t-170) REVERT: A 1729 GLU cc_start: 0.8021 (pm20) cc_final: 0.7709 (pm20) REVERT: A 1790 ARG cc_start: 0.6558 (OUTLIER) cc_final: 0.6083 (mmt180) REVERT: B 54 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: B 89 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7224 (tp) REVERT: C 37 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7592 (m90) REVERT: D 93 ARG cc_start: 0.7237 (mtp85) cc_final: 0.6751 (mtp180) REVERT: D 94 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7402 (mm-30) REVERT: D 101 PHE cc_start: 0.6894 (OUTLIER) cc_final: 0.5893 (t80) REVERT: D 151 GLU cc_start: 0.7689 (mp0) cc_final: 0.7337 (mp0) REVERT: D 232 LYS cc_start: 0.8761 (OUTLIER) cc_final: 0.8559 (tttp) REVERT: D 317 ASN cc_start: 0.8050 (m-40) cc_final: 0.7683 (m-40) REVERT: E 15 ARG cc_start: 0.7629 (OUTLIER) cc_final: 0.6717 (mtt-85) REVERT: E 91 TYR cc_start: 0.7489 (OUTLIER) cc_final: 0.5946 (m-80) REVERT: E 105 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6811 (ttp80) REVERT: E 112 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7079 (mt) REVERT: E 117 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6011 (mt0) REVERT: F 25 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7186 (pp20) REVERT: F 28 TRP cc_start: 0.8123 (m100) cc_final: 0.7729 (m100) REVERT: F 199 MET cc_start: 0.7456 (tmm) cc_final: 0.7149 (tmm) REVERT: G 91 ARG cc_start: 0.7248 (tmm160) cc_final: 0.7020 (tmm160) REVERT: H 116 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6901 (ptm) REVERT: H 175 LEU cc_start: 0.4916 (tt) cc_final: 0.4475 (tt) outliers start: 117 outliers final: 84 residues processed: 373 average time/residue: 0.3389 time to fit residues: 194.4011 Evaluate side-chains 374 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 277 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 871 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 VAL Chi-restraints excluded: chain A residue 1307 VAL Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1691 GLU Chi-restraints excluded: chain A residue 1708 LEU Chi-restraints excluded: chain A residue 1742 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1777 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain A residue 1790 ARG Chi-restraints excluded: chain A residue 1794 ILE Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 333 SER Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 98 ILE Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 232 LYS Chi-restraints excluded: chain D residue 238 LEU Chi-restraints excluded: chain D residue 258 THR Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 15 ARG Chi-restraints excluded: chain E residue 91 TYR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 87 ILE Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 112 SER Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 196 THR Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 27 CYS Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 177 ASN Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 200 ASN Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 247 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 49 optimal weight: 0.0000 chunk 121 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 63 optimal weight: 0.9980 chunk 186 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 97 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1069 ASN A1789 ASN B 332 ASN E 301 HIS F 95 ASN G 84 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.195158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.152574 restraints weight = 28077.295| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 2.38 r_work: 0.3634 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22052 Z= 0.113 Angle : 0.567 13.486 29812 Z= 0.281 Chirality : 0.041 0.201 3461 Planarity : 0.003 0.044 3792 Dihedral : 7.318 108.350 3023 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.06 % Allowed : 23.94 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.16), residues: 2717 helix: 1.06 (0.15), residues: 1265 sheet: -0.58 (0.23), residues: 507 loop : -0.86 (0.20), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1403 HIS 0.004 0.001 HIS E 331 PHE 0.015 0.001 PHE A1717 TYR 0.015 0.001 TYR G 249 ARG 0.007 0.000 ARG C 150 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 1151) hydrogen bonds : angle 4.46244 ( 3318) covalent geometry : bond 0.00257 (22052) covalent geometry : angle 0.56734 (29812) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 313 time to evaluate : 2.