Starting phenix.real_space_refine on Thu Mar 5 10:27:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s5y_24843/03_2026/7s5y_24843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5y_24843/03_2026/7s5y_24843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s5y_24843/03_2026/7s5y_24843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5y_24843/03_2026/7s5y_24843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s5y_24843/03_2026/7s5y_24843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5y_24843/03_2026/7s5y_24843.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.005 sd= 0.075 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 5 5.49 5 Mg 2 5.21 5 S 119 5.16 5 C 13639 2.51 5 N 3594 2.21 5 O 3747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 121 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21106 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2519 Classifications: {'peptide': 321} Link IDs: {'PTRANS': 13, 'TRANS': 307} Chain: "E" Number of atoms: 10970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1402, 10970 Classifications: {'peptide': 1402} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 42, 'TRANS': 1359} Chain breaks: 7 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 1, 'ARG:plan': 2, 'PHE:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 64 Chain: "E" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Restraints were copied for chains: B, C, D Time building chain proxies: 4.63, per 1000 atoms: 0.22 Number of scatterers: 21106 At special positions: 0 Unit cell: (143, 145.6, 136.5, 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 119 16.00 P 5 15.00 Mg 2 11.99 O 3747 8.00 N 3594 7.00 C 13639 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 950.6 milliseconds 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5068 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 25 sheets defined 48.3% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 59 through 65 Processing helix chain 'A' and resid 67 through 97 Processing helix chain 'A' and resid 116 through 129 removed outlier: 3.747A pdb=" N ALA A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL A 129 " --> pdb=" O ILE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 172 Processing helix chain 'A' and resid 173 through 179 removed outlier: 4.246A pdb=" N ARG A 176 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.601A pdb=" N LEU A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 65 Processing helix chain 'B' and resid 67 through 97 Processing helix chain 'B' and resid 116 through 129 removed outlier: 3.747A pdb=" N ALA B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 129 " --> pdb=" O ILE B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 172 Processing helix chain 'B' and resid 173 through 179 removed outlier: 4.246A pdb=" N ARG B 176 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 271 through 275 removed outlier: 3.601A pdb=" N LEU B 275 " --> pdb=" O PRO B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 59 through 65 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 116 through 129 removed outlier: 3.747A pdb=" N ALA C 120 " --> pdb=" O SER C 116 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL C 129 " --> pdb=" O ILE C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 172 Processing helix chain 'C' and resid 173 through 179 removed outlier: 4.246A pdb=" N ARG C 176 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 275 removed outlier: 3.601A pdb=" N LEU C 275 " --> pdb=" O PRO C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 65 Processing helix chain 'D' and resid 67 through 97 Processing helix chain 'D' and resid 116 through 129 removed outlier: 3.747A pdb=" N ALA D 120 " --> pdb=" O SER D 116 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N VAL D 129 " --> pdb=" O ILE D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 172 Processing helix chain 'D' and resid 173 through 179 removed outlier: 4.246A pdb=" N ARG D 176 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 removed outlier: 3.601A pdb=" N LEU D 275 " --> pdb=" O PRO D 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 Processing helix chain 'E' and resid 25 through 33 Processing helix chain 'E' and resid 34 through 51 Proline residue: E 46 - end of helix Processing helix chain 'E' and resid 74 through 94 removed outlier: 3.812A pdb=" N CYS E 88 " --> pdb=" O PHE E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 130 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 138 through 161 removed outlier: 5.514A pdb=" N ILE E 149 " --> pdb=" O THR E 145 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N LYS E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N HIS E 161 " --> pdb=" O LYS E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 194 removed outlier: 3.831A pdb=" N CYS E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 175 " --> pdb=" O CYS E 171 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 231 Processing helix chain 'E' and resid 259 through 274 removed outlier: 3.711A pdb=" N ALA E 273 " --> pdb=" O GLU E 269 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 313 removed outlier: 6.294A pdb=" N ARG E 298 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG E 299 " --> pdb=" O ALA E 295 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N ASP E 311 " --> pdb=" O ARG E 307 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 312 " --> pdb=" O ILE E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 315 through 330 removed outlier: 3.800A pdb=" N LEU E 319 " --> pdb=" O PHE E 315 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N HIS E 327 " --> pdb=" O GLY E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 355 Processing helix chain 'E' and resid 355 through 401 removed outlier: 3.727A pdb=" N LEU E 359 " --> pdb=" O ASN E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 405 through 410 Processing helix chain 'E' and resid 414 through 424 Processing helix chain 'E' and resid 426 through 435 Processing helix chain 'E' and resid 435 through 458 removed outlier: 3.546A pdb=" N LEU E 439 " --> pdb=" O LEU E 435 " (cutoff:3.500A) Proline residue: E 443 - end of helix removed outlier: 3.654A pdb=" N VAL E 448 " --> pdb=" O VAL E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 461 No H-bonds generated for 'chain 'E' and resid 459 through 461' Processing helix chain 'E' and resid 465 through 506 removed outlier: 5.963A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) Proline residue: E 473 - end of helix Processing helix chain 'E' and resid 506 through 512 Processing helix chain 'E' and resid 515 through 565 Proline residue: E 552 - end of helix removed outlier: 3.519A pdb=" N VAL E 564 " --> pdb=" O PHE E 560 " (cutoff:3.500A) Processing helix chain 'E' and resid 574 through 589 Processing helix chain 'E' and resid 590 through 600 removed outlier: 3.590A pdb=" N SER E 595 " --> pdb=" O LEU E 591 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER E 596 " --> pdb=" O PHE E 592 " (cutoff:3.500A) Processing helix chain 'E' and resid 601 through 616 Processing helix chain 'E' and resid 719 through 728 removed outlier: 4.156A pdb=" N LEU E 724 " --> pdb=" O LYS E 720 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 790 removed outlier: 3.531A pdb=" N PHE E 790 " --> pdb=" O GLU E 786 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 806 Processing helix chain 'E' and resid 808 through 814 Processing helix chain 'E' and resid 817 through 821 removed outlier: 3.846A pdb=" N GLN E 820 " --> pdb=" O HIS E 817 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N THR E 821 " --> pdb=" O GLY E 818 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 817 through 821' Processing helix chain 'E' and resid 832 through 842 Processing helix chain 'E' and resid 861 through 871 Processing helix chain 'E' and resid 890 through 894 Processing helix chain 'E' and resid 913 through 920 Processing helix chain 'E' and resid 923 through 932 Processing helix chain 'E' and resid 999 through 1009 Processing helix chain 'E' and resid 1009 through 1039 removed outlier: 3.613A pdb=" N ASP E1039 " --> pdb=" O ALA E1035 " (cutoff:3.500A) Processing helix chain 'E' and resid 1062 through 1097 Processing helix chain 'E' and resid 1100 through 1106 Processing helix chain 'E' and resid 1109 through 1116 removed outlier: 3.621A pdb=" N PHE E1113 " --> pdb=" O PRO E1109 " (cutoff:3.500A) Processing helix chain 'E' and resid 1117 through 1134 removed outlier: 3.728A pdb=" N ILE E1121 " --> pdb=" O PRO E1117 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASP E1128 " --> pdb=" O ARG E1124 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N CYS E1129 " --> pdb=" O PHE E1125 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1161 removed outlier: 3.836A pdb=" N THR E1139 " --> pdb=" O HIS E1135 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL E1160 " --> pdb=" O VAL E1156 " (cutoff:3.500A) Processing helix chain 'E' and resid 1162 through 1169 Processing helix chain 'E' and resid 1170 through 1196 removed outlier: 4.338A pdb=" N VAL E1184 " --> pdb=" O LYS E1180 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA E1185 " --> pdb=" O TYR E1181 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N GLN E1191 " --> pdb=" O ARG E1187 " (cutoff:3.500A) Processing helix chain 'E' and resid 1199 through 1207 Processing helix chain 'E' and resid 1210 through 1218 Processing helix chain 'E' and resid 1219 through 1273 removed outlier: 3.737A pdb=" N HIS E1273 " --> pdb=" O SER E1269 " (cutoff:3.500A) Processing helix chain 'E' and resid 1279 through 1318 removed outlier: 5.926A pdb=" N ASN E1296 " --> pdb=" O SER E1292 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP E1297 " --> pdb=" O ASN E1293 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA E1311 " --> pdb=" O LEU E1307 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E1312 " --> pdb=" O GLN E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1384 through 1390 removed outlier: 3.848A pdb=" N LEU E1390 " --> pdb=" O SER E1386 " (cutoff:3.500A) Processing helix chain 'E' and resid 1414 through 1421 Processing helix chain 'E' and resid 1436 through 1441 Processing helix chain 'E' and resid 1447 through 1457 removed outlier: 3.764A pdb=" N LEU E1451 " --> pdb=" O SER