Starting phenix.real_space_refine on Sat Jul 4 14:42:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s5y_24843/07_2026/7s5y_24843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5y_24843/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7s5y_24843/07_2026/7s5y_24843.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s5y_24843/07_2026/7s5y_24843.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s5y_24843/07_2026/7s5y_24843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5y_24843/07_2026/7s5y_24843.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s5y_24843/07_2026/7s5y_24843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5y_24843/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 4.89, per 1000 atoms: 0.23 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: 1.75 Conformation dependent library (CDL) restraints added in 866.9 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: 0.81 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: 4.35 Time building geometry restraints manager: 2.34 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: 11718 24.98 - 49.96: 896 49.96 - 74.93: 155 74.93 - 99.91: 5 99.91 - 124.89: 1 Dihedral angle restraints: 12775 sinusoidal: 4975 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 12772 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: 3.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.440 Find NCS groups from input model: 0.210 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: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 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 : 17.609 124.888 7707 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/Z covalent geometry : bond 0.00951 / 0.45 (21567) covalent geometry : angle 1.48384 / 0.81 (29310) hydrogen bonds : bond 0.13063 / 8.60 ( 1065) hydrogen bonds : angle 8.19976 / 5.74 ( 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 : 0.856 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: 0.1450 time to fit residues: 153.0607 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 : 0.813 ------------------------------------------------------------------------------- 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... 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 ** 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.069651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.057443 restraints weight = 89721.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.059294 restraints weight = 44705.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.060552 restraints weight = 27806.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.061413 restraints weight = 19825.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.061940 restraints weight = 15563.964| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 21567 Z= 0.160 Angle : 0.725 12.431 29310 Z= 0.375 Chirality : 0.045 0.240 3469 Planarity : 0.006 0.053 3646 Dihedral : 8.501 109.426 2956 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.51 % Rotamer: Outliers : 3.84 % Allowed : 17.31 % Favored : 78.85 % 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: -2.45 (0.14), residues: 2662 helix: -1.43 (0.12), residues: 1317 sheet: -0.73 (0.32), residues: 260 loop : -1.96 (0.17), residues: 1085 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 221 TYR 0.024 0.002 TYR E 124 PHE 0.023 0.001 PHE E 6 TRP 0.022 0.002 TRP E1033 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (21567) covalent geometry : angle 0.72466 / 0.38 (29310) hydrogen bonds : bond 0.04431 / 3.00 ( 1065) hydrogen bonds : angle 5.04202 / 3.56 ( 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 507 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 419 time to evaluate : 0.753 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 43 ASN cc_start: 0.8613 (t0) cc_final: 0.8130 (t0) REVERT: A 56 LEU cc_start: 0.9042 (mm) cc_final: 0.8827 (pp) REVERT: A 65 ASP cc_start: 0.9002 (t0) cc_final: 0.8632 (t0) REVERT: A 158 MET cc_start: 0.8131 (tmm) cc_final: 0.7798 (tmm) REVERT: A 163 MET cc_start: 0.9258 (mmm) cc_final: 0.8929 (mmm) REVERT: A 209 MET cc_start: 0.8891 (tpp) cc_final: 0.8657 (tpp) REVERT: A 247 ASN cc_start: 0.8445 (p0) cc_final: 0.8204 (p0) REVERT: A 250 PHE cc_start: 0.8826 (t80) cc_final: 0.8587 (t80) REVERT: B 57 GLN cc_start: 0.8870 (mt0) cc_final: 0.8047 (tp-100) REVERT: B 163 MET cc_start: 0.9135 (mmm) cc_final: 0.8844 (mmm) REVERT: B 181 LEU cc_start: 0.8853 (mt) cc_final: 0.8595 (tp) REVERT: B 218 GLN cc_start: 0.8480 (mt0) cc_final: 0.8139 (mt0) REVERT: B 247 ASN cc_start: 0.7649 (p0) cc_final: 0.7314 (p0) REVERT: B 304 TYR cc_start: 0.8553 (m-10) cc_final: 0.8225 (m-80) REVERT: B 313 GLN cc_start: 0.7633 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: C 65 ASP cc_start: 0.8092 (t0) cc_final: 0.7640 (t0) REVERT: C 170 LYS cc_start: 0.8826 (tptt) cc_final: 0.8612 (tptm) REVERT: C 209 MET cc_start: 0.8831 (tpp) cc_final: 0.8498 (mmm) REVERT: C 237 ASP cc_start: 0.8481 (OUTLIER) cc_final: 0.8086 (m-30) REVERT: C 240 MET cc_start: 0.8113 (tmm) cc_final: 0.7862 (tmm) REVERT: C 247 ASN cc_start: 0.8325 (p0) cc_final: 0.8020 (p0) REVERT: C 292 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7595 (tm-30) REVERT: C 313 GLN cc_start: 0.8989 (mt0) cc_final: 0.8233 (mt0) REVERT: D 43 ASN cc_start: 0.8037 (t0) cc_final: 0.7389 (t0) REVERT: D 110 CYS cc_start: 0.8685 (m) cc_final: 0.8050 (m) REVERT: D 163 MET cc_start: 0.9090 (mmm) cc_final: 0.8309 (mmm) REVERT: D 166 SER cc_start: 0.9430 (t) cc_final: 0.9050 (p) REVERT: D 185 LYS cc_start: 0.9117 (ttpp) cc_final: 0.8682 (ttpt) REVERT: D 198 PHE cc_start: 0.8792 (t80) cc_final: 0.8387 (t80) REVERT: D 199 MET cc_start: 0.8073 (mtm) cc_final: 0.6620 (mpp) REVERT: D 216 HIS cc_start: 0.7774 (m170) cc_final: 0.7479 (m170) REVERT: D 217 MET cc_start: 0.8706 (mtp) cc_final: 0.8462 (mtt) REVERT: D 240 MET cc_start: 0.8853 (ptm) cc_final: 0.8532 (ppp) REVERT: D 286 ILE cc_start: 0.9341 (mp) cc_final: 0.9080 (mp) REVERT: D 298 THR cc_start: 0.8940 (t) cc_final: 0.8731 (t) REVERT: D 334 ASP cc_start: 0.8591 (p0) cc_final: 0.7925 (t70) REVERT: E 75 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8332 (ttm-80) REVERT: E 146 LEU cc_start: 0.9570 (mm) cc_final: 0.9283 (mm) REVERT: E 170 PHE cc_start: 0.8488 (t80) cc_final: 0.8176 (t80) REVERT: E 258 MET cc_start: 0.8714 (ptp) cc_final: 0.8491 (ptt) REVERT: E 353 LEU cc_start: 0.9384 (mm) cc_final: 0.8892 (pp) REVERT: E 364 PHE cc_start: 0.8856 (t80) cc_final: 0.8347 (t80) REVERT: E 425 ASP cc_start: 0.7946 (m-30) cc_final: 0.7712 (m-30) REVERT: E 546 PHE cc_start: 0.8821 (t80) cc_final: 0.8581 (t80) REVERT: E 603 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.5604 (mtmm) REVERT: E 857 PHE cc_start: 0.8261 (m-80) cc_final: 0.8030 (m-80) REVERT: E 1020 GLN cc_start: 0.8961 (mm110) cc_final: 0.8340 (mm-40) REVERT: E 1140 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9274 (mm) REVERT: E 1194 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8552 (t0) REVERT: E 1261 LEU cc_start: 0.8854 (tp) cc_final: 0.8612 (tp) REVERT: E 1290 MET cc_start: 0.9397 (tpp) cc_final: 0.9184 (tpp) REVERT: E 1293 ASN cc_start: 0.9098 (m-40) cc_final: 0.8622 (t0) REVERT: E 1389 SER cc_start: 0.9516 (t) cc_final: 0.9266 (p) REVERT: E 1390 LEU cc_start: 0.9547 (mm) cc_final: 0.9243 (mt) REVERT: E 1395 MET cc_start: 0.8688 (mmt) cc_final: 0.8218 (mmp) REVERT: E 1428 ASP cc_start: 0.8603 (t0) cc_final: 0.8285 (m-30) outliers start: 88 outliers final: 44 residues processed: 478 average time/residue: 0.1411 time to fit residues: 107.0214 Evaluate side-chains 378 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 329 time to evaluate : 0.770 ------------------------------------------------------------------------------- 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 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 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 D residue 339 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 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 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: 0.9990 chunk 247 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 244 optimal weight: 7.9990 chunk 255 optimal weight: 0.9980 chunk 16 optimal weight: 7.9990 chunk 184 optimal weight: 0.8980 chunk 188 optimal weight: 0.9990 chunk 224 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN ** A 242 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 128 GLN C 186 HIS D 173 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.068759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.056533 restraints weight = 90064.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058358 restraints weight = 45072.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.059610 restraints weight = 28114.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.060443 restraints weight = 20054.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.060981 restraints weight = 15795.456| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21567 Z= 0.136 Angle : 0.683 10.903 29310 Z= 0.346 Chirality : 0.045 0.232 3469 Planarity : 0.004 0.040 3646 Dihedral : 7.002 104.084 2903 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 3.27 % Allowed : 20.32 % Favored : 76.41 % 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: -1.45 (0.15), residues: 2662 helix: -0.41 (0.14), residues: 1344 sheet: -0.38 (0.32), residues: 275 loop : -1.76 (0.18), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 221 TYR 0.019 0.001 TYR E 124 PHE 0.025 0.001 PHE C 250 TRP 0.021 0.001 TRP A 83 HIS 0.019 0.001 HIS E 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (21567) covalent geometry : angle 0.68315 / 0.35 (29310) hydrogen bonds : bond 0.04098 / 2.77 ( 1065) hydrogen bonds : angle 4.58773 / 3.24 ( 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 424 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 349 time to evaluate : 0.817 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: 0.8606 (t0) cc_final: 0.8144 (t0) REVERT: A 48 ASN cc_start: 0.8818 (t0) cc_final: 0.8548 (t0) REVERT: A 56 LEU cc_start: 0.9116 (mm) cc_final: 0.8888 (pp) REVERT: A 65 ASP cc_start: 0.9089 (t0) cc_final: 0.8635 (t0) REVERT: A 158 MET cc_start: 0.8131 (tmm) cc_final: 0.7720 (tmm) REVERT: A 163 MET cc_start: 0.9274 (mmm) cc_final: 0.8885 (mmm) REVERT: A 247 ASN cc_start: 0.8474 (p0) cc_final: 0.8092 (p0) REVERT: A 250 PHE cc_start: 0.8861 (t80) cc_final: 0.8634 (t80) REVERT: B 247 ASN cc_start: 0.8000 (p0) cc_final: 0.7695 (p0) REVERT: B 257 ILE cc_start: 0.9576 (mm) cc_final: 0.9098 (tp) REVERT: B 287 LEU cc_start: 0.9426 (tp) cc_final: 0.9053 (pt) REVERT: C 65 ASP cc_start: 0.8193 (t0) cc_final: 0.7775 (t0) REVERT: C 77 MET cc_start: 0.8760 (tpp) cc_final: 0.8322 (ttt) REVERT: C 170 LYS cc_start: 0.8784 (tptt) cc_final: 0.8567 (tptm) REVERT: C 179 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7819 (mt-10) REVERT: C 199 MET cc_start: 0.8409 (mtt) cc_final: 0.8185 (mtt) REVERT: C 237 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.8046 (m-30) REVERT: C 240 MET cc_start: 0.8064 (tmm) cc_final: 0.7789 (tmm) REVERT: C 247 ASN cc_start: 0.8491 (p0) cc_final: 0.8131 (p0) REVERT: C 292 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 332 LYS cc_start: 0.9118 (tppt) cc_final: 0.8871 (tppt) REVERT: D 43 ASN cc_start: 0.8058 (t0) cc_final: 0.7367 (t0) REVERT: D 110 CYS cc_start: 0.8653 (m) cc_final: 0.8006 (m) REVERT: D 163 MET cc_start: 0.9226 (mmm) cc_final: 0.8514 (mmm) REVERT: D 166 SER cc_start: 0.9498 (t) cc_final: 0.9156 (p) REVERT: D 170 LYS cc_start: 0.9017 (tppt) cc_final: 0.8667 (tptm) REVERT: D 185 LYS cc_start: 0.9103 (ttpp) cc_final: 0.8663 (ttpt) REVERT: D 198 PHE cc_start: 0.8843 (t80) cc_final: 0.8318 (t80) REVERT: D 199 MET cc_start: 0.8177 (mtm) cc_final: 0.6685 (mpp) REVERT: D 216 HIS cc_start: 0.7557 (m170) cc_final: 0.7226 (m170) REVERT: D 240 MET cc_start: 0.8937 (ptm) cc_final: 0.8473 (ppp) REVERT: D 286 ILE cc_start: 0.9388 (mp) cc_final: 0.9114 (mp) REVERT: D 334 ASP cc_start: 0.8485 (p0) cc_final: 0.7753 (t70) REVERT: E 7 CYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7811 (m) REVERT: E 75 ARG cc_start: 0.8582 (mtp85) cc_final: 0.8319 (ttm-80) REVERT: E 146 LEU cc_start: 0.9628 (mm) cc_final: 0.9401 (mm) REVERT: E 170 PHE cc_start: 0.8442 (t80) cc_final: 0.8099 (t80) REVERT: E 364 PHE cc_start: 0.8819 (t80) cc_final: 0.8509 (t80) REVERT: E 368 LEU cc_start: 0.9223 (mm) cc_final: 0.8570 (mm) REVERT: E 603 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.5828 (mtmm) REVERT: E 683 MET cc_start: 0.8441 (mpp) cc_final: 0.8173 (mpp) REVERT: E 723 LEU cc_start: 0.9404 (mt) cc_final: 0.9197 (mt) REVERT: E 857 PHE cc_start: 0.8501 (m-80) cc_final: 0.8175 (m-80) REVERT: E 919 ARG cc_start: 0.8982 (ptm160) cc_final: 0.8488 (ptm-80) REVERT: E 1020 GLN cc_start: 0.8975 (mm110) cc_final: 0.8308 (mm-40) REVERT: E 1066 MET cc_start: 0.6662 (tpt) cc_final: 0.6061 (ptm) REVERT: E 1140 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9069 (mm) REVERT: E 1194 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8619 (t0) REVERT: E 1252 MET cc_start: 0.8787 (mtm) cc_final: 0.8567 (mpp) REVERT: E 1290 MET cc_start: 0.9386 (tpp) cc_final: 0.9179 (tpp) REVERT: E 1293 ASN cc_start: 0.9161 (m-40) cc_final: 0.8518 (t0) REVERT: E 1390 LEU cc_start: 0.9585 (mm) cc_final: 0.9274 (mt) REVERT: E 1395 MET cc_start: 0.8803 (mmt) cc_final: 0.8344 (mmp) REVERT: E 1428 ASP cc_start: 0.8593 (t0) cc_final: 0.8309 (m-30) REVERT: E 1507 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7821 (mp0) outliers start: 75 outliers final: 43 residues processed: 399 average time/residue: 0.1381 time to fit residues: 87.9209 Evaluate side-chains 359 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 311 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 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 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 336 THR 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 125 ILE 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 339 VAL Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 78 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 1016 LEU 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: 0.6980 chunk 92 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 145 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 128 GLN A 153 ASN ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS B 299 GLN C 97 HIS C 186 HIS D 97 HIS D 160 ASN D 173 GLN D 242 ASN E 12 HIS E 60 HIS ** E 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 235 ASN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 817 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 892 GLN E1439 ASN E1518 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.066803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.054619 restraints weight = 90907.