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5898 (mp) REVERT: A 1344 MET cc_start: 0.8511 (mmt) cc_final: 0.6616 (ptp) REVERT: A 1490 HIS cc_start: 0.7800 (t-170) cc_final: 0.7592 (t-170) REVERT: A 1729 GLU cc_start: 0.7821 (pm20) cc_final: 0.7584 (pm20) REVERT: B 54 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7416 (mp0) REVERT: B 89 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.6956 (tp) REVERT: C 37 HIS cc_start: 0.7775 (OUTLIER) cc_final: 0.7454 (m90) REVERT: D 93 ARG cc_start: 0.7084 (mtp85) cc_final: 0.6593 (mtp180) REVERT: D 101 PHE cc_start: 0.6720 (OUTLIER) cc_final: 0.5837 (t80) REVERT: D 151 GLU cc_start: 0.7578 (mp0) cc_final: 0.7267 (mp0) REVERT: D 317 ASN cc_start: 0.7842 (m-40) cc_final: 0.7516 (m-40) REVERT: E 105 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.6752 (ttp80) REVERT: E 112 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7114 (mt) REVERT: F 25 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: F 28 TRP cc_start: 0.8024 (m100) cc_final: 0.7684 (m100) REVERT: F 89 THR cc_start: 0.7693 (m) cc_final: 0.7457 (m) REVERT: F 198 GLU cc_start: 0.6901 (mt-10) cc_final: 0.6417 (tm-30) REVERT: F 199 MET cc_start: 0.7267 (tmm) cc_final: 0.6955 (tmm) REVERT: H 116 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6834 (ptp) REVERT: H 177 ASN cc_start: 0.6485 (t0) cc_final: 0.6226 (m-40) REVERT: H 251 LEU cc_start: 0.8117 (tp) cc_final: 0.7772 (tt) outliers start: 74 outliers final: 54 residues processed: 367 average time/residue: 0.3474 time to fit residues: 196.1750 Evaluate side-chains 360 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 297 time to evaluate : 2.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1369 ILE Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1397 ILE Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1657 SER Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 101 PHE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 196 LYS Chi-restraints excluded: chain D residue 202 LEU Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain D residue 354 THR Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 184 GLN Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 255 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 45 VAL Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 182 LEU Chi-restraints excluded: chain H residue 206 THR Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 65 optimal weight: 2.9990 chunk 231 optimal weight: 0.4980 chunk 182 optimal weight: 0.0270 chunk 156 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 179 optimal weight: 0.4980 chunk 125 optimal weight: 1.9990 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1789 ASN B 332 ASN E 206 ASN E 301 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.196562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.153911 restraints weight = 28157.850| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.30 r_work: 0.3655 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22052 Z= 0.104 Angle : 0.553 10.956 29812 Z= 0.273 Chirality : 0.041 0.204 3461 Planarity : 0.003 0.044 3792 Dihedral : 7.145 110.852 3023 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.48 % Allowed : 24.47 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.16), residues: 2717 helix: 1.31 (0.15), residues: 1265 sheet: -0.49 (0.23), residues: 508 loop : -0.78 (0.20), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1403 HIS 0.006 0.001 HIS F 44 PHE 0.031 0.001 PHE D 126 TYR 0.017 0.001 TYR G 60 ARG 0.007 0.000 ARG E 270 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 1151) hydrogen bonds : angle 4.29475 ( 3318) covalent geometry : bond 0.00239 (22052) covalent geometry : angle 0.55296 (29812) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5434 Ramachandran restraints generated. 2717 Oldfield, 0 Emsley, 2717 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 308 time to evaluate : 2.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1089 LEU cc_start: 0.6304 (OUTLIER) cc_final: 0.5813 (mp) REVERT: A 1325 MET cc_start: 0.5747 (mmm) cc_final: 0.4834 (mmm) REVERT: A 1344 MET cc_start: 0.8505 (mmt) cc_final: 0.6620 (ptp) REVERT: A 1501 MET cc_start: 0.6812 (mmp) cc_final: 0.6569 (mmm) REVERT: B 54 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: B 89 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.6991 (tp) REVERT: B 296 ILE cc_start: 0.8606 (tp) cc_final: 0.8312 (tp) REVERT: C 37 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7415 (m90) REVERT: D 151 GLU cc_start: 0.7490 (mp0) cc_final: 0.7165 (mp0) REVERT: D 317 ASN cc_start: 0.7841 (m-40) cc_final: 