E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1460 through 1465 Processing helix chain 'E' and resid 1483 through 1496 Processing helix chain 'E' and resid 1507 through 1511 removed outlier: 3.622A pdb=" N ALA E1510 " --> pdb=" O GLU E1507 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N SER E1511 " --> pdb=" O ALA E1508 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1507 through 1511' Processing helix chain 'E' and resid 1513 through 1528 removed outlier: 3.609A pdb=" N PHE E1528 " --> pdb=" O VAL E1524 " (cutoff:3.500A) Processing helix chain 'E' and resid 1539 through 1543 removed outlier: 3.794A pdb=" N THR E1542 " --> pdb=" O ARG E1539 " (cutoff:3.500A) Processing helix chain 'E' and resid 1562 through 1569 Processing helix chain 'E' and resid 1572 through 1582 Processing sheet with id=AA1, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 removed outlier: 6.707A pdb=" N ALA A 187 " --> pdb=" O LEU A 310 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET A 217 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ALA A 213 " --> pdb=" O GLU A 288 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU A 288 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE A 215 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ILE A 286 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET A 217 " --> pdb=" O ILE A 284 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE A 284 " --> pdb=" O MET A 217 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL A 219 " --> pdb=" O GLU A 282 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU A 282 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 319 through 322 Processing sheet with id=AA5, first strand: chain 'B' and resid 181 through 182 Processing sheet with id=AA6, first strand: chain 'B' and resid 181 through 182 removed outlier: 6.707A pdb=" N ALA B 187 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET B 217 " --> pdb=" O ILE B 238 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA B 213 " --> pdb=" O GLU B 288 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU B 288 " --> pdb=" O ALA B 213 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE B 215 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE B 286 " --> pdb=" O ILE B 215 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N MET B 217 " --> pdb=" O ILE B 284 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 284 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL B 219 " --> pdb=" O GLU B 282 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU B 282 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AA9, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AB1, first strand: chain 'C' and resid 181 through 182 removed outlier: 6.708A pdb=" N ALA C 187 " --> pdb=" O LEU C 310 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 234 through 238 removed outlier: 4.363A pdb=" N MET C 217 " --> pdb=" O ILE C 238 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA C 213 " --> pdb=" O GLU C 288 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU C 288 " --> pdb=" O ALA C 213 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE C 215 " --> pdb=" O ILE C 286 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILE C 286 " --> pdb=" O ILE C 215 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET C 217 " --> pdb=" O ILE C 284 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE C 284 " --> pdb=" O MET C 217 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N VAL C 219 " --> pdb=" O GLU C 282 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU C 282 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 319 through 322 Processing sheet with id=AB4, first strand: chain 'D' and resid 181 through 182 Processing sheet with id=AB5, first strand: chain 'D' and resid 181 through 182 removed outlier: 6.707A pdb=" N ALA D 187 " --> pdb=" O LEU D 310 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 234 through 238 removed outlier: 4.364A pdb=" N MET D 217 " --> pdb=" O ILE D 238 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ALA D 213 " --> pdb=" O GLU D 288 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU D 288 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ILE D 215 " --> pdb=" O ILE D 286 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE D 286 " --> pdb=" O ILE D 215 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N MET D 217 " --> pdb=" O ILE D 284 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE D 284 " --> pdb=" O MET D 217 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL D 219 " --> pdb=" O GLU D 282 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU D 282 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 319 through 322 Processing sheet with id=AB8, first strand: chain 'E' and resid 678 through 680 removed outlier: 3.770A pdb=" N VAL E 680 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 683 through 685 Processing sheet with id=AC1, first strand: chain 'E' and resid 687 through 688 Processing sheet with id=AC2, first strand: chain 'E' and resid 771 through 773 removed outlier: 6.538A pdb=" N ALA E 771 " --> pdb=" O PHE E 852 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL E 887 " --> pdb=" O LEU E 853 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N MET E 711 " --> pdb=" O ILE E 901 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET E 903 " --> pdb=" O MET E 711 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL E 713 " --> pdb=" O MET E 903 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE E 900 " --> pdb=" O GLU E 911 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU E 911 " --> pdb=" O ILE E 900 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA E 902 " --> pdb=" O GLN E 909 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR E 907 " --> pdb=" O LYS E 904 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 1345 through 1348 Processing sheet with id=AC4, first strand: chain 'E' and resid 1351 through 1353 removed outlier: 7.172A pdb=" N SER E1351 " --> pdb=" O PHE E1399 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N PHE E1399 " --> pdb=" O SER E1351 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 1502 through 1505 removed outlier: 6.892A pdb=" N PHE E1503 " --> pdb=" O VAL E1534 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ILE E1536 " --> pdb=" O PHE E1503 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N MET E1505 " --> pdb=" O ILE E1536 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE E1375 " --> pdb=" O THR E1535 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LYS E1374 " --> pdb=" O LEU E1548 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N ILE E1550 " --> pdb=" O LYS E1374 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N GLY E1376 " --> pdb=" O ILE E1550 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU E1552 " --> pdb=" O GLY E1376 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS E1378 " --> pdb=" O LEU E1552 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL E1549 " --> pdb=" O PHE E1560 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE E1560 " --> pdb=" O VAL E1549 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL E1551 " --> pdb=" O LEU E1558 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 1404 through 1405 Processing sheet with id=AC7, first strand: chain 'E' and resid 1434 through 1435 removed outlier: 3.529A pdb=" N ILE E1475 " --> pdb=" O GLY E1434 " (cutoff:3.500A) 1073 hydrogen bonds defined for protein. 3063 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: 3.73 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6091 1.34 - 1.46: 5348 1.46 - 1.58: 9925 1.58 - 1.71: 13 1.71 - 1.83: 190 Bond restraints: 21567 Sorted by residual: bond pdb=" C4 ATP E1604 " pdb=" C5 ATP E1604 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.17e+01 bond pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 1.374 1.319 0.055 1.00e-02 1.00e+04 3.02e+01 bond pdb=" C5 ATP E1604 " pdb=" N7 ATP E1604 " ideal model delta sigma weight residual 1.387 1.333 0.054 1.00e-02 1.00e+04 2.89e+01 bond pdb=" C5 ATP E1604 " pdb=" C6 ATP E1604 " ideal model delta sigma weight residual 1.409 1.462 -0.053 1.00e-02 1.00e+04 2.86e+01 bond pdb=" C ILE E1136 " pdb=" N PRO E1137 " ideal model delta sigma weight residual 1.334 1.453 -0.119 2.34e-02 1.83e+03 2.59e+01 ... (remaining 21562 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.93: 28505 3.93 - 7.85: 687 7.85 - 11.78: 104 11.78 - 15.71: 8 15.71 - 19.64: 6 Bond angle restraints: 29310 Sorted by residual: angle pdb=" PB ATP E1604 " pdb=" O3B ATP E1604 " pdb=" PG ATP E1604 " ideal model delta sigma weight residual 139.87 122.05 17.82 1.00e+00 1.00e+00 3.18e+02 angle pdb=" PA ATP E1604 " pdb=" O3A ATP E1604 " pdb=" PB ATP E1604 " ideal model delta sigma weight residual 136.83 124.59 12.24 1.00e+00 1.00e+00 1.50e+02 angle pdb=" C ALA E 310 " pdb=" N ASP E 311 " pdb=" CA ASP E 311 " ideal model delta sigma weight residual 121.54 135.64 -14.10 1.91e+00 2.74e-01 5.45e+01 angle pdb=" C5 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N3 ATP E1604 " ideal model delta sigma weight residual 126.80 119.74 7.06 1.00e+00 1.00e+00 4.98e+01 angle pdb=" N3 ATP E1604 " pdb=" C4 ATP E1604 " pdb=" N9 ATP E1604 " ideal model delta sigma weight residual 127.04 134.86 -7.82 1.15e+00 7.59e-01 4.64e+01 ... (remaining 29305 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.98: 11727 24.98 - 49.96: 915 49.96 - 74.93: 158 74.93 - 99.91: 5 99.91 - 124.89: 1 Dihedral angle restraints: 12806 sinusoidal: 5006 harmonic: 7800 Sorted by residual: dihedral pdb=" CA GLY E 343 " pdb=" C GLY E 343 " pdb=" N VAL E 344 " pdb=" CA VAL E 344 " ideal model delta harmonic sigma weight residual -180.00 -118.48 -61.52 0 5.00e+00 4.00e-02 1.51e+02 dihedral pdb=" CA PHE E1182 " pdb=" C PHE E1182 " pdb=" N ARG E1183 " pdb=" CA ARG E1183 " ideal model delta harmonic sigma weight residual -180.00 -129.32 -50.68 0 5.00e+00 4.00e-02 1.03e+02 dihedral pdb=" CA LEU E 137 " pdb=" C LEU E 137 " pdb=" N ILE E 138 " pdb=" CA ILE E 138 " ideal model delta harmonic sigma weight residual -180.00 -136.18 -43.82 0 5.00e+00 4.00e-02 7.68e+01 ... (remaining 12803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.141: 3193 0.141 - 0.282: 244 0.282 - 0.422: 23 0.422 - 0.563: 5 0.563 - 0.704: 4 Chirality