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.056365 restraints weight = 45931.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.057565 restraints weight = 28864.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.058379 restraints weight = 20726.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.058894 restraints weight = 16373.523| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 21567 Z= 0.166 Angle : 0.673 12.596 29310 Z= 0.338 Chirality : 0.045 0.245 3469 Planarity : 0.004 0.054 3646 Dihedral : 6.340 94.915 2897 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.66 % Allowed : 20.72 % Favored : 75.62 % 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: -0.84 (0.16), residues: 2662 helix: 0.19 (0.14), residues: 1354 sheet: -0.33 (0.32), residues: 279 loop : -1.56 (0.18), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 301 TYR 0.016 0.001 TYR B 304 PHE 0.015 0.001 PHE B 75 TRP 0.018 0.001 TRP E1033 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.17 (21567) covalent geometry : angle 0.67347 / 0.34 (29310) hydrogen bonds : bond 0.03992 / 2.70 ( 1065) hydrogen bonds : angle 4.39330 / 3.11 ( 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 408 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 324 time to evaluate : 0.836 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: 0.8627 (t0) cc_final: 0.8185 (t0) REVERT: A 47 LYS cc_start: 0.8308 (tppt) cc_final: 0.8056 (tppt) REVERT: A 56 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8952 (pp) REVERT: A 65 ASP cc_start: 0.9182 (t0) cc_final: 0.8636 (t0) REVERT: A 158 MET cc_start: 0.8161 (tmm) cc_final: 0.7791 (tmm) REVERT: A 163 MET cc_start: 0.9192 (mmm) cc_final: 0.8830 (mmm) REVERT: A 250 PHE cc_start: 0.8856 (t80) cc_final: 0.8641 (t80) REVERT: B 77 MET cc_start: 0.9260 (tpp) cc_final: 0.8980 (tpp) REVERT: B 152 GLN cc_start: 0.9417 (OUTLIER) cc_final: 0.8091 (tp40) REVERT: B 159 ILE cc_start: 0.8979 (pt) cc_final: 0.8656 (mm) REVERT: B 247 ASN cc_start: 0.8459 (p0) cc_final: 0.8039 (p0) REVERT: B 292 GLU cc_start: 0.8410 (tm-30) cc_final: 0.8019 (tm-30) REVERT: C 65 ASP cc_start: 0.8272 (t0) cc_final: 0.7879 (t0) REVERT: C 85 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9109 (tp) REVERT: C 179 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8016 (mt-10) REVERT: C 199 MET cc_start: 0.8576 (mtt) cc_final: 0.8238 (mtt) REVERT: C 237 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8155 (m-30) REVERT: C 240 MET cc_start: 0.8033 (tmm) cc_final: 0.7778 (tmm) REVERT: C 247 ASN cc_start: 0.8568 (p0) cc_final: 0.8119 (p0) REVERT: C 292 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.7615 (tm-30) REVERT: D 110 CYS cc_start: 0.8594 (m) cc_final: 0.8188 (m) REVERT: D 122 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9036 (mm) REVERT: D 163 MET cc_start: 0.9298 (mmm) cc_final: 0.8648 (mmm) REVERT: D 166 SER cc_start: 0.9562 (t) cc_final: 0.9240 (p) REVERT: D 185 LYS cc_start: 0.9179 (ttpp) cc_final: 0.8752 (ttpt) REVERT: D 198 PHE cc_start: 0.8862 (t80) cc_final: 0.8313 (t80) REVERT: D 199 MET cc_start: 0.8254 (mtm) cc_final: 0.6630 (mpp) REVERT: D 240 MET cc_start: 0.8963 (ptm) cc_final: 0.8532 (ppp) REVERT: D 286 ILE cc_start: 0.9562 (mp) cc_final: 0.9275 (mp) REVERT: D 288 GLU cc_start: 0.7938 (pt0) cc_final: 0.7537 (pt0) REVERT: E 7 CYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8086 (m) REVERT: E 138 ILE cc_start: 0.9636 (mm) cc_final: 0.9260 (tp) REVERT: E 353 LEU cc_start: 0.9211 (mm) cc_final: 0.8913 (pp) REVERT: E 364 PHE cc_start: 0.8861 (t80) cc_final: 0.8651 (t80) REVERT: E 368 LEU cc_start: 0.9312 (mm) cc_final: 0.8658 (mm) REVERT: E 442 MET cc_start: 0.8190 (tpp) cc_final: 0.7915 (tpt) REVERT: E 603 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.6296 (mtmm) REVERT: E 683 MET cc_start: 0.8515 (mpp) cc_final: 0.8184 (mpp) REVERT: E 723 LEU cc_start: 0.9348 (mt) cc_final: 0.9123 (mt) REVERT: E 1020 GLN cc_start: 0.8921 (mm110) cc_final: 0.8236 (mm-40) REVERT: E 1066 MET cc_start: 0.6683 (tpt) cc_final: 0.6126 (ptm) REVERT: E 1293 ASN cc_start: 0.9061 (m-40) cc_final: 0.8410 (t0) REVERT: E 1298 MET cc_start: 0.9269 (tmm) cc_final: 0.8954 (tmm) REVERT: E 1390 LEU cc_start: 0.9586 (mm) cc_final: 0.9293 (mt) REVERT: E 1395 MET cc_start: 0.8852 (mmt) cc_final: 0.8314 (mmp) outliers start: 84 outliers final: 49 residues processed: 378 average time/residue: 0.1388 time to fit residues: 83.9665 Evaluate side-chains 352 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 295 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ILE 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 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 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 152 GLN 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 299 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 VAL 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 122 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 182 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 190 VAL 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 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 1193 ASP 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: 5.9990 chunk 117 optimal weight: 9.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 202 optimal weight: 6.9990 chunk 209 optimal weight: 4.9990 chunk 174 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 175 HIS B 299 GLN C 175 HIS D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN E 220 GLN ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN E1427 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.064168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.052093 restraints weight = 91326.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.053790 restraints weight = 45743.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.054936 restraints weight = 28617.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055653 restraints weight = 20612.