0.7553 (m-40) REVERT: E 105 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.6698 (ttp80) REVERT: E 112 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7078 (mt) REVERT: F 25 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7418 (pm20) REVERT: F 28 TRP cc_start: 0.7987 (m100) cc_final: 0.7670 (m100) REVERT: F 198 GLU cc_start: 0.6799 (mt-10) cc_final: 0.6354 (tm-30) REVERT: F 199 MET cc_start: 0.7147 (tmm) cc_final: 0.6861 (tmm) REVERT: G 124 GLU cc_start: 0.5499 (mt-10) cc_final: 0.4817 (pm20) REVERT: H 21 ASP cc_start: 0.7478 (t0) cc_final: 0.7125 (t0) REVERT: H 116 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6537 (ptp) REVERT: H 162 CYS cc_start: 0.5511 (m) cc_final: 0.4302 (p) REVERT: H 251 LEU cc_start: 0.8106 (tp) cc_final: 0.7794 (tt) outliers start: 60 outliers final: 44 residues processed: 352 average time/residue: 0.3433 time to fit residues: 185.6165 Evaluate side-chains 349 residues out of total 2419 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 297 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1089 LEU Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1376 ARG Chi-restraints excluded: chain A residue 1483 ILE Chi-restraints excluded: chain A residue 1664 THR Chi-restraints excluded: chain A residue 1759 SER Chi-restraints excluded: chain A residue 1781 SER Chi-restraints excluded: chain B residue 54 GLU Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 226 GLN Chi-restraints excluded: chain C residue 37 HIS Chi-restraints excluded: chain C residue 70 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 249 ASN Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 86 SER Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 295 ASP Chi-restraints excluded: chain E residue 105 ARG Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 117 GLN Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 199 VAL Chi-restraints excluded: chain E residue 206 ASN Chi-restraints excluded: chain E residue 230 CYS Chi-restraints excluded: chain E residue 250 ASP Chi-restraints excluded: chain E residue 275 ARG Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain F residue 25 GLU Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 97 ASP Chi-restraints excluded: chain F residue 121 LEU Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 151 LEU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain G residue 52 LEU Chi-restraints excluded: chain G residue 66 LEU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 175 LEU Chi-restraints excluded: chain G residue 219 THR Chi-restraints excluded: chain G residue 233 VAL Chi-restraints excluded: chain G residue 246 HIS Chi-restraints excluded: chain H residue 59 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 89 THR Chi-restraints excluded: chain H residue 116 MET Chi-restraints excluded: chain H residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 271 random chunks: chunk 199 optimal weight: 0.9980 chunk 243 optimal weight: 7.9990 chunk 128 optimal weight: 0.4980 chunk 46 optimal weight: 0.8980 chunk 113 optimal weight: 9.9990 chunk 147 optimal weight: 0.5980 chunk 269 optimal weight: 10.0000 chunk 239 optimal weight: 0.8980 chunk 245 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1490 HIS A1789 ASN B 332 ASN E 301 HIS F 95 ASN G 179 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.196792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.154646 restraints weight = 28188.101| |-----------------------------------------------------------------------------| r_work (start): 0.3864 rms_B_bonded: 2.29 r_work: 0.3660 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3516 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22052 Z= 0.111 Angle : 0.555 12.399 29812 Z= 0.273 Chirality : 0.041 0.208 3461 Planarity : 0.003 0.043 3792 Dihedral : 7.098 111.107 3023 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.77 % Allowed : 24.39 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.16), residues: 2717 helix: 1.37 (0.15), residues: 1267 sheet: -0.48 (0.22), residues: 516 loop : -0.73 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1403 HIS 0.004 0.001 HIS A1490 PHE 0.029 0.001 PHE D 126 TYR 0.026 0.001 TYR G 249 ARG 0.009 0.000 ARG E 270 Details of bonding type rmsd hydrogen bonds : bond 0.03088 ( 1151) hydrogen bonds : angle 4.24504 ( 3318) covalent geometry : bond 0.00259 (22052) covalent geometry : angle 0.55523 (29812) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12906.87 seconds wall clock time: 224 minutes 22.05 seconds (13462.05 seconds total)