restraints: 3469 Sorted by residual: chirality pdb=" CB VAL D 337 " pdb=" CA VAL D 337 " pdb=" CG1 VAL D 337 " pdb=" CG2 VAL D 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.24e+01 chirality pdb=" CB VAL C 337 " pdb=" CA VAL C 337 " pdb=" CG1 VAL C 337 " pdb=" CG2 VAL C 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 chirality pdb=" CB VAL A 337 " pdb=" CA VAL A 337 " pdb=" CG1 VAL A 337 " pdb=" CG2 VAL A 337 " both_signs ideal model delta sigma weight residual False -2.63 -1.93 -0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 3466 not shown) Planarity restraints: 3646 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS E1180 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.16e+01 pdb=" C LYS E1180 " -0.080 2.00e-02 2.50e+03 pdb=" O LYS E1180 " 0.030 2.00e-02 2.50e+03 pdb=" N TYR E1181 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 149 " -0.023 2.00e-02 2.50e+03 4.62e-02 2.14e+01 pdb=" C ILE E 149 " 0.080 2.00e-02 2.50e+03 pdb=" O ILE E 149 " -0.030 2.00e-02 2.50e+03 pdb=" N THR E 150 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP E 144 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.01e+01 pdb=" C TRP E 144 " 0.078 2.00e-02 2.50e+03 pdb=" O TRP E 144 " -0.029 2.00e-02 2.50e+03 pdb=" N THR E 145 " -0.026 2.00e-02 2.50e+03 ... (remaining 3643 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 309 2.61 - 3.18: 16113 3.18 - 3.75: 35082 3.75 - 4.33: 46078 4.33 - 4.90: 73953 Nonbonded interactions: 171535 Sorted by model distance: nonbonded pdb=" SG CYS E 7 " pdb=" SG CYS E 27 " model vdw 2.032 3.760 nonbonded pdb=" O1B ADP E1601 " pdb="MG MG E1603 " model vdw 2.160 2.170 nonbonded pdb=" OE1 GLN E 775 " pdb="MG MG E1602 " model vdw 2.166 2.170 nonbonded pdb="MG MG E1602 " pdb=" O2B ATP E1604 " model vdw 2.166 2.170 nonbonded pdb=" OG SER E1386 " pdb="MG MG E1603 " model vdw 2.172 2.170 ... (remaining 171530 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 18.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.010 0.119 21567 Z= 0.453 Angle : 1.484 19.636 29310 Z= 0.813 Chirality : 0.083 0.704 3469 Planarity : 0.012 0.095 3646 Dihedral : 17.699 124.888 7738 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.26 % Favored : 94.67 % Rotamer: Outliers : 7.41 % Allowed : 12.39 % Favored : 80.20 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.62 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.12 (0.11), residues: 2662 helix: -4.11 (0.07), residues: 1321 sheet: -1.57 (0.30), residues: 271 loop : -2.65 (0.15), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 177 TYR 0.029 0.003 TYR E 379 PHE 0.042 0.004 PHE E 373 TRP 0.027 0.003 TRP E1033 HIS 0.014 0.002 HIS A 276 Details of bonding type rmsd covalent geometry : bond 0.00951 (21567) covalent geometry : angle 1.48384 (29310) hydrogen bonds : bond 0.13063 ( 1065) hydrogen bonds : angle 8.19976 ( 3063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 170 poor density : 552 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8287 (t0) cc_final: 0.7708 (t0) REVERT: A 52 GLN cc_start: 0.8107 (tt0) cc_final: 0.7254 (pp30) REVERT: A 65 ASP cc_start: 0.8662 (t0) cc_final: 0.8398 (t0) REVERT: A 83 TRP cc_start: 0.9431 (m-10) cc_final: 0.9031 (m-90) REVERT: A 84 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8928 (mt) REVERT: A 126 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8276 (mp0) REVERT: A 160 ASN cc_start: 0.9121 (m-40) cc_final: 0.8913 (t0) REVERT: A 163 MET cc_start: 0.9091 (mmm) cc_final: 0.8829 (mmm) REVERT: A 247 ASN cc_start: 0.8498 (p0) cc_final: 0.8176 (p0) REVERT: A 250 PHE cc_start: 0.8791 (t80) cc_final: 0.8490 (t80) REVERT: B 48 ASN cc_start: 0.8944 (m-40) cc_final: 0.7627 (m-40) REVERT: B 57 GLN cc_start: 0.8793 (mt0) cc_final: 0.8261 (tp-100) REVERT: B 86 PHE cc_start: 0.9254 (m-80) cc_final: 0.9052 (m-10) REVERT: B 151 VAL cc_start: 0.9619 (OUTLIER) cc_final: 0.9416 (t) REVERT: B 152 GLN cc_start: 0.9213 (tp40) cc_final: 0.8556 (tp-100) REVERT: B 170 LYS cc_start: 0.8524 (tptt) cc_final: 0.8271 (tptt) REVERT: B 262 ASP cc_start: 0.8649 (p0) cc_final: 0.8020 (p0) REVERT: B 292 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: B 316 VAL cc_start: 0.8543 (OUTLIER) cc_final: 0.8306 (m) REVERT: B 331 SER cc_start: 0.9069 (OUTLIER) cc_final: 0.8213 (p) REVERT: C 65 ASP cc_start: 0.7489 (t0) cc_final: 0.7253 (t0) REVERT: C 77 MET cc_start: 0.8432 (tpp) cc_final: 0.8158 (ttt) REVERT: C 170 LYS cc_start: 0.8870 (tptt) cc_final: 0.8434 (tptm) REVERT: C 179 GLU cc_start: 0.7952 (mt-10) cc_final: 0.7566 (tp30) REVERT: C 185 LYS cc_start: 0.8546 (ttpp) cc_final: 0.7813 (ttpt) REVERT: C 214 THR cc_start: 0.8889 (m) cc_final: 0.8545 (p) REVERT: C 237 ASP cc_start: 0.8726 (m-30) cc_final: 0.7836 (m-30) REVERT: C 281 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8641 (tt) REVERT: C 286 ILE cc_start: 0.9396 (mp) cc_final: 0.9113 (tp) REVERT: C 292 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7429 (tm-30) REVERT: C 313 GLN cc_start: 0.8829 (mt0) cc_final: 0.8234 (mm110) REVERT: C 316 VAL cc_start: 0.9150 (OUTLIER) cc_final: 0.8932 (p) REVERT: D 43 ASN cc_start: 0.8027 (t0) cc_final: 0.7325 (t0) REVERT: D 150 ILE cc_start: 0.9606 (mt) cc_final: 0.9391 (mt) REVERT: D 163 MET cc_start: 0.8653 (mmm) cc_final: 0.8013 (mmm) REVERT: D 173 GLN cc_start: 0.8518 (pt0) cc_final: 0.7921 (mt0) REVERT: D 179 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7971 (mt-10) REVERT: D 185 LYS cc_start: 0.8892 (ttpp) cc_final: 0.8634 (ttpt) REVERT: D 216 HIS cc_start: 0.7753 (m170) cc_final: 0.7473 (m-70) REVERT: D 240 MET cc_start: 0.8823 (ptm) cc_final: 0.8354 (ppp) REVERT: D 280 ASP cc_start: 0.8005 (t70) cc_final: 0.7695 (t0) REVERT: D 281 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8974 (tt) REVERT: D 286 ILE cc_start: 0.9309 (mp) cc_final: 0.9007 (mp) REVERT: D 331 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.8096 (p) REVERT: D 334 ASP cc_start: 0.8424 (p0) cc_final: 0.7782 (t0) REVERT: D 348 GLN cc_start: 0.9240 (mt0) cc_final: 0.8616 (tm-30) REVERT: E 32 LEU cc_start: 0.9585 (mt) cc_final: 0.9252 (mp) REVERT: E 39 PHE cc_start: 0.9006 (t80) cc_final: 0.8675 (t80) REVERT: E 75 ARG cc_start: 0.8264 (mtp85) cc_final: 0.8058 (ttm-80) REVERT: E 80 PHE cc_start: 0.8761 (m-10) cc_final: 0.8142 (m-80) REVERT: E 113 MET cc_start: 0.8855 (mmp) cc_final: 0.8587 (mmp) REVERT: E 146 LEU cc_start: 0.9518 (mm) cc_final: 0.9285 (mm) REVERT: E 153 ILE cc_start: 0.9343 (mm) cc_final: 0.9107 (mm) REVERT: E 168 LEU cc_start: 0.8712 (pt) cc_final: 0.8273 (tp) REVERT: E 353 LEU cc_start: 0.9389 (mm) cc_final: 0.8795 (pp) REVERT: E 364 PHE cc_start: 0.8955 (t80) cc_final: 0.8170 (t80) REVERT: E 368 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8571 (mm) REVERT: E 425 ASP cc_start: 0.7733 (m-30) cc_final: 0.7272 (m-30) REVERT: E 446 ILE cc_start: 0.9496 (pt) cc_final: 0.9275 (tp) REVERT: E 508 LYS cc_start: 0.9353 (tttt) cc_final: 0.9069 (ttmm) REVERT: E 546 PHE cc_start: 0.8872 (t80) cc_final: 0.8643 (t80) REVERT: E 723 LEU cc_start: 0.9285 (mt) cc_final: 0.9044 (mt) REVERT: E 857 PHE cc_start: 0.8465 (m-80) cc_final: 0.8132 (m-80) REVERT: E 903 MET cc_start: 0.7799 (ptm) cc_final: 0.7331 (ptm) REVERT: E 1074 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8948 (mp) REVERT: E 1232 ASP cc_start: 0.8126 (t70) cc_final: 0.7894 (t70) REVERT: E 1261 LEU cc_start: 0.8847 (tp) cc_final: 0.8597 (tp) REVERT: E 1290 MET cc_start: 0.9269 (tpp) cc_final: 0.9021 (tpp) REVERT: E 1293 ASN cc_start: 0.9021 (m-40) cc_final: 0.8613 (t0) REVERT: E 1305 MET cc_start: 0.8617 (tpp) cc_final: 0.8276 (mmt) REVERT: E 1395 MET cc_start: 0.8461 (mmt) cc_final: 0.7961 (mmp) REVERT: E 1428 ASP cc_start: 0.8535 (t0) cc_final: 0.8239 (m-30) outliers start: 170 outliers final: 39 residues processed: 669 average time/residue: 0.1392 time to fit residues: 146.7202 Evaluate side-chains 400 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 349 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 142 CYS Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 331 SER Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 244 VAL Chi-restraints excluded: chain C residue 281 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 182 ILE Chi-restraints excluded: chain D residue 220 VAL Chi-restraints excluded: chain D residue 255 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 GLU Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain D residue 331 SER Chi-restraints excluded: chain E residue 308 ILE Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 942 GLU Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1074 LEU Chi-restraints excluded: chain E residue 1175 CYS Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 HIS A 153 ASN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 46 HIS B 48 ASN B 70 HIS B 313 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS E 127 ASN E 375 GLN E 486 GLN E 609 GLN E 681 GLN E 787 ASN E 817 HIS E 867 HIS E 892 GLN E1486 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057426 restraints weight = 89722.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.059295 restraints weight = 44768.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060546 restraints weight = 27814.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061405 restraints weight = 19819.