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.056210 restraints weight = 16553.718| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 21567 Z= 0.241 Angle : 0.722 11.085 29310 Z= 0.367 Chirality : 0.046 0.219 3469 Planarity : 0.004 0.042 3646 Dihedral : 6.131 84.954 2890 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 4.58 % Allowed : 22.07 % Favored : 73.35 % 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: 0.45 (0.14), residues: 1348 sheet: -0.57 (0.29), residues: 336 loop : -1.33 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 50 TYR 0.015 0.002 TYR E 379 PHE 0.019 0.002 PHE B 183 TRP 0.020 0.002 TRP E1033 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.24 (21567) covalent geometry : angle 0.72208 / 0.37 (29310) hydrogen bonds : bond 0.04184 / 2.81 ( 1065) hydrogen bonds : angle 4.44637 / 3.14 ( 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 410 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 305 time to evaluate : 0.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8726 (t0) cc_final: 0.8262 (t0) REVERT: A 47 LYS cc_start: 0.8281 (tppt) cc_final: 0.8068 (tppt) REVERT: A 56 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8969 (pp) REVERT: A 65 ASP cc_start: 0.9166 (t0) cc_final: 0.8709 (t0) REVERT: A 158 MET cc_start: 0.8172 (tmm) cc_final: 0.7780 (tmm) REVERT: A 163 MET cc_start: 0.9202 (mmm) cc_final: 0.8823 (mmm) REVERT: A 257 ILE cc_start: 0.9604 (mm) cc_final: 0.9390 (mm) REVERT: B 152 GLN cc_start: 0.9501 (OUTLIER) cc_final: 0.8244 (tp40) REVERT: B 159 ILE cc_start: 0.9150 (pt) cc_final: 0.8822 (mm) REVERT: B 247 ASN cc_start: 0.8785 (p0) cc_final: 0.8118 (p0) REVERT: B 292 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8244 (tm-30) REVERT: B 304 TYR cc_start: 0.8589 (m-10) cc_final: 0.8341 (m-10) REVERT: B 316 VAL cc_start: 0.9173 (OUTLIER) cc_final: 0.8881 (m) REVERT: B 326 TYR cc_start: 0.8841 (m-80) cc_final: 0.8518 (m-80) REVERT: C 36 VAL cc_start: 0.8532 (OUTLIER) cc_final: 0.8245 (p) REVERT: C 81 CYS cc_start: 0.9455 (m) cc_final: 0.8980 (m) REVERT: C 85 LEU cc_start: 0.9450 (tt) cc_final: 0.9181 (tp) REVERT: C 88 MET cc_start: 0.8505 (tmm) cc_final: 0.8036 (tmm) REVERT: C 126 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8418 (mt-10) REVERT: C 152 GLN cc_start: 0.9406 (OUTLIER) cc_final: 0.8617 (tp-100) REVERT: C 179 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8090 (mt-10) REVERT: C 199 MET cc_start: 0.8652 (mtt) cc_final: 0.8378 (mtt) REVERT: C 240 MET cc_start: 0.8132 (tmm) cc_final: 0.7880 (tmm) REVERT: C 247 ASN cc_start: 0.8830 (p0) cc_final: 0.8254 (p0) REVERT: C 292 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: D 43 ASN cc_start: 0.7911 (m-40) cc_final: 0.7350 (p0) REVERT: D 110 CYS cc_start: 0.8476 (m) cc_final: 0.8121 (m) REVERT: D 115 HIS cc_start: 0.7790 (OUTLIER) cc_final: 0.7053 (p-80) REVERT: D 163 MET cc_start: 0.9371 (mmm) cc_final: 0.8735 (mmm) REVERT: D 166 SER cc_start: 0.9607 (t) cc_final: 0.9383 (p) REVERT: D 170 LYS cc_start: 0.9234 (tppt) cc_final: 0.8620 (tptm) REVERT: D 185 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8878 (ttpt) REVERT: D 199 MET cc_start: 0.8376 (mtm) cc_final: 0.7402 (mpp) REVERT: D 240 MET cc_start: 0.9083 (ptm) cc_final: 0.8443 (ppp) REVERT: E 7 CYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8087 (m) REVERT: E 353 LEU cc_start: 0.9215 (mm) cc_final: 0.8904 (pp) REVERT: E 368 LEU cc_start: 0.9222 (mm) cc_final: 0.8581 (mm) REVERT: E 388 LEU cc_start: 0.9600 (tp) cc_final: 0.9388 (tt) REVERT: E 683 MET cc_start: 0.8410 (mpp) cc_final: 0.8006 (mpp) REVERT: E 1016 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9206 (tp) REVERT: E 1020 GLN cc_start: 0.8939 (mm110) cc_final: 0.8293 (mm-40) REVERT: E 1066 MET cc_start: 0.7160 (tpt) cc_final: 0.6679 (ptm) REVERT: E 1290 MET cc_start: 0.9208 (tpp) cc_final: 0.8696 (tpp) REVERT: E 1293 ASN cc_start: 0.9086 (m-40) cc_final: 0.8504 (t0) REVERT: E 1298 MET cc_start: 0.9320 (tmm) cc_final: 0.9014 (tmm) REVERT: E 1395 MET cc_start: 0.8789 (mmt) cc_final: 0.8186 (mmp) outliers start: 105 outliers final: 71 residues processed: 382 average time/residue: 0.1424 time to fit residues: 86.6824 Evaluate side-chains 363 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 282 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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 244 VAL Chi-restraints excluded: chain A residue 251 LEU 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 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 299 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 76 THR Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 155 VAL 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 7 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 PHE 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 232 TRP Chi-restraints excluded: chain E residue 271 PHE 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 350 GLN 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 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 941 LYS Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1016 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 1283 LEU Chi-restraints excluded: chain E residue 1334 LEU Chi-restraints excluded: chain E residue 1509 THR 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: 10.0000 chunk 178 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 138 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 251 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 846 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1521 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.064336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.052267 restraints weight = 90207.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.053970 restraints weight = 45238.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.055114 restraints weight = 28354.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.055901 restraints weight = 20377.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.056397 restraints weight = 16101.309| |-----------------------------------------------------------------------------| r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.4551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21567 Z= 0.194 Angle : 0.696 11.981 29310 Z= 0.349 Chirality : 0.045 0.206 3469 Planarity : 0.004 0.068 3646 Dihedral : 5.931 93.245 2887 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.58 % Allowed : 22.72 % 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: -0.37 (0.16), residues: 2662 helix: 0.61 (0.14), residues: 1350 sheet: -0.56 (0.29), residues: 336 loop : -1.24 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 703 TYR 0.017 0.001 TYR B 304 PHE 0.017 0.002 PHE B 75 TRP 0.016 0.001 TRP E1033 HIS 0.020 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.19 (21567) covalent geometry : angle 0.69633 / 0.35 (29310) hydrogen bonds : bond 0.04096 / 2.75 ( 1065) hydrogen bonds : angle 4.35858 / 3.08 ( 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 404 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 299 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8763 (t0) cc_final: 0.8290 (t0) REVERT: A 56 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8971 (pp) REVERT: A 65 ASP cc_start: 0.9178 (t0) cc_final: 0.8708 (t0) REVERT: A 158 MET cc_start: 0.8205 (tmm) cc_final: 0.7786 (tmm) REVERT: A 163 MET cc_start: 0.9214 (mmm) cc_final: 0.8839 (mmm) REVERT: A 257 ILE cc_start: 0.9603 (mm) cc_final: 0.9392 (mm) REVERT: B 81 CYS cc_start: 0.8615 (m) cc_final: 0.7766 (t) REVERT: B 152 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.8339 (tp40) REVERT: B 159 ILE cc_start: 0.9131 (pt) cc_final: 0.8876 (mm) REVERT: B 163 MET cc_start: 0.9122 (mmm) cc_final: 0.8911 (mmt) REVERT: B 247 ASN cc_start: 0.8806 (p0) cc_final: 0.8044 (p0) REVERT: B 292 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8230 (tm-30) REVERT: B 304 TYR cc_start: 0.8569 (m-10) cc_final: 0.8271 (m-10) REVERT: B 316 VAL cc_start: 0.9111 (OUTLIER) cc_final: 0.8895 (m) REVERT: B 326 TYR cc_start: 0.8907 (m-80) cc_final: 0.8635 (m-80) REVERT: C 36 VAL cc_start: 0.8399 (OUTLIER) cc_final: 0.7998 (p) REVERT: C 81 CYS cc_start: 0.9459 (m) cc_final: 0.8988 (m) REVERT: C 88 MET cc_start: 0.8510 (tmm) cc_final: 0.8048 (tmm) REVERT: C 126 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8363 (mt-10) REVERT: C 152 GLN cc_start: 0.9333 (OUTLIER) cc_final: 0.8627 (tp-100) REVERT: C 199 MET cc_start: 0.8702 (mtt) cc_final: 0.8427 (mtt) REVERT: C 247 ASN cc_start: 0.8815 (p0) cc_final: 0.8178 (p0) REVERT: C 292 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7859 (tm-30) REVERT: D 110 CYS cc_start: 0.8546 (m) cc_final: 0.8211 (m) REVERT: D 115 HIS cc_start: 0.7848 (OUTLIER) cc_final: 0.7296 (p-80) REVERT: D 163 MET cc_start: 0.9374 (mmm) cc_final: 0.8649 (mmm) REVERT: D 166 SER cc_start: 0.9565 (t) cc_final: 0.9324 (p) REVERT: D 170 LYS cc_start: 0.9217 (tppt) cc_final: 0.8607 (tptm) REVERT: D 185 LYS cc_start: 0.9271 (ttpp) cc_final: 0.8873 (ttpt) REVERT: D 199 MET cc_start: 0.8340 (mtm) cc_final: 0.7246 (mpp) REVERT: D 240 MET cc_start: 0.9149 (ptm) cc_final: 0.8510 (ppp) REVERT: D 318 ILE cc_start: 0.9247 (pt) cc_final: 0.8452 (mm) REVERT: E 7 CYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8104 (m) REVERT: E 266 ARG cc_start: 0.9242 (OUTLIER) cc_final: 0.8932 (mtp-110) REVERT: E 353 LEU cc_start: 0.9298 (mm) cc_final: 0.8955 (pp) REVERT: E 364 PHE cc_start: 0.8984 (t80) cc_final: 0.8566 (t80) REVERT: E 368 LEU cc_start: 0.9226 (mm) cc_final: 0.8504 (mm) REVERT: E 683 MET cc_start: 0.8457 (mpp) cc_final: 0.8017 (mpp) REVERT: E 1020 GLN cc_start: 0.8947 (mm110) cc_final: 0.8205 (mm-40) REVERT: E 1066 MET cc_start: 0.7243 (tpt) cc_final: 0.6781 (ptm) REVERT: E 1173 ILE cc_start: 0.9226 (mm) cc_final: 0.8866 (pt) REVERT: E 1252 MET cc_start: 0.8585 (mpp) cc_final: 0.8184 (mpp) REVERT: E 1293 ASN cc_start: 0.9056 (m-40) cc_final: 0.8510 (t0) REVERT: E 1298 MET cc_start: 0.9340 (tmm) cc_final: 0.9017 (tmm) REVERT: E 1395 MET cc_start: 0.8764 (mmt) cc_final: 0.8259 (mmp) REVERT: E 1483 SER cc_start: 0.8061 (OUTLIER) cc_final: 0.7174 (t) outliers start: 105 outliers final: 71 residues processed: 375 average time/residue: 0.1411 time to fit residues: 84.9204 Evaluate side-chains 360 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 278 time to evaluate : 1.010 ------------------------------------------------------------------------------- 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 153 ASN Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 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 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 125 ILE 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 299 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 181 LEU 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 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 7 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 266 ARG 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 350 GLN 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 817 HIS 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 1283 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1462 LEU Chi-restraints excluded: chain E residue 1483 SER 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: 2.9990 chunk 241 optimal weight: 7.9990 chunk 161 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 132 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.051665 restraints weight = 90247.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.053357 restraints weight = 44946.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.054515 restraints weight = 28137.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.055286 restraints weight = 20168.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055749 restraints weight = 15977.323| |-----------------------------------------------------------------------------| r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21567 Z= 0.181 Angle : 0.699 12.198 29310 Z= 0.347 Chirality : 0.045 0.198 3469 Planarity : 0.003 0.040 3646 Dihedral : 5.870 101.155 2887 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 4.67 % Allowed : 23.64 % Favored : 71.70 % 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: -0.20 (0.16), residues: 2662 helix: 0.68 (0.14), residues: 1359 sheet: -0.55 (0.29), residues: 324 loop : -1.05 (0.20), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 703 TYR 0.015 0.001 TYR B 304 PHE 0.019 0.002 PHE B 75 TRP 0.014 0.001 TRP E1033 HIS 0.016 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (21567) covalent geometry : angle 0.69872 / 0.35 (29310) hydrogen bonds : bond 0.04060 / 2.72 ( 1065) hydrogen bonds : angle 4.29716 / 3.04 ( 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 404 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 297 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8768 (t0) cc_final: 0.8311 (t0) REVERT: A 56 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8961 (pp) REVERT: A 65 ASP cc_start: 0.9206 (t0) cc_final: 0.8730 (t0) REVERT: A 158 MET cc_start: 0.8268 (tmm) cc_final: 0.7844 (tmm) REVERT: A 163 MET cc_start: 0.9219 (mmm) cc_final: 0.8835 (mmm) REVERT: A 257 ILE cc_start: 0.9595 (mm) cc_final: 0.9385 (mm) REVERT: B 81 CYS cc_start: 0.8512 (m) cc_final: 0.7720 (t) REVERT: B 152 GLN cc_start: 0.9518 (OUTLIER) cc_final: 0.8416 (tp40) REVERT: B 247 ASN cc_start: 0.8842 (p0) cc_final: 0.8027 (p0) REVERT: B 292 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8246 (tm-30) REVERT: B 304 TYR cc_start: 0.8577 (m-10) cc_final: 0.8213 (m-10) REVERT: B 313 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.8249 (mp10) REVERT: B 316 VAL cc_start: 0.9100 (OUTLIER) cc_final: 0.8877 (m) REVERT: B 326 TYR cc_start: 0.8926 (m-80) cc_final: 0.8681 (m-80) REVERT: B 338 LYS cc_start: 0.8662 (tptp) cc_final: 0.8121 (tptt) REVERT: C 36 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.7992 (p) REVERT: C 81 CYS cc_start: 0.9473 (m) cc_final: 0.8986 (m) REVERT: C 88 MET cc_start: 0.8522 (tmm) cc_final: 0.8051 (tmm) REVERT: C 