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.061951 restraints weight = 15569.918| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21567 Z= 0.150 Angle : 0.722 11.887 29310 Z= 0.373 Chirality : 0.045 0.232 3469 Planarity : 0.006 0.056 3646 Dihedral : 9.042 109.932 2987 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 3.79 % Allowed : 17.79 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.14), residues: 2662 helix: -1.55 (0.12), residues: 1316 sheet: -0.77 (0.32), residues: 260 loop : -1.97 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 221 TYR 0.024 0.002 TYR E 124 PHE 0.023 0.001 PHE E 6 TRP 0.022 0.001 TRP E1033 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd covalent geometry : bond 0.00325 (21567) covalent geometry : angle 0.72229 (29310) hydrogen bonds : bond 0.04524 ( 1065) hydrogen bonds : angle 5.11577 ( 3063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 419 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8606 (t0) cc_final: 0.8131 (t0) REVERT: A 65 ASP cc_start: 0.9002 (t0) cc_final: 0.8637 (t0) REVERT: A 83 TRP cc_start: 0.9397 (m-10) cc_final: 0.9173 (m-90) REVERT: A 158 MET cc_start: 0.8125 (tmm) cc_final: 0.7838 (tmm) REVERT: A 163 MET cc_start: 0.9257 (mmm) cc_final: 0.8927 (mmm) REVERT: A 209 MET cc_start: 0.8894 (tpp) cc_final: 0.8657 (tpp) REVERT: A 247 ASN cc_start: 0.8493 (p0) cc_final: 0.8225 (p0) REVERT: A 250 PHE cc_start: 0.8839 (t80) cc_final: 0.8600 (t80) REVERT: B 57 GLN cc_start: 0.8876 (mt0) cc_final: 0.8048 (tp-100) REVERT: B 163 MET cc_start: 0.9158 (mmm) cc_final: 0.8862 (mmm) REVERT: B 181 LEU cc_start: 0.8846 (mt) cc_final: 0.8588 (tp) REVERT: B 218 GLN cc_start: 0.8501 (mt0) cc_final: 0.8165 (mt0) REVERT: B 247 ASN cc_start: 0.7727 (p0) cc_final: 0.7314 (p0) REVERT: B 304 TYR cc_start: 0.8501 (m-10) cc_final: 0.8169 (m-80) REVERT: B 313 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: C 65 ASP cc_start: 0.7971 (t0) cc_final: 0.7614 (t0) REVERT: C 77 MET cc_start: 0.8688 (tpp) cc_final: 0.8172 (ttt) REVERT: C 170 LYS cc_start: 0.8853 (tptt) cc_final: 0.8618 (tptm) REVERT: C 209 MET cc_start: 0.8867 (tpp) cc_final: 0.8483 (mmm) REVERT: C 237 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: C 240 MET cc_start: 0.8090 (tmm) cc_final: 0.7832 (tmm) REVERT: C 247 ASN cc_start: 0.8312 (p0) cc_final: 0.8003 (p0) REVERT: C 292 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7589 (tm-30) REVERT: C 313 GLN cc_start: 0.8990 (mt0) cc_final: 0.8176 (mm110) REVERT: D 43 ASN cc_start: 0.8043 (t0) cc_final: 0.7389 (t0) REVERT: D 110 CYS cc_start: 0.8678 (m) cc_final: 0.8345 (m) REVERT: D 126 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8288 (mt-10) REVERT: D 163 MET cc_start: 0.9083 (mmm) cc_final: 0.8306 (mmm) REVERT: D 166 SER cc_start: 0.9425 (t) cc_final: 0.9028 (p) REVERT: D 185 LYS cc_start: 0.9108 (ttpp) cc_final: 0.8681 (ttpt) REVERT: D 198 PHE cc_start: 0.8799 (t80) cc_final: 0.8386 (t80) REVERT: D 199 MET cc_start: 0.8079 (mtm) cc_final: 0.6615 (mpp) REVERT: D 216 HIS cc_start: 0.7772 (m170) cc_final: 0.7466 (m170) REVERT: D 217 MET cc_start: 0.8750 (mtp) cc_final: 0.8508 (mtt) REVERT: D 240 MET cc_start: 0.8853 (ptm) cc_final: 0.8526 (ppp) REVERT: D 286 ILE cc_start: 0.9326 (mp) cc_final: 0.9060 (mp) REVERT: D 298 THR cc_start: 0.8960 (t) cc_final: 0.8745 (t) REVERT: D 334 ASP cc_start: 0.8644 (p0) cc_final: 0.7934 (t70) REVERT: E 35 VAL cc_start: 0.9644 (m) cc_final: 0.9442 (p) REVERT: E 75 ARG cc_start: 0.8592 (mtp85) cc_final: 0.8316 (ttm-80) REVERT: E 146 LEU cc_start: 0.9571 (mm) cc_final: 0.9280 (mm) REVERT: E 168 LEU cc_start: 0.8884 (pt) cc_final: 0.8537 (tp) REVERT: E 258 MET cc_start: 0.8717 (ptp) cc_final: 0.8509 (ptt) REVERT: E 353 LEU cc_start: 0.9386 (mm) cc_final: 0.8887 (pp) REVERT: E 364 PHE cc_start: 0.8871 (t80) cc_final: 0.8355 (t80) REVERT: E 425 ASP cc_start: 0.7959 (m-30) cc_final: 0.7724 (m-30) REVERT: E 546 PHE cc_start: 0.8831 (t80) cc_final: 0.8598 (t80) REVERT: E 603 LYS cc_start: 0.8058 (OUTLIER) cc_final: 0.5633 (mtmm) REVERT: E 857 PHE cc_start: 0.8276 (m-80) cc_final: 0.8055 (m-80) REVERT: E 1020 GLN cc_start: 0.8969 (mm110) cc_final: 0.8343 (mm-40) REVERT: E 1140 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9276 (mm) REVERT: E 1191 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8687 (pp30) REVERT: E 1194 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8550 (t0) REVERT: E 1235 ASN cc_start: 0.9191 (m-40) cc_final: 0.8989 (m-40) REVERT: E 1261 LEU cc_start: 0.8845 (tp) cc_final: 0.8609 (tp) REVERT: E 1290 MET cc_start: 0.9395 (tpp) cc_final: 0.9159 (tpp) REVERT: E 1293 ASN cc_start: 0.9107 (m-40) cc_final: 0.8623 (t0) REVERT: E 1389 SER cc_start: 0.9529 (t) cc_final: 0.9250 (p) REVERT: E 1395 MET cc_start: 0.8679 (mmt) cc_final: 0.8195 (mmp) REVERT: E 1428 ASP cc_start: 0.8607 (t0) cc_final: 0.8282 (m-30) REVERT: E 1436 ILE cc_start: 0.9235 (mt) cc_final: 0.8996 (pt) outliers start: 87 outliers final: 45 residues processed: 478 average time/residue: 0.1453 time to fit residues: 110.0974 Evaluate side-chains 383 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 333 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 608 VAL Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1194 ASP Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 216 optimal weight: 2.9990 chunk 247 optimal weight: 6.9990 chunk 167 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 255 optimal weight: 0.4980 chunk 16 optimal weight: 5.9990 chunk 184 optimal weight: 0.9980 chunk 188 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 62 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 HIS B 299 GLN ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 52 GLN C 128 GLN C 186 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057446 restraints weight = 89732.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059308 restraints weight = 45041.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060565 restraints weight = 28006.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061420 restraints weight = 19973.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061967 restraints weight = 15668.382| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21567 Z= 0.125 Angle : 0.680 11.205 29310 Z= 0.342 Chirality : 0.045 0.229 3469 Planarity : 0.004 0.040 3646 Dihedral : 7.671 106.224 2935 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.98 % Favored : 95.98 % Rotamer: Outliers : 2.97 % Allowed : 20.41 % Favored : 76.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.15), residues: 2662 helix: -0.46 (0.14), residues: 1341 sheet: -0.39 (0.32), residues: 275 loop : -1.81 (0.17), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 266 TYR 0.019 0.001 TYR E 124 PHE 0.026 0.001 PHE C 250 TRP 0.018 0.001 TRP B 311 HIS 0.016 0.001 HIS E 817 Details of bonding type rmsd covalent geometry : bond 0.00266 (21567) covalent geometry : angle 0.68043 (29310) hydrogen bonds : bond 0.04059 ( 1065) hydrogen bonds : angle 4.59996 ( 3063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 360 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8566 (t0) cc_final: 0.8111 (t0) REVERT: A 48 ASN cc_start: 0.8828 (t0) cc_final: 0.8514 (t0) REVERT: A 56 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8799 (pp) REVERT: A 65 ASP cc_start: 0.9104 (t0) cc_final: 0.8599 (t0) REVERT: A 158 MET cc_start: 0.8224 (tmm) cc_final: 0.7820 (tmm) REVERT: A 163 MET cc_start: 0.9293 (mmm) cc_final: 0.8919 (mmm) REVERT: A 247 ASN cc_start: 0.8416 (p0) cc_final: 0.8054 (p0) REVERT: A 250 PHE cc_start: 0.8854 (t80) cc_final: 0.8616 (t80) REVERT: B 183 PHE cc_start: 0.8762 (m-80) cc_final: 0.8284 (m-80) REVERT: B 247 ASN cc_start: 0.8059 (p0) cc_final: 0.7695 (p0) REVERT: B 257 ILE cc_start: 0.9584 (mm) cc_final: 0.9076 (tp) REVERT: B 287 LEU cc_start: 0.9407 (tp) cc_final: 0.9131 (pt) REVERT: C 65 ASP cc_start: 0.8168 (t0) cc_final: 0.7733 (t0) REVERT: C 170 LYS cc_start: 0.8772 (tptt) cc_final: 0.8540 (tptm) REVERT: C 179 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7778 (mt-10) REVERT: C 199 MET cc_start: 0.8366 (mtt) cc_final: 0.8149 (mtt) REVERT: C 237 ASP cc_start: 0.8337 (OUTLIER) cc_final: 0.8014 (m-30) REVERT: C 240 MET cc_start: 0.8048 (tmm) cc_final: 0.7767 (tmm) REVERT: C 247 ASN cc_start: 0.8438 (p0) cc_final: 0.8089 (p0) REVERT: C 292 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7663 (tm-30) REVERT: C 332 LYS cc_start: 0.9072 (tppt) cc_final: 0.8786 (tppt) REVERT: D 43 ASN cc_start: 0.8048 (t0) cc_final: 0.7352 (t0) REVERT: D 83 TRP cc_start: 0.9059 (m-10) cc_final: 0.8260 (m-90) REVERT: D 110 CYS cc_start: 0.8617 (m) cc_final: 0.7942 (m) REVERT: D 126 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7848 (mp0) REVERT: D 163 MET cc_start: 0.9203 (mmm) cc_final: 0.8511 (mmm) REVERT: D 166 SER cc_start: 0.9475 (t) cc_final: 0.9105 (p) REVERT: D 170 LYS cc_start: 0.9014 (tppt) cc_final: 0.8633 (tptm) REVERT: D 185 LYS cc_start: 0.9089 (ttpp) cc_final: 0.8658 (ttpt) REVERT: D 198 PHE cc_start: 0.8786 (t80) cc_final: 0.8284 (t80) REVERT: D 199 MET cc_start: 0.8142 (mtm) cc_final: 0.6660 (mpp) REVERT: D 217 MET cc_start: 0.8592 (mtp) cc_final: 0.8283 (mtp) REVERT: D 240 MET cc_start: 0.8906 (ptm) cc_final: 0.8462 (ppp) REVERT: D 281 LEU cc_start: 0.9264 (tt) cc_final: 0.8798 (tp) REVERT: D 286 ILE cc_start: 0.9299 (mp) cc_final: 0.8940 (mp) REVERT: D 288 GLU cc_start: 0.7892 (pt0) cc_final: 0.7427 (pt0) REVERT: D 332 LYS cc_start: 0.8930 (mtmm) cc_final: 0.8720 (mtmm) REVERT: D 334 ASP cc_start: 0.8484 (p0) cc_final: 0.7757 (t70) REVERT: E 75 ARG cc_start: 0.8553 (mtp85) cc_final: 0.8299 (ttm-80) REVERT: E 146 LEU cc_start: 0.9616 (mm) cc_final: 0.9389 (mm) REVERT: E 353 LEU cc_start: 0.9358 (mm) cc_final: 0.8904 (pp) REVERT: E 364 PHE cc_start: 0.8805 (t80) cc_final: 0.8497 (t80) REVERT: E 368 LEU cc_start: 0.9210 (mm) cc_final: 0.8558 (mm) REVERT: E 603 LYS cc_start: 0.7823 (OUTLIER) cc_final: 0.5797 (mtmm) REVERT: E 683 MET cc_start: 0.8588 (mpp) cc_final: 0.8326 (mpp) REVERT: E 723 LEU cc_start: 0.9397 (mt) cc_final: 0.9183 (mt) REVERT: E 857 PHE cc_start: 0.8458 (m-80) cc_final: 0.8092 (m-80) REVERT: E 919 ARG cc_start: 0.8962 (ptm160) cc_final: 0.8546 (ptm-80) REVERT: E 1020 GLN cc_start: 0.8957 (mm110) cc_final: 0.8388 (mm-40) REVERT: E 1066 MET cc_start: 0.6588 (tpt) cc_final: 0.5975 (ptm) REVERT: E 1140 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9096 (mm) REVERT: E 1194 ASP cc_start: 0.8925 (OUTLIER) cc_final: 0.8724 (t70) REVERT: E 1252 MET cc_start: 0.8779 (mtm) cc_final: 0.8576 (mpp) REVERT: E 1293 ASN cc_start: 0.9155 (m-40) cc_final: 0.8521 (t0) REVERT: E 1395 MET cc_start: 0.8837 (mmt) cc_final: 0.8252 (mmp) REVERT: E 1428 ASP cc_start: 0.8584 (t0) cc_final: 0.8292 (m-30) REVERT: E 1507 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7813 (mp0) outliers start: 68 outliers final: 40 residues processed: 404 average time/residue: 0.1477 time to fit residues: 95.2775 Evaluate side-chains 368 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 323 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1194 ASP Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 95 optimal weight: 0.8980 chunk 92 optimal weight: 5.9990 chunk 78 optimal weight: 0.0970 chunk 264 optimal weight: 3.9990 chunk 229 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 203 optimal weight: 9.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 153 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 ASN B 48 ASN B 299 GLN C 97 HIS C 186 HIS D 97 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN ** D 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS E 12 HIS E 235 ASN E 708 GLN E 817 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 892 GLN E1518 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.067909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055655 restraints weight = 90377.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.057458 restraints weight = 45382.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058690 restraints weight = 28264.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.059514 restraints weight = 20170.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.060059 restraints weight = 15883.931| |-----------------------------------------------------------------------------| r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21567 Z= 0.143 Angle : 0.660 13.008 29310 Z= 0.329 Chirality : 0.044 0.232 3469 Planarity : 0.004 0.056 3646 Dihedral : 7.070 98.024 2929 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.71 % Allowed : 20.50 % Favored : 75.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.82 (0.16), residues: 2662 helix: 0.20 (0.14), residues: 1356 sheet: -0.22 (0.33), residues: 279 loop : -1.57 (0.18), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 703 TYR 0.017 0.001 TYR B 304 PHE 0.017 0.001 PHE B 75 TRP 0.026 0.001 TRP A 83 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00308 (21567) covalent geometry : angle 0.66004 (29310) hydrogen bonds : bond 0.03915 ( 1065) hydrogen bonds : angle 4.29754 ( 3063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 339 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8638 (t0) cc_final: 0.8202 (t0) REVERT: A 47 LYS cc_start: 0.8308 (tppt) cc_final: 0.8075 (tppt) REVERT: A 56 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8848 (pp) REVERT: A 65 ASP cc_start: 0.9178 (t0) cc_final: 0.8652 (t0) REVERT: A 158 MET cc_start: 0.8140 (tmm) cc_final: 0.7831 (tmm) REVERT: A 163 MET cc_start: 0.9259 (mmm) cc_final: 0.8884 (mmm) REVERT: A 247 ASN cc_start: 0.8427 (p0) cc_final: 0.8021 (p0) REVERT: A 250 PHE cc_start: 0.8890 (t80) cc_final: 0.8641 (t80) REVERT: B 77 MET cc_start: 0.9240 (tpp) cc_final: 0.8933 (tpp) REVERT: B 159 ILE cc_start: 0.8815 (pt) cc_final: 0.8559 (mm) REVERT: B 247 ASN cc_start: 0.8383 (p0) cc_final: 0.7973 (p0) REVERT: C 65 ASP cc_start: 0.8311 (t0) cc_final: 0.7878 (t0) REVERT: C 77 MET cc_start: 0.8827 (tpp) cc_final: 0.8333 (ttt) REVERT: C 170 LYS cc_start: 0.8794 (tptt) cc_final: 0.8517 (tptm) REVERT: C 179 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7990 (mt-10) REVERT: C 199 MET cc_start: 0.8620 (mtt) cc_final: 0.8296 (mtt) REVERT: C 209 MET cc_start: 0.8604 (mmm) cc_final: 0.8302 (mmm) REVERT: C 237 ASP cc_start: 0.8410 (OUTLIER) cc_final: 0.8136 (m-30) REVERT: C 240 MET cc_start: 0.8001 (tmm) cc_final: 0.7748 (tmm) REVERT: C 247 ASN cc_start: 0.8541 (p0) cc_final: 0.8103 (p0) REVERT: C 292 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7634 (tm-30) REVERT: D 83 TRP cc_start: 0.9223 (m-10) cc_final: 0.8460 (m-90) REVERT: D 110 CYS cc_start: 0.8564 (m) cc_final: 0.8139 (m) REVERT: D 163 MET cc_start: 0.9292 (mmm) cc_final: 0.8659 (mmm) REVERT: D 166 SER cc_start: 0.9550 (t) cc_final: 0.9221 (p) REVERT: D 170 LYS cc_start: 0.9097 (tppt) cc_final: 0.8603 (tptm) REVERT: D 179 GLU cc_start: 0.8669 (mt-10) cc_final: 0.8333 (tt0) REVERT: D 185 LYS cc_start: 0.9140 (ttpp) cc_final: 0.8709 (ttpt) REVERT: D 198 PHE cc_start: 0.8889 (t80) cc_final: 0.8299 (t80) REVERT: D 199 MET cc_start: 0.8210 (mtm) cc_final: 0.6673 (mpp) REVERT: D 201 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7511 (mtm180) REVERT: D 240 MET cc_start: 0.8926 (ptm) cc_final: 0.8519 (ppp) REVERT: D 286 ILE cc_start: 0.9448 (mp) cc_final: 0.9141 (mp) REVERT: D 288 GLU cc_start: 0.8010 (pt0) cc_final: 0.7706 (pt0) REVERT: D 334 ASP cc_start: 0.8601 (p0) cc_final: 0.7905 (t70) REVERT: E 28 PHE cc_start: 0.8813 (t80) cc_final: 0.8564 (t80) REVERT: E 115 PHE cc_start: 0.9354 (t80) cc_final: 0.9147 (t80) REVERT: E 138 ILE cc_start: 0.9616 (mm) cc_final: 0.9327 (tp) REVERT: E 364 PHE cc_start: 0.8864 (t80) cc_final: 0.8604 (t80) REVERT: E 368 LEU cc_start: 0.9298 (mm) cc_final: 0.8657 (mm) REVERT: E 401 MET cc_start: 0.9353 (tpp) cc_final: 0.8881 (mmm) REVERT: E 413 MET cc_start: 0.8463 (tpp) cc_final: 0.8254 (tpp) REVERT: E 425 ASP cc_start: 0.8051 (m-30) cc_final: 0.7838 (m-30) REVERT: E 442 MET cc_start: 0.8256 (tpp) cc_final: 0.7935 (tpt) REVERT: E 603 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.5649 (mtmm) REVERT: E 683 MET cc_start: 0.8564 (mpp) cc_final: 0.7993 (mpp) REVERT: E 723 LEU cc_start: 0.9394 (mt) cc_final: 0.9153 (mt) REVERT: E 1020 GLN cc_start: 0.8992 (mm110) cc_final: 0.8335 (mm-40) REVERT: E 1066 MET cc_start: 0.6637 (tpt) cc_final: 0.6044 (ptm) REVERT: E 1252 MET cc_start: 0.8743 (mtm) cc_final: 0.8508 (mpp) REVERT: E 1293 ASN cc_start: 0.9103 (m-40) cc_final: 0.8451 (t0) REVERT: E 1305 MET cc_start: 0.8560 (tpp) cc_final: 0.8350 (mmt) REVERT: E 1395 MET cc_start: 0.8779 (mmt) cc_final: 0.8279 (mmp) REVERT: E 1428 ASP cc_start: 0.8607 (t0) cc_final: 0.8370 (m-30) REVERT: E 1507 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7803 (mp0) outliers start: 85 outliers final: 50 residues processed: 394 average time/residue: 0.1435 time to fit residues: 90.6693 Evaluate side-chains 363 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 308 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 299 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 237 ASP Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 201 ARG Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 18 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 chunk 202 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 160 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 GLN A 175 HIS B 97 HIS B 128 GLN B 299 GLN ** C 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 ASN ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 GLN ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN E1427 GLN E1439 ASN E1521 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.063749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.051694 restraints weight = 91401.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.053382 restraints weight = 46038.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.054512 restraints weight = 28862.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.055289 restraints weight = 20812.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055748 restraints weight = 16501.335| |-----------------------------------------------------------------------------| r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 21567 Z= 0.277 Angle : 0.753 11.445 29310 Z= 0.384 Chirality : 0.046 0.215 3469 Planarity : 0.004 0.036 3646 Dihedral : 6.967 83.228 2922 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.80 % Allowed : 21.11 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.16), residues: 2662 helix: 0.43 (0.14), residues: 1344 sheet: -0.54 (0.29), residues: 332 loop : -1.31 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 301 TYR 0.027 0.002 TYR B 258 PHE 0.020 0.002 PHE E 578 TRP 0.022 0.002 TRP E1033 HIS 0.016 0.001 HIS E 62 Details of bonding type rmsd covalent geometry : bond 0.00591 (21567) covalent geometry : angle 0.75286 (29310) hydrogen bonds : bond 0.04255 ( 1065) hydrogen bonds : angle 4.48541 ( 3063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 301 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8754 (t0) cc_final: 0.8214 (t0) REVERT: A 56 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8916 (pp) REVERT: A 65 ASP cc_start: 0.9196 (t0) cc_final: 0.8720 (t0) REVERT: A 137 MET cc_start: 0.8695 (ttp) cc_final: 0.8449 (ttp) REVERT: A 158 MET cc_start: 0.8186 (tmm) cc_final: 0.7809 (tmm) REVERT: A 163 MET cc_start: 0.9184 (mmm) cc_final: 0.8812 (mmm) REVERT: B 65 ASP cc_start: 0.8888 (t0) cc_final: 0.8593 (t70) REVERT: B 159 ILE cc_start: 0.9131 (pt) cc_final: 0.8755 (mm) REVERT: B 247 ASN cc_start: 0.8768 (p0) cc_final: 0.8152 (p0) REVERT: B 292 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8220 (tm-30) REVERT: B 304 TYR cc_start: 0.8753 (m-10) cc_final: 0.8297 (m-10) REVERT: B 316 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8860 (m) REVERT: B 326 TYR cc_start: 0.8850 (m-80) cc_final: 0.8515 (m-80) REVERT: C 36 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8247 (p) REVERT: C 65 ASP cc_start: 0.8350 (t0) cc_final: 0.8137 (t0) REVERT: C 81 CYS cc_start: 0.9461 (m) cc_final: 0.8975 (m) REVERT: C 85 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9192 (tp) REVERT: C 88 MET cc_start: 0.8536 (tmm) cc_final: 0.8066 (tmm) REVERT: C 152 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.8621 (tp-100) REVERT: C 179 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8091 (mt-10) REVERT: C 199 MET cc_start: 0.8685 (mtt) cc_final: 0.8389 (mtt) REVERT: C 209 MET cc_start: 0.8511 (mmm) cc_final: 0.8278 (mmm) REVERT: C 240 MET cc_start: 0.8195 (tmm) cc_final: 0.7927 (tmm) REVERT: C 247 ASN cc_start: 0.8840 (p0) cc_final: 0.8240 (p0) REVERT: C 292 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: D 43 ASN cc_start: 0.8010 (m-40) cc_final: 0.7475 (p0) REVERT: D 110 CYS cc_start: 0.8386 (m) cc_final: 0.8012 (m) REVERT: D 115 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7091 (p-80) REVERT: D 163 MET cc_start: 0.9389 (mmm) cc_final: 0.8785 (mmm) REVERT: D 166 SER cc_start: 0.9603 (t) cc_final: 0.9391 (p) REVERT: D 170 LYS cc_start: 0.9217 (tppt) cc_final: 0.8635 (tptm) REVERT: D 179 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8267 (pt0) REVERT: D 185 LYS cc_start: 0.9236 (ttpp) cc_final: 0.8861 (ttpt) REVERT: D 199 MET cc_start: 0.8351 (mtm) cc_final: 0.6347 (mpp) REVERT: D 240 MET cc_start: 0.9089 (ptm) cc_final: 0.8535 (ppp) REVERT: D 258 TYR cc_start: 0.8454 (p90) cc_final: 0.8189 (p90) REVERT: D 334 ASP cc_start: 0.8666 (p0) cc_final: 0.7662 (t70) REVERT: E 353 LEU cc_start: 0.9217 (mm) cc_final: 0.8948 (pp) REVERT: E 368 LEU cc_start: 0.9215 (mm) cc_final: 0.8558 (mm) REVERT: E 442 MET cc_start: 0.8208 (tpp) cc_final: 0.7955 (tpt) REVERT: E 683 MET cc_start: 0.8305 (mpp) cc_final: 0.7813 (mpp) REVERT: E 1020 GLN cc_start: 0.9002 (mm110) cc_final: 0.8474 (mm-40) REVERT: E 1066 MET cc_start: 0.7170 (tpt) cc_final: 0.6680 (ptm) REVERT: E 1173 ILE cc_start: 0.9206 (mm) cc_final: 0.8854 (pt) REVERT: E 1293 ASN cc_start: 0.9090 (m-40) cc_final: 0.8502 (t0) REVERT: E 1395 MET cc_start: 0.8751 (mmt) cc_final: 0.8124 (mmp) REVERT: E 1428 ASP cc_start: 0.8643 (t0) cc_final: 0.8440 (m-30) outliers start: 110 outliers final: 74 residues processed: 376 average time/residue: 0.1450 time to fit residues: 87.5485 Evaluate side-chains 366 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 284 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 153 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 188 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain C residue 328 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 362 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 447 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 523 VAL Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 844 LEU Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1232 ASP Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1265 VAL Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1548 LEU Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 6.9990 chunk 178 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 234 optimal weight: 0.8980 chunk 138 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 218 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 251 optimal weight: 10.0000 chunk 232 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.065609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.053526 restraints weight = 90071.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.055251 restraints weight = 45281.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.056421 restraints weight = 28279.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057215 restraints weight = 20315.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.057708 restraints weight = 16054.628| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21567 Z= 0.146 Angle : 0.678 12.248 29310 Z= 0.335 Chirality : 0.044 0.206 3469 Planarity : 0.003 0.030 3646 Dihedral : 6.651 92.108 2918 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.66 % Allowed : 22.81 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2662 helix: 0.63 (0.14), residues: 1354 sheet: -0.42 (0.30), residues: 324 loop : -1.09 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 599 TYR 0.027 0.001 TYR E 124 PHE 0.031 0.001 PHE E 433 TRP 0.013 0.001 TRP E1033 HIS 0.018 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00321 (21567) covalent geometry : angle 0.67829 (29310) hydrogen bonds : bond 0.04033 ( 1065) hydrogen bonds : angle 4.26994 ( 3063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 312 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8655 (t0) cc_final: 0.8166 (t0) REVERT: A 56 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8901 (pp) REVERT: A 65 ASP cc_start: 0.9146 (t0) cc_final: 0.8664 (t0) REVERT: A 137 MET cc_start: 0.8704 (ttp) cc_final: 0.8441 (ttp) REVERT: A 158 MET cc_start: 0.8160 (tmm) cc_final: 0.7747 (tmm) REVERT: A 163 MET cc_start: 0.9225 (mmm) cc_final: 0.8837 (mmm) REVERT: B 81 CYS cc_start: 0.8604 (m) cc_final: 0.7756 (t) REVERT: B 152 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.8233 (tp40) REVERT: B 159 ILE cc_start: 0.9049 (pt) cc_final: 0.8798 (mm) REVERT: B 163 MET cc_start: 0.9099 (mmm) cc_final: 0.8894 (mmt) REVERT: B 247 ASN cc_start: 0.8842 (p0) cc_final: 0.8070 (p0) REVERT: B 292 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8167 (tm-30) REVERT: B 304 TYR cc_start: 0.8726 (m-10) cc_final: 0.8224 (m-10) REVERT: B 326 TYR cc_start: 0.8894 (m-80) cc_final: 0.8593 (m-80) REVERT: C 36 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.7982 (p) REVERT: C 81 CYS cc_start: 0.9388 (m) cc_final: 0.8930 (m) REVERT: C 88 MET cc_start: 0.8447 (tmm) cc_final: 0.7993 (tmm) REVERT: C 126 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 199 MET cc_start: 0.8649 (mtt) cc_final: 0.8341 (mtt) REVERT: C 207 LYS cc_start: 0.8791 (ttmt) cc_final: 0.8381 (tppt) REVERT: C 209 MET cc_start: 0.8502 (mmm) cc_final: 0.8271 (mmm) REVERT: C 240 MET cc_start: 0.8028 (tmm) cc_final: 0.7644 (tmm) REVERT: C 247 ASN cc_start: 0.8818 (p0) cc_final: 0.8229 (p0) REVERT: C 292 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7838 (tm-30) REVERT: D 43 ASN cc_start: 0.7891 (m-40) cc_final: 0.7348 (p0) REVERT: D 110 CYS cc_start: 0.8497 (m) cc_final: 0.8032 (m) REVERT: D 115 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7180 (p-80) REVERT: D 163 MET cc_start: 0.9390 (mmm) cc_final: 0.8783 (mmm) REVERT: D 166 SER cc_start: 0.9536 (t) cc_final: 0.9315 (p) REVERT: D 170 LYS cc_start: 0.9174 (tppt) cc_final: 0.8549 (tptm) REVERT: D 179 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8235 (pt0) REVERT: D 185 LYS cc_start: 0.9216 (ttpp) cc_final: 0.8808 (ttpt) REVERT: D 199 MET cc_start: 0.8308 (mtm) cc_final: 0.6444 (mpp) REVERT: D 240 MET cc_start: 0.9032 (ptm) cc_final: 0.8610 (ppp) REVERT: D 334 ASP cc_start: 0.8582 (p0) cc_final: 0.7676 (t70) REVERT: E 138 ILE cc_start: 0.9627 (mm) cc_final: 0.9271 (tp) REVERT: E 153 ILE cc_start: 0.9396 (mm) cc_final: 0.9193 (mm) REVERT: E 353 LEU cc_start: 0.9209 (mm) cc_final: 0.8910 (pp) REVERT: E 364 PHE cc_start: 0.8918 (t80) cc_final: 0.8485 (t80) REVERT: E 368 LEU cc_start: 0.9220 (mm) cc_final: 0.8487 (mm) REVERT: E 388 LEU cc_start: 0.9715 (OUTLIER) cc_final: 0.9425 (tt) REVERT: E 425 ASP cc_start: 0.7901 (m-30) cc_final: 0.7352 (m-30) REVERT: E 603 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6424 (mtmm) REVERT: E 683 MET cc_start: 0.8533 (mpp) cc_final: 0.8158 (mpp) REVERT: E 1020 GLN cc_start: 0.8952 (mm110) cc_final: 0.8416 (mm-40) REVERT: E 1066 MET cc_start: 0.7197 (tpt) cc_final: 0.6723 (ptm) REVERT: E 1173 ILE cc_start: 0.9194 (mm) cc_final: 0.8851 (pt) REVERT: E 1293 ASN cc_start: 0.9014 (m-40) cc_final: 0.8462 (t0) REVERT: E 1305 MET cc_start: 0.8592 (mmt) cc_final: 0.8389 (mmt) REVERT: E 1395 MET cc_start: 0.8774 (mmt) cc_final: 0.8224 (mmp) REVERT: E 1428 ASP cc_start: 0.8637 (t0) cc_final: 0.8429 (m-30) REVERT: E 1514 MET cc_start: 0.8627 (mtt) cc_final: 0.8345 (mtm) outliers start: 84 outliers final: 57 residues processed: 372 average time/residue: 0.1445 time to fit residues: 86.1408 Evaluate side-chains 350 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 285 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 292 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 241 optimal weight: 8.9990 chunk 161 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 234 optimal weight: 0.6980 chunk 227 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 117 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.053654 restraints weight = 90331.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.055387 restraints weight = 45728.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056581 restraints weight = 28648.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.057336 restraints weight = 20609.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057908 restraints weight = 16457.518| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21567 Z= 0.137 Angle : 0.684 12.826 29310 Z= 0.335 Chirality : 0.044 0.267 3469 Planarity : 0.003 0.035 3646 Dihedral : 6.518 99.659 2918 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.19 % Allowed : 23.11 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.16), residues: 2662 helix: 0.72 (0.14), residues: 1361 sheet: -0.40 (0.30), residues: 324 loop : -1.02 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 919 TYR 0.022 0.001 TYR E 124 PHE 0.014 0.001 PHE E 364 TRP 0.012 0.001 TRP E1033 HIS 0.008 0.001 HIS D 115 Details of bonding type rmsd covalent geometry : bond 0.00301 (21567) covalent geometry : angle 0.68416 (29310) hydrogen bonds : bond 0.03985 ( 1065) hydrogen bonds : angle 4.21529 ( 3063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 315 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8691 (t0) cc_final: 0.8257 (t0) REVERT: A 47 LYS cc_start: 0.8411 (tppt) cc_final: 0.7922 (tppt) REVERT: A 56 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8901 (pp) REVERT: A 65 ASP cc_start: 0.9156 (t0) cc_final: 0.8649 (t0) REVERT: A 137 MET cc_start: 0.8719 (ttp) cc_final: 0.8474 (ttp) REVERT: A 152 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.8863 (tp40) REVERT: A 158 MET cc_start: 0.8238 (tmm) cc_final: 0.7821 (tmm) REVERT: A 163 MET cc_start: 0.9184 (mmm) cc_final: 0.8782 (mmm) REVERT: B 81 CYS cc_start: 0.8613 (m) cc_final: 0.7764 (t) REVERT: B 152 GLN cc_start: 0.9509 (OUTLIER) cc_final: 0.8300 (tp40) REVERT: B 159 ILE cc_start: 0.9043 (pt) cc_final: 0.8823 (mm) REVERT: B 247 ASN cc_start: 0.8823 (p0) cc_final: 0.8057 (p0) REVERT: B 292 GLU cc_start: 0.8473 (OUTLIER) cc_final: 0.8021 (tm-30) REVERT: B 304 TYR cc_start: 0.8729 (m-10) cc_final: 0.8248 (m-10) REVERT: B 313 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 316 VAL cc_start: 0.9126 (OUTLIER) cc_final: 0.8891 (m) REVERT: B 326 TYR cc_start: 0.8866 (m-80) cc_final: 0.8601 (m-80) REVERT: B 338 LYS cc_start: 0.8483 (tptt) cc_final: 0.8265 (tppt) REVERT: C 36 VAL cc_start: 0.8337 (OUTLIER) cc_final: 0.7970 (p) REVERT: C 81 CYS cc_start: 0.9391 (m) cc_final: 0.8937 (m) REVERT: C 88 MET cc_start: 0.8407 (tmm) cc_final: 0.7940 (tmm) REVERT: C 152 GLN cc_start: 0.9299 (OUTLIER) cc_final: 0.8864 (tp40) REVERT: C 179 GLU cc_start: 0.8422 (mt-10) cc_final: 0.7594 (tp30) REVERT: C 199 MET cc_start: 0.8639 (mtt) cc_final: 0.8374 (mtt) REVERT: C 209 MET cc_start: 0.8557 (mmm) cc_final: 0.8323 (mmm) REVERT: C 240 MET cc_start: 0.7963 (tmm) cc_final: 0.7596 (tmm) REVERT: C 247 ASN cc_start: 0.8805 (p0) cc_final: 0.8187 (p0) REVERT: C 292 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: D 110 CYS cc_start: 0.8522 (m) cc_final: 0.8051 (m) REVERT: D 163 MET cc_start: 0.9430 (mmm) cc_final: 0.8763 (mmm) REVERT: D 166 SER cc_start: 0.9555 (t) cc_final: 0.9276 (p) REVERT: D 170 LYS cc_start: 0.9170 (tppt) cc_final: 0.8544 (tptm) REVERT: D 179 GLU cc_start: 0.8604 (mt-10) cc_final: 0.8251 (pt0) REVERT: D 185 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8779 (ttpt) REVERT: D 240 MET cc_start: 0.9102 (ptm) cc_final: 0.8636 (ppp) REVERT: D 334 ASP cc_start: 0.8558 (p0) cc_final: 0.7646 (t70) REVERT: E 138 ILE cc_start: 0.9624 (mm) cc_final: 0.9267 (tp) REVERT: E 153 ILE cc_start: 0.9402 (mm) cc_final: 0.9190 (mm) REVERT: E 353 LEU cc_start: 0.9211 (mm) cc_final: 0.8888 (pp) REVERT: E 364 PHE cc_start: 0.8964 (t80) cc_final: 0.8457 (t80) REVERT: E 368 LEU cc_start: 0.9300 (mm) cc_final: 0.8557 (mm) REVERT: E 388 LEU cc_start: 0.9722 (OUTLIER) cc_final: 0.9510 (tt) REVERT: E 425 ASP cc_start: 0.7873 (m-30) cc_final: 0.7234 (m-30) REVERT: E 599 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.9073 (tpp80) REVERT: E 603 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.6989 (mtmm) REVERT: E 683 MET cc_start: 0.8497 (mpp) cc_final: 0.8042 (mpp) REVERT: E 903 MET cc_start: 0.8081 (ptp) cc_final: 0.7872 (tmm) REVERT: E 1020 GLN cc_start: 0.8987 (mm110) cc_final: 0.8266 (mm-40) REVERT: E 1066 MET cc_start: 0.7197 (tpt) cc_final: 0.6732 (ptm) REVERT: E 1173 ILE cc_start: 0.9222 (mm) cc_final: 0.8844 (pt) REVERT: E 1293 ASN cc_start: 0.9002 (m-40) cc_final: 0.8424 (t0) REVERT: E 1305 MET cc_start: 0.8683 (mmt) cc_final: 0.8469 (mmt) REVERT: E 1395 MET cc_start: 0.8682 (mmt) cc_final: 0.8220 (mmp) REVERT: E 1428 ASP cc_start: 0.8639 (t0) cc_final: 0.8426 (m-30) outliers start: 96 outliers final: 61 residues processed: 380 average time/residue: 0.1353 time to fit residues: 82.5340 Evaluate side-chains 364 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 291 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 57 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 34 optimal weight: 0.0670 chunk 267 optimal weight: 4.9990 chunk 191 optimal weight: 0.9980 chunk 225 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 66 optimal weight: 0.1980 chunk 65 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.2520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 892 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.065895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.053890 restraints weight = 89287.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055634 restraints weight = 44515.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.056818 restraints weight = 27508.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057616 restraints weight = 19595.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058126 restraints weight = 15390.316| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21567 Z= 0.144 Angle : 0.702 12.724 29310 Z= 0.342 Chirality : 0.045 0.243 3469 Planarity : 0.003 0.034 3646 Dihedral : 6.381 106.743 2916 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.97 % Allowed : 23.90 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.16), residues: 2662 helix: 0.79 (0.14), residues: 1359 sheet: -0.39 (0.29), residues: 324 loop : -0.96 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 919 TYR 0.019 0.001 TYR E 124 PHE 0.015 0.001 PHE C 168 TRP 0.013 0.001 TRP D 90 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00317 (21567) covalent geometry : angle 0.70210 (29310) hydrogen bonds : bond 0.03994 ( 1065) hydrogen bonds : angle 4.23227 ( 3063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 310 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8883 (tttt) cc_final: 0.8561 (tttp) REVERT: A 43 ASN cc_start: 0.8748 (t0) cc_final: 0.8361 (t0) REVERT: A 47 LYS cc_start: 0.8527 (tppt) cc_final: 0.8061 (tppt) REVERT: A 56 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8891 (pp) REVERT: A 65 ASP cc_start: 0.9191 (t0) cc_final: 0.8682 (t0) REVERT: A 137 MET cc_start: 0.8738 (ttp) cc_final: 0.8480 (ttp) REVERT: A 152 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.8844 (tp40) REVERT: A 158 MET cc_start: 0.8450 (tmm) cc_final: 0.7994 (tmm) REVERT: A 163 MET cc_start: 0.9294 (mmm) cc_final: 0.8871 (mmm) REVERT: A 250 PHE cc_start: 0.8978 (t80) cc_final: 0.8672 (t80) REVERT: B 81 CYS cc_start: 0.8530 (m) cc_final: 0.7723 (t) REVERT: B 152 GLN cc_start: 0.9506 (OUTLIER) cc_final: 0.8280 (tp40) REVERT: B 159 ILE cc_start: 0.9038 (pt) cc_final: 0.8833 (mm) REVERT: B 247 ASN cc_start: 0.8794 (p0) cc_final: 0.8050 (p0) REVERT: B 292 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: B 304 TYR cc_start: 0.8708 (m-10) cc_final: 0.8233 (m-10) REVERT: B 313 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8088 (mp10) REVERT: B 326 TYR cc_start: 0.8909 (m-80) cc_final: 0.8632 (m-80) REVERT: B 338 LYS cc_start: 0.8507 (tptt) cc_final: 0.8087 (tppt) REVERT: C 36 VAL cc_start: 0.8366 (OUTLIER) cc_final: 0.7990 (p) REVERT: C 39 LYS cc_start: 0.8678 (tttp) cc_final: 0.8196 (tttp) REVERT: C 81 CYS cc_start: 0.9405 (m) cc_final: 0.8916 (m) REVERT: C 88 MET cc_start: 0.8436 (tmm) cc_final: 0.7981 (tmm) REVERT: C 179 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8153 (mt-10) REVERT: C 199 MET cc_start: 0.8701 (mtt) cc_final: 0.8419 (mtt) REVERT: C 209 MET cc_start: 0.8562 (mmm) cc_final: 0.8358 (mmm) REVERT: C 247 ASN cc_start: 0.8952 (p0) cc_final: 0.8439 (p0) REVERT: C 292 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7920 (tm-30) REVERT: D 43 ASN cc_start: 0.7896 (m-40) cc_final: 0.7319 (p0) REVERT: D 110 CYS cc_start: 0.8537 (m) cc_final: 0.8029 (m) REVERT: D 115 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.6807 (p90) REVERT: D 126 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8188 (mt-10) REVERT: D 163 MET cc_start: 0.9437 (mmm) cc_final: 0.8827 (mmm) REVERT: D 166 SER cc_start: 0.9560 (t) cc_final: 0.9291 (p) REVERT: D 170 LYS cc_start: 0.9120 (tppt) cc_final: 0.8457 (tptm) REVERT: D 185 LYS cc_start: 0.9236 (ttpp) cc_final: 0.8787 (ttpt) REVERT: D 240 MET cc_start: 0.9124 (ptm) cc_final: 0.8662 (ppp) REVERT: D 334 ASP cc_start: 0.8621 (p0) cc_final: 0.7648 (t70) REVERT: E 138 ILE cc_start: 0.9632 (mm) cc_final: 0.9277 (tp) REVERT: E 153 ILE cc_start: 0.9383 (mm) cc_final: 0.9175 (mm) REVERT: E 266 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.8894 (mmm-85) REVERT: E 353 LEU cc_start: 0.9213 (mm) cc_final: 0.8886 (pp) REVERT: E 364 PHE cc_start: 0.8963 (t80) cc_final: 0.8445 (t80) REVERT: E 368 LEU cc_start: 0.9287 (mm) cc_final: 0.8527 (mm) REVERT: E 442 MET cc_start: 0.8689 (tpp) cc_final: 0.8471 (tpt) REVERT: E 599 ARG cc_start: 0.9329 (OUTLIER) cc_final: 0.9109 (tpp80) REVERT: E 603 LYS cc_start: 0.8025 (OUTLIER) cc_final: 0.7082 (mtmm) REVERT: E 683 MET cc_start: 0.8484 (mpp) cc_final: 0.8064 (mpp) REVERT: E 903 MET cc_start: 0.7978 (ptp) cc_final: 0.7687 (ptt) REVERT: E 1020 GLN cc_start: 0.9026 (mm110) cc_final: 0.8307 (mm-40) REVERT: E 1066 MET cc_start: 0.7258 (tpt) cc_final: 0.6800 (ptm) REVERT: E 1173 ILE cc_start: 0.9210 (mm) cc_final: 0.8841 (pt) REVERT: E 1293 ASN cc_start: 0.9028 (m-40) cc_final: 0.8424 (t0) REVERT: E 1395 MET cc_start: 0.8712 (mmt) cc_final: 0.8286 (mmp) REVERT: E 1428 ASP cc_start: 0.8669 (t0) cc_final: 0.8457 (m-30) outliers start: 91 outliers final: 68 residues processed: 373 average time/residue: 0.1487 time to fit residues: 88.5934 Evaluate side-chains 371 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 292 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 702 ILE Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1274 ARG Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 169 optimal weight: 0.9990 chunk 126 optimal weight: 0.3980 chunk 244 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 202 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 42 optimal weight: 9.9990 chunk 138 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.066636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.054764 restraints weight = 90030.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.056512 restraints weight = 44915.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.057701 restraints weight = 27804.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.058453 restraints weight = 19797.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059039 restraints weight = 15694.380| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21567 Z= 0.137 Angle : 0.708 14.953 29310 Z= 0.342 Chirality : 0.045 0.291 3469 Planarity : 0.003 0.032 3646 Dihedral : 6.310 111.803 2916 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.58 % Allowed : 24.33 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.17), residues: 2662 helix: 0.95 (0.15), residues: 1329 sheet: -0.46 (0.29), residues: 334 loop : -0.81 (0.19), residues: 999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 919 TYR 0.020 0.001 TYR E 124 PHE 0.029 0.001 PHE E 433 TRP 0.011 0.001 TRP E1037 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00303 (21567) covalent geometry : angle 0.70755 (29310) hydrogen bonds : bond 0.03943 ( 1065) hydrogen bonds : angle 4.24533 ( 3063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 314 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8846 (tttt) cc_final: 0.8523 (tttp) REVERT: A 43 ASN cc_start: 0.8788 (t0) cc_final: 0.8445 (t0) REVERT: A 47 LYS cc_start: 0.8327 (tppt) cc_final: 0.7908 (tppt) REVERT: A 56 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8883 (pp) REVERT: A 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8538 (t0) REVERT: A 137 MET cc_start: 0.8733 (ttp) cc_final: 0.8477 (ttp) REVERT: A 152 GLN cc_start: 0.9489 (OUTLIER) cc_final: 0.8855 (tp40) REVERT: A 158 MET cc_start: 0.8581 (tmm) cc_final: 0.8104 (tmm) REVERT: A 163 MET cc_start: 0.9277 (mmm) cc_final: 0.8790 (mmm) REVERT: A 207 LYS cc_start: 0.8071 (pttt) cc_final: 0.7702 (ptpt) REVERT: A 250 PHE cc_start: 0.8954 (t80) cc_final: 0.8641 (t80) REVERT: B 65 ASP cc_start: 0.8819 (t70) cc_final: 0.8445 (t0) REVERT: B 81 CYS cc_start: 0.8532 (m) cc_final: 0.7713 (t) REVERT: B 152 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8293 (tp40) REVERT: B 247 ASN cc_start: 0.8836 (p0) cc_final: 0.8109 (p0) REVERT: B 292 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8194 (tm-30) REVERT: B 304 TYR cc_start: 0.8727 (m-10) cc_final: 0.8235 (m-10) REVERT: B 313 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 326 TYR cc_start: 0.8898 (m-80) cc_final: 0.8686 (m-80) REVERT: B 338 LYS cc_start: 0.8516 (tptt) cc_final: 0.8118 (tppt) REVERT: C 36 VAL cc_start: 0.8411 (OUTLIER) cc_final: 0.8069 (p) REVERT: C 39 LYS cc_start: 0.8689 (tttp) cc_final: 0.8223 (tttp) REVERT: C 88 MET cc_start: 0.8384 (tmm) cc_final: 0.7950 (tmm) REVERT: C 152 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8933 (tp40) REVERT: C 179 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7589 (tp30) REVERT: C 199 MET cc_start: 0.8627 (mtt) cc_final: 0.8328 (mtt) REVERT: C 209 MET cc_start: 0.8497 (mmm) cc_final: 0.8296 (mmm) REVERT: C 240 MET cc_start: 0.7937 (tmm) cc_final: 0.7651 (tmm) REVERT: C 247 ASN cc_start: 0.8972 (p0) cc_final: 0.8503 (p0) REVERT: C 292 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: D 43 ASN cc_start: 0.7894 (m-40) cc_final: 0.7358 (p0) REVERT: D 110 CYS cc_start: 0.8382 (m) cc_final: 0.7691 (m) REVERT: D 115 HIS cc_start: 0.7838 (OUTLIER) cc_final: 0.6795 (p90) REVERT: D 163 MET cc_start: 0.9391 (mmm) cc_final: 0.8848 (mmm) REVERT: D 166 SER cc_start: 0.9539 (t) cc_final: 0.9277 (p) REVERT: D 170 LYS cc_start: 0.9128 (tppt) cc_final: 0.8437 (tptm) REVERT: D 185 LYS cc_start: 0.9193 (ttpp) cc_final: 0.8817 (ttpt) REVERT: D 240 MET cc_start: 0.9071 (ptm) cc_final: 0.8755 (ppp) REVERT: D 334 ASP cc_start: 0.8549 (p0) cc_final: 0.7627 (t70) REVERT: E 138 ILE cc_start: 0.9609 (mm) cc_final: 0.9229 (tp) REVERT: E 153 ILE cc_start: 0.9390 (mm) cc_final: 0.9179 (mm) REVERT: E 353 LEU cc_start: 0.9208 (mm) cc_final: 0.8887 (pp) REVERT: E 364 PHE cc_start: 0.8931 (t80) cc_final: 0.8357 (t80) REVERT: E 368 LEU cc_start: 0.9295 (mm) cc_final: 0.8472 (mm) REVERT: E 442 MET cc_start: 0.8697 (tpp) cc_final: 0.8482 (tpt) REVERT: E 599 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.9086 (tpp80) REVERT: E 603 LYS cc_start: 0.7879 (OUTLIER) cc_final: 0.6987 (mtmm) REVERT: E 683 MET cc_start: 0.8434 (mpp) cc_final: 0.8101 (mpp) REVERT: E 1020 GLN cc_start: 0.8945 (mm110) cc_final: 0.8270 (mm-40) REVERT: E 1066 MET cc_start: 0.7271 (tpt) cc_final: 0.6822 (ptm) REVERT: E 1173 ILE cc_start: 0.9144 (mm) cc_final: 0.8793 (pt) REVERT: E 1248 LEU cc_start: 0.8679 (tp) cc_final: 0.8268 (tp) REVERT: E 1252 MET cc_start: 0.8461 (mpp) cc_final: 0.7738 (mpp) REVERT: E 1293 ASN cc_start: 0.9013 (m-40) cc_final: 0.8391 (t0) REVERT: E 1395 MET cc_start: 0.8678 (mmt) cc_final: 0.8206 (mmp) REVERT: E 1428 ASP cc_start: 0.8642 (t0) cc_final: 0.8439 (m-30) outliers start: 82 outliers final: 59 residues processed: 375 average time/residue: 0.1499 time to fit residues: 90.0911 Evaluate side-chains 364 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 294 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1274 ARG Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 175 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 256 optimal weight: 0.0980 chunk 246 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 212 optimal weight: 1.9990 chunk 240 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 257 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.054493 restraints weight = 90078.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.056222 restraints weight = 45497.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057403 restraints weight = 28445.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058152 restraints weight = 20436.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058731 restraints weight = 16281.439| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.4998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21567 Z= 0.134 Angle : 0.717 13.879 29310 Z= 0.346 Chirality : 0.045 0.308 3469 Planarity : 0.003 0.032 3646 Dihedral : 6.207 114.677 2914 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.31 % Allowed : 24.55 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.17), residues: 2662 helix: 0.97 (0.15), residues: 1327 sheet: -0.36 (0.32), residues: 294 loop : -0.70 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 919 TYR 0.017 0.001 TYR E 124 PHE 0.043 0.001 PHE E 433 TRP 0.012 0.001 TRP E1033 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00298 (21567) covalent geometry : angle 0.71691 (29310) hydrogen bonds : bond 0.03917 ( 1065) hydrogen bonds : angle 4.22952 ( 3063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5324 Ramachandran restraints generated. 2662 Oldfield, 0 Emsley, 2662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 315 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8847 (tttt) cc_final: 0.8515 (tttp) REVERT: A 43 ASN cc_start: 0.8846 (t0) cc_final: 0.8452 (t0) REVERT: A 47 LYS cc_start: 0.8441 (tppt) cc_final: 0.8044 (tppt) REVERT: A 56 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8882 (pp) REVERT: A 65 ASP cc_start: 0.9100 (t0) cc_final: 0.8462 (t0) REVERT: A 137 MET cc_start: 0.8694 (ttp) cc_final: 0.8437 (ttp) REVERT: A 152 GLN cc_start: 0.9473 (OUTLIER) cc_final: 0.8871 (tp40) REVERT: A 158 MET cc_start: 0.8633 (tmm) cc_final: 0.8179 (tmm) REVERT: A 163 MET cc_start: 0.9247 (mmm) cc_final: 0.8730 (mmm) REVERT: A 207 LYS cc_start: 0.8037 (pttt) cc_final: 0.7679 (ptpt) REVERT: A 250 PHE cc_start: 0.8934 (t80) cc_final: 0.8612 (t80) REVERT: B 65 ASP cc_start: 0.8811 (t70) cc_final: 0.8440 (t0) REVERT: B 81 CYS cc_start: 0.8547 (m) cc_final: 0.7706 (t) REVERT: B 152 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.8286 (tp40) REVERT: B 247 ASN cc_start: 0.8864 (p0) cc_final: 0.8174 (p0) REVERT: B 292 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: B 304 TYR cc_start: 0.8730 (m-10) cc_final: 0.8270 (m-10) REVERT: B 313 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: B 326 TYR cc_start: 0.8905 (m-80) cc_final: 0.8701 (m-80) REVERT: B 338 LYS cc_start: 0.8493 (tptt) cc_final: 0.8149 (tppt) REVERT: C 36 VAL cc_start: 0.8332 (OUTLIER) cc_final: 0.7959 (p) REVERT: C 39 LYS cc_start: 0.8702 (tttp) cc_final: 0.8237 (tttp) REVERT: C 88 MET cc_start: 0.8371 (tmm) cc_final: 0.7897 (tmm) REVERT: C 152 GLN cc_start: 0.9256 (OUTLIER) cc_final: 0.8874 (tp40) REVERT: C 179 GLU cc_start: 0.8434 (mt-10) cc_final: 0.7574 (tp30) REVERT: C 199 MET cc_start: 0.8622 (mtt) cc_final: 0.8365 (mtt) REVERT: C 209 MET cc_start: 0.8480 (mmm) cc_final: 0.8269 (mmm) REVERT: C 240 MET cc_start: 0.7813 (tmm) cc_final: 0.7559 (tmm) REVERT: C 247 ASN cc_start: 0.8989 (p0) cc_final: 0.8640 (p0) REVERT: C 292 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7889 (tm-30) REVERT: D 43 ASN cc_start: 0.7914 (m-40) cc_final: 0.7254 (p0) REVERT: D 110 CYS cc_start: 0.8515 (m) cc_final: 0.8001 (m) REVERT: D 115 HIS cc_start: 0.7862 (OUTLIER) cc_final: 0.6766 (p90) REVERT: D 163 MET cc_start: 0.9372 (mmm) cc_final: 0.8843 (mmm) REVERT: D 166 SER cc_start: 0.9540 (t) cc_final: 0.9160 (p) REVERT: D 170 LYS cc_start: 0.9121 (tppt) cc_final: 0.8455 (tptm) REVERT: D 185 LYS cc_start: 0.9182 (ttpp) cc_final: 0.8788 (ttpt) REVERT: D 240 MET cc_start: 0.9094 (ptm) cc_final: 0.8700 (ppp) REVERT: D 334 ASP cc_start: 0.8593 (p0) cc_final: 0.7638 (t70) REVERT: E 138 ILE cc_start: 0.9632 (mm) cc_final: 0.9261 (tp) REVERT: E 153 ILE cc_start: 0.9381 (mm) cc_final: 0.9174 (mm) REVERT: E 182 MET cc_start: 0.8511 (ptp) cc_final: 0.8278 (mpp) REVERT: E 353 LEU cc_start: 0.9205 (mm) cc_final: 0.8884 (pp) REVERT: E 364 PHE cc_start: 0.8925 (t80) cc_final: 0.8378 (t80) REVERT: E 368 LEU cc_start: 0.9302 (mm) cc_final: 0.8490 (mm) REVERT: E 442 MET cc_start: 0.8707 (tpp) cc_final: 0.8491 (tpt) REVERT: E 599 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.9024 (tpp80) REVERT: E 603 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7062 (mtmm) REVERT: E 683 MET cc_start: 0.8435 (mpp) cc_final: 0.8149 (mpp) REVERT: E 903 MET cc_start: 0.7947 (ptt) cc_final: 0.6916 (pmm) REVERT: E 1020 GLN cc_start: 0.8960 (mm110) cc_final: 0.8330 (mm-40) REVERT: E 1066 MET cc_start: 0.7151 (tpt) cc_final: 0.6760 (ptm) REVERT: E 1173 ILE cc_start: 0.9219 (mm) cc_final: 0.8851 (pt) REVERT: E 1248 LEU cc_start: 0.8680 (tp) cc_final: 0.8166 (tp) REVERT: E 1252 MET cc_start: 0.8365 (mpp) cc_final: 0.7721 (mpp) REVERT: E 1253 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8477 (mm-30) REVERT: E 1293 ASN cc_start: 0.9013 (m-40) cc_final: 0.8500 (t0) REVERT: E 1305 MET cc_start: 0.8775 (mmt) cc_final: 0.8403 (mmt) REVERT: E 1395 MET cc_start: 0.8659 (mmt) cc_final: 0.8270 (mmp) outliers start: 76 outliers final: 57 residues processed: 371 average time/residue: 0.1411 time to fit residues: 83.3128 Evaluate side-chains 368 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 300 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 152 GLN Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 181 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 294 THR Chi-restraints excluded: chain D residue 62 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 115 HIS Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 392 ILE Chi-restraints excluded: chain E residue 408 LEU Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1259 VAL Chi-restraints excluded: chain E residue 1274 ARG Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1285 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1509 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 chunk 150 optimal weight: 6.9990 chunk 222 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.066547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054312 restraints weight = 90991.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056065 restraints weight = 46251.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.057253 restraints weight = 29000.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.058049 restraints weight = 20884.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.058611 restraints weight = 16557.161| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21567 Z= 0.138 Angle : 0.718 13.542 29310 Z= 0.346 Chirality : 0.045 0.280 3469 Planarity : 0.003 0.032 3646 Dihedral : 6.188 115.863 2913 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.31 % Allowed : 24.86 % Favored : 71.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.17), residues: 2662 helix: 1.01 (0.15), residues: 1325 sheet: -0.35 (0.31), residues: 294 loop : -0.66 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 919 TYR 0.017 0.001 TYR E 124 PHE 0.038 0.001 PHE E 433 TRP 0.011 0.001 TRP E1037 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd covalent geometry : bond 0.00307 (21567) covalent geometry : angle 0.71824 (29310) hydrogen bonds : bond 0.03901 ( 1065) hydrogen bonds : angle 4.22990 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3370.25 seconds wall clock time: 59 minutes 27.94 seconds (3567.94 seconds total)