152 GLN cc_start: 0.9332 (OUTLIER) cc_final: 0.8587 (tp-100) REVERT: C 179 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7573 (tp30) REVERT: C 199 MET cc_start: 0.8684 (mtt) cc_final: 0.8379 (mtt) REVERT: C 240 MET cc_start: 0.8011 (tmm) cc_final: 0.7707 (tmm) REVERT: C 247 ASN cc_start: 0.8983 (p0) cc_final: 0.8515 (p0) REVERT: C 292 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7906 (tm-30) REVERT: D 43 ASN cc_start: 0.7924 (OUTLIER) cc_final: 0.7334 (p0) REVERT: D 110 CYS cc_start: 0.8558 (m) cc_final: 0.8088 (m) REVERT: D 163 MET cc_start: 0.9442 (mmm) cc_final: 0.8811 (mmm) REVERT: D 166 SER cc_start: 0.9583 (t) cc_final: 0.9314 (p) REVERT: D 170 LYS cc_start: 0.9211 (tppt) cc_final: 0.8596 (tptm) REVERT: D 185 LYS cc_start: 0.9282 (ttpp) cc_final: 0.8878 (ttpt) REVERT: D 240 MET cc_start: 0.9179 (ptm) cc_final: 0.8550 (ppp) REVERT: D 318 ILE cc_start: 0.9251 (pt) cc_final: 0.8471 (mm) REVERT: E 7 CYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8225 (m) REVERT: E 153 ILE cc_start: 0.9415 (mm) cc_final: 0.9205 (mm) REVERT: E 353 LEU cc_start: 0.9304 (mm) cc_final: 0.8968 (pp) REVERT: E 364 PHE cc_start: 0.9021 (t80) cc_final: 0.8576 (t80) REVERT: E 368 LEU cc_start: 0.9203 (mm) cc_final: 0.8510 (mm) REVERT: E 683 MET cc_start: 0.8386 (mpp) cc_final: 0.8042 (mpp) REVERT: E 1020 GLN cc_start: 0.9022 (mm110) cc_final: 0.8267 (mm-40) REVERT: E 1066 MET cc_start: 0.7282 (tpt) cc_final: 0.6851 (ptm) REVERT: E 1173 ILE cc_start: 0.9212 (mm) cc_final: 0.8876 (pt) REVERT: E 1252 MET cc_start: 0.8651 (mpp) cc_final: 0.8378 (mpp) REVERT: E 1293 ASN cc_start: 0.9060 (m-40) cc_final: 0.8509 (t0) REVERT: E 1298 MET cc_start: 0.9389 (tmm) cc_final: 0.9096 (tmm) REVERT: E 1395 MET cc_start: 0.8761 (mmt) cc_final: 0.8267 (mmp) REVERT: E 1483 SER cc_start: 0.7869 (OUTLIER) cc_final: 0.6914 (t) outliers start: 107 outliers final: 79 residues processed: 372 average time/residue: 0.1414 time to fit residues: 84.6757 Evaluate side-chains 368 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 278 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 153 ASN 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 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 125 ILE 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 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 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 299 GLN 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 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 D residue 43 ASN 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 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 7 CYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 158 PHE 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 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE 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 350 GLN 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 547 MET Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 682 ILE Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 830 LEU 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 1016 LEU Chi-restraints excluded: chain E residue 1193 ASP 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 1483 SER 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: 7.9990 chunk 34 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 191 optimal weight: 0.0980 chunk 225 optimal weight: 2.9990 chunk 116 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN B 335 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 892 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.063438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.051550 restraints weight = 90247.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.053260 restraints weight = 45803.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.054416 restraints weight = 28931.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.055169 restraints weight = 20757.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.055781 restraints weight = 16559.424| |-----------------------------------------------------------------------------| r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21567 Z= 0.171 Angle : 0.699 12.563 29310 Z= 0.346 Chirality : 0.045 0.192 3469 Planarity : 0.004 0.040 3646 Dihedral : 5.824 107.008 2886 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.62 % Allowed : 23.86 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.16), residues: 2662 helix: 0.80 (0.14), residues: 1352 sheet: -0.58 (0.29), residues: 334 loop : -0.99 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 919 TYR 0.016 0.001 TYR B 304 PHE 0.019 0.001 PHE B 75 TRP 0.013 0.001 TRP E1033 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (21567) covalent geometry : angle 0.69906 / 0.35 (29310) hydrogen bonds : bond 0.04056 / 2.72 ( 1065) hydrogen bonds : angle 4.28660 / 3.03 ( 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 407 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 301 time to evaluate : 0.804 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: 0.8834 (t0) cc_final: 0.8401 (t0) REVERT: A 56 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8972 (pp) REVERT: A 65 ASP cc_start: 0.9194 (t0) cc_final: 0.8721 (t0) REVERT: A 152 GLN cc_start: 0.9549 (OUTLIER) cc_final: 0.8850 (tp40) REVERT: A 158 MET cc_start: 0.8429 (tmm) cc_final: 0.7982 (tmm) REVERT: A 163 MET cc_start: 0.9209 (mmm) cc_final: 0.8825 (mmm) REVERT: A 257 ILE cc_start: 0.9594 (mm) cc_final: 0.9379 (mm) REVERT: B 81 CYS cc_start: 0.8540 (m) cc_final: 0.7755 (t) REVERT: B 152 GLN cc_start: 0.9530 (OUTLIER) cc_final: 0.8504 (tp40) REVERT: B 247 ASN cc_start: 0.8885 (p0) cc_final: 0.8098 (p0) REVERT: B 292 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8260 (tm-30) REVERT: B 304 TYR cc_start: 0.8559 (m-10) cc_final: 0.8168 (m-10) REVERT: B 313 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.8183 (mp10) REVERT: B 326 TYR cc_start: 0.8946 (m-80) cc_final: 0.8728 (m-80) REVERT: B 338 LYS cc_start: 0.8742 (tptp) cc_final: 0.8285 (tptt) REVERT: C 36 VAL cc_start: 0.8498 (OUTLIER) cc_final: 0.8094 (p) REVERT: C 81 CYS cc_start: 0.9474 (m) cc_final: 0.8986 (m) REVERT: C 88 MET cc_start: 0.8514 (tmm) cc_final: 0.8038 (tmm) REVERT: C 152 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8685 (tp40) REVERT: C 179 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8130 (mt-10) REVERT: C 199 MET cc_start: 0.8673 (mtt) cc_final: 0.8375 (mtt) REVERT: C 240 MET cc_start: 0.7974 (tmm) cc_final: 0.7675 (tmm) REVERT: C 247 ASN cc_start: 0.8958 (p0) cc_final: 0.8486 (p0) REVERT: C 292 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: D 43 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.7281 (p0) REVERT: D 110 CYS cc_start: 0.8569 (m) cc_final: 0.8098 (m) REVERT: D 163 MET cc_start: 0.9421 (mmm) cc_final: 0.8777 (mmm) REVERT: D 166 SER cc_start: 0.9588 (t) cc_final: 0.9284 (p) REVERT: D 170 LYS cc_start: 0.9205 (tppt) cc_final: 0.8573 (tptm) REVERT: D 185 LYS cc_start: 0.9280 (ttpp) cc_final: 0.8882 (ttpt) REVERT: D 240 MET cc_start: 0.9168 (ptm) cc_final: 0.8590 (ppp) REVERT: D 318 ILE cc_start: 0.9249 (pt) cc_final: 0.8465 (mm) REVERT: E 7 CYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8250 (m) REVERT: E 153 ILE cc_start: 0.9411 (mm) cc_final: 0.9204 (mm) REVERT: E 353 LEU cc_start: 0.9304 (mm) cc_final: 0.8935 (pp) REVERT: E 364 PHE cc_start: 0.9036 (t80) cc_final: 0.8604 (t80) REVERT: E 368 LEU cc_start: 0.9306 (mm) cc_final: 0.8621 (mm) REVERT: E 683 MET cc_start: 0.8347 (mpp) cc_final: 0.7970 (mpp) REVERT: E 869 MET cc_start: 0.9547 (mmm) cc_final: 0.9204 (mmm) REVERT: E 1020 GLN cc_start: 0.9022 (mm110) cc_final: 0.8274 (mm-40) REVERT: E 1066 MET cc_start: 0.7289 (tpt) cc_final: 0.6865 (ptm) REVERT: E 1173 ILE cc_start: 0.9220 (mm) cc_final: 0.8831 (pt) REVERT: E 1292 SER cc_start: 0.9388 (OUTLIER) cc_final: 0.9154 (p) REVERT: E 1293 ASN cc_start: 0.9044 (m-40) cc_final: 0.8621 (t0) REVERT: E 1298 MET cc_start: 0.9409 (tmm) cc_final: 0.9204 (tmm) REVERT: E 1395 MET cc_start: 0.8650 (mmt) cc_final: 0.8211 (mmp) outliers start: 106 outliers final: 78 residues processed: 378 average time/residue: 0.1366 time to fit residues: 83.5649 Evaluate side-chains 371 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 282 time to evaluate : 0.831 ------------------------------------------------------------------------------- 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 153 ASN 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 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 288 GLU Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 299 GLN 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 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 D residue 43 ASN 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 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 7 CYS Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 158 PHE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 350 GLN 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 523 VAL Chi-restraints excluded: chain E residue 547 MET 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 830 LEU 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 1016 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 1292 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 169 optimal weight: 1.9990 chunk 126 optimal weight: 0.0670 chunk 244 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 202 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 155 optimal weight: 0.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN B 299 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 836 GLN E 892 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.055062 restraints weight = 88814.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056805 restraints weight = 44289.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057985 restraints weight = 27541.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.058794 restraints weight = 19739.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.059311 restraints weight = 15629.412| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.4959 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= 0.134 Angle : 0.700 13.388 29310 Z= 0.340 Chirality : 0.044 0.275 3469 Planarity : 0.003 0.044 3646 Dihedral : 5.690 111.245 2884 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.97 % Allowed : 24.60 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.17), residues: 2662 helix: 0.88 (0.14), residues: 1352 sheet: -0.45 (0.29), residues: 334 loop : -0.95 (0.20), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 703 TYR 0.015 0.001 TYR B 304 PHE 0.021 0.001 PHE B 75 TRP 0.013 0.001 TRP D 90 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (21567) covalent geometry : angle 0.70046 / 0.34 (29310) hydrogen bonds : bond 0.03986 / 2.67 ( 1065) hydrogen bonds : angle 4.22122 / 2.98 ( 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 405 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 314 time to evaluate : 0.610 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 39 LYS cc_start: 0.8860 (tttt) cc_final: 0.8568 (tttp) REVERT: A 43 ASN cc_start: 0.8786 (t0) cc_final: 0.8373 (t0) REVERT: A 56 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8982 (pp) REVERT: A 65 ASP cc_start: 0.9106 (t0) cc_final: 0.8547 (t0) REVERT: A 158 MET cc_start: 0.8555 (tmm) cc_final: 0.8105 (tmm) REVERT: A 163 MET cc_start: 0.9199 (mmm) cc_final: 0.8741 (mmm) REVERT: A 250 PHE cc_start: 0.8933 (t80) cc_final: 0.8642 (t80) REVERT: A 257 ILE cc_start: 0.9615 (mm) cc_final: 0.9411 (mm) REVERT: B 65 ASP cc_start: 0.8757 (t70) cc_final: 0.8390 (t0) REVERT: B 81 CYS cc_start: 0.8517 (m) cc_final: 0.7710 (t) REVERT: B 152 GLN cc_start: 0.9504 (OUTLIER) cc_final: 0.8491 (tp40) REVERT: B 247 ASN cc_start: 0.8873 (p0) cc_final: 0.8179 (p0) REVERT: B 292 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8100 (tm-30) REVERT: B 304 TYR cc_start: 0.8523 (m-10) cc_final: 0.8224 (m-10) REVERT: B 338 LYS cc_start: 0.8724 (tptp) cc_final: 0.8280 (tptt) REVERT: C 36 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8083 (p) REVERT: C 81 CYS cc_start: 0.9430 (m) cc_final: 0.8948 (m) REVERT: C 88 MET cc_start: 0.8423 (tmm) cc_final: 0.7952 (tmm) REVERT: C 168 PHE cc_start: 0.9521 (t80) cc_final: 0.9304 (t80) REVERT: C 179 GLU cc_start: 0.8474 (mt-10) cc_final: 0.7610 (tp30) REVERT: C 199 MET cc_start: 0.8558 (mtt) cc_final: 0.8299 (mtt) REVERT: C 240 MET cc_start: 0.7939 (tmm) cc_final: 0.7685 (tmm) REVERT: C 247 ASN cc_start: 0.8903 (p0) cc_final: 0.8472 (p0) REVERT: C 292 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7867 (tm-30) REVERT: D 43 ASN cc_start: 0.7827 (m-40) cc_final: 0.7335 (p0) REVERT: D 83 TRP cc_start: 0.9384 (m-10) cc_final: 0.8732 (m-90) REVERT: D 110 CYS cc_start: 0.8525 (m) cc_final: 0.8066 (m) REVERT: D 163 MET cc_start: 0.9430 (mmm) cc_final: 0.8791 (mmm) REVERT: D 166 SER cc_start: 0.9541 (t) cc_final: 0.9258 (p) REVERT: D 170 LYS cc_start: 0.9191 (tppt) cc_final: 0.8561 (tptm) REVERT: D 185 LYS cc_start: 0.9229 (ttpp) cc_final: 0.8892 (tmtt) REVERT: D 240 MET cc_start: 0.9091 (ptm) cc_final: 0.8750 (ppp) REVERT: D 318 ILE cc_start: 0.9230 (pt) cc_final: 0.8472 (mm) REVERT: E 7 CYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8270 (m) REVERT: E 153 ILE cc_start: 0.9401 (mm) cc_final: 0.9196 (mm) REVERT: E 353 LEU cc_start: 0.9289 (mm) cc_final: 0.8949 (pp) REVERT: E 364 PHE cc_start: 0.9013 (t80) cc_final: 0.8609 (t80) REVERT: E 368 LEU cc_start: 0.9312 (mm) cc_final: 0.8668 (mm) REVERT: E 683 MET cc_start: 0.8261 (mpp) cc_final: 0.8007 (mpp) REVERT: E 869 MET cc_start: 0.9487 (mmm) cc_final: 0.9207 (mmm) REVERT: E 903 MET cc_start: 0.8015 (tmm) cc_final: 0.7772 (tmm) REVERT: E 1016 LEU cc_start: 0.9486 (tp) cc_final: 0.9112 (tp) REVERT: E 1020 GLN cc_start: 0.8959 (mm110) cc_final: 0.8248 (mm-40) REVERT: E 1066 MET cc_start: 0.7248 (tpt) cc_final: 0.6840 (ptm) REVERT: E 1173 ILE cc_start: 0.9243 (mm) cc_final: 0.8857 (pt) REVERT: E 1249 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8672 (tp30) REVERT: E 1293 ASN cc_start: 0.8961 (m-40) cc_final: 0.8562 (t0) REVERT: E 1298 MET cc_start: 0.9354 (tmm) cc_final: 0.9105 (tmm) REVERT: E 1395 MET cc_start: 0.8729 (mmt) cc_final: 0.8287 (mmp) REVERT: E 1507 GLU cc_start: 0.8537 (mt-10) cc_final: 0.7860 (mp0) outliers start: 91 outliers final: 67 residues processed: 377 average time/residue: 0.1348 time to fit residues: 81.4001 Evaluate side-chains 365 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 291 time to evaluate : 0.819 ------------------------------------------------------------------------------- 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 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 154 ILE Chi-restraints excluded: chain C residue 155 VAL 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 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 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 339 VAL Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 179 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 350 GLN Chi-restraints excluded: chain E residue 358 VAL 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 547 MET Chi-restraints excluded: chain E residue 557 LEU 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 1249 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 175 optimal weight: 1.9990 chunk 255 optimal weight: 0.4980 chunk 256 optimal weight: 0.0670 chunk 246 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 212 optimal weight: 8.9990 chunk 240 optimal weight: 5.9990 chunk 215 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 257 optimal weight: 0.3980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.066677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.054428 restraints weight = 90131.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.056219 restraints weight = 45106.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.057432 restraints weight = 28076.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058202 restraints weight = 20098.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.058790 restraints weight = 15982.860| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21567 Z= 0.126 Angle : 0.712 13.741 29310 Z= 0.344 Chirality : 0.045 0.291 3469 Planarity : 0.003 0.039 3646 Dihedral : 5.555 114.132 2884 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.45 % Allowed : 25.21 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2662 helix: 0.98 (0.15), residues: 1324 sheet: -0.34 (0.30), residues: 334 loop : -0.85 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 703 TYR 0.016 0.001 TYR B 304 PHE 0.022 0.001 PHE B 75 TRP 0.012 0.001 TRP E1037 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (21567) covalent geometry : angle 0.71225 / 0.34 (29310) hydrogen bonds : bond 0.03925 / 2.63 ( 1065) hydrogen bonds : angle 4.17993 / 2.94 ( 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 389 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 310 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8852 (tttt) cc_final: 0.8553 (tttp) REVERT: A 43 ASN cc_start: 0.8807 (t0) cc_final: 0.8453 (t0) REVERT: A 56 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8940 (pp) REVERT: A 65 ASP cc_start: 0.9131 (t0) cc_final: 0.8487 (t0) REVERT: A 152 GLN cc_start: 0.9467 (OUTLIER) cc_final: 0.8904 (tm-30) REVERT: A 158 MET cc_start: 0.8641 (tmm) cc_final: 0.8215 (tmm) REVERT: A 163 MET cc_start: 0.9235 (mmm) cc_final: 0.8759 (mmm) REVERT: A 169 MET cc_start: 0.9064 (ttm) cc_final: 0.8823 (mtp) REVERT: A 207 LYS cc_start: 0.8084 (pttt) cc_final: 0.7695 (ptpt) REVERT: A 247 ASN cc_start: 0.8350 (p0) cc_final: 0.7807 (p0) REVERT: A 250 PHE cc_start: 0.8910 (t80) cc_final: 0.8563 (t80) REVERT: B 65 ASP cc_start: 0.8854 (t70) cc_final: 0.8474 (t0) REVERT: B 152 GLN cc_start: 0.9485 (OUTLIER) cc_final: 0.8441 (tp40) REVERT: B 247 ASN cc_start: 0.8876 (p0) cc_final: 0.8032 (p0) REVERT: B 292 GLU cc_start: 0.8394 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: B 299 GLN cc_start: 0.9353 (OUTLIER) cc_final: 0.8305 (pt0) REVERT: B 304 TYR cc_start: 0.8502 (m-10) cc_final: 0.8224 (m-10) REVERT: C 36 VAL cc_start: 0.8271 (OUTLIER) cc_final: 0.7892 (p) REVERT: C 88 MET cc_start: 0.8345 (tmm) cc_final: 0.7906 (tmm) REVERT: C 148 ILE cc_start: 0.9648 (tp) cc_final: 0.9409 (tp) REVERT: C 179 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7588 (tp30) REVERT: C 199 MET cc_start: 0.8612 (mtt) cc_final: 0.8336 (mtt) REVERT: C 209 MET cc_start: 0.8541 (mmm) cc_final: 0.8092 (mmm) REVERT: C 240 MET cc_start: 0.7764 (tmm) cc_final: 0.7546 (tmm) REVERT: C 247 ASN cc_start: 0.8952 (p0) cc_final: 0.8496 (p0) REVERT: C 292 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: D 43 ASN cc_start: 0.7803 (m-40) cc_final: 0.7163 (p0) REVERT: D 83 TRP cc_start: 0.9357 (m-10) cc_final: 0.8705 (m-90) REVERT: D 110 CYS cc_start: 0.8533 (m) cc_final: 0.7990 (m) REVERT: D 163 MET cc_start: 0.9389 (mmm) cc_final: 0.8859 (mmm) REVERT: D 166 SER cc_start: 0.9522 (t) cc_final: 0.9223 (p) REVERT: D 240 MET cc_start: 0.9105 (ptm) cc_final: 0.8627 (ppp) REVERT: D 318 ILE cc_start: 0.9228 (pt) cc_final: 0.8395 (mm) REVERT: E 7 CYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8302 (m) REVERT: E 153 ILE cc_start: 0.9396 (mm) cc_final: 0.9187 (mm) REVERT: E 182 MET cc_start: 0.8628 (ptp) cc_final: 0.8384 (mpp) REVERT: E 353 LEU cc_start: 0.9232 (mm) cc_final: 0.8887 (pp) REVERT: E 364 PHE cc_start: 0.9029 (t80) cc_final: 0.8604 (t80) REVERT: E 368 LEU cc_start: 0.9297 (mm) cc_final: 0.8642 (mm) REVERT: E 433 PHE cc_start: 0.9431 (m-10) cc_final: 0.9197 (m-10) REVERT: E 683 MET cc_start: 0.8248 (mpp) cc_final: 0.8034 (mpp) REVERT: E 869 MET cc_start: 0.9521 (mmm) cc_final: 0.9288 (mmm) REVERT: E 903 MET cc_start: 0.7790 (tmm) cc_final: 0.7436 (tmm) REVERT: E 932 MET cc_start: 0.8204 (ttp) cc_final: 0.7651 (tmm) REVERT: E 1016 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9167 (tp) REVERT: E 1020 GLN cc_start: 0.9029 (mm110) cc_final: 0.8319 (mm-40) REVERT: E 1066 MET cc_start: 0.7285 (tpt) cc_final: 0.6788 (ptm) REVERT: E 1173 ILE cc_start: 0.9235 (mm) cc_final: 0.8871 (pt) REVERT: E 1249 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8744 (tp30) REVERT: E 1293 ASN cc_start: 0.9047 (m-40) cc_final: 0.8515 (t0) REVERT: E 1298 MET cc_start: 0.9335 (tmm) cc_final: 0.9026 (tmm) REVERT: E 1395 MET cc_start: 0.8736 (mmt) cc_final: 0.8346 (mmp) REVERT: E 1432 PHE cc_start: 0.8813 (m-80) cc_final: 0.8388 (m-10) outliers start: 79 outliers final: 55 residues processed: 366 average time/residue: 0.1411 time to fit residues: 82.5529 Evaluate side-chains 360 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 295 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 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 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 268 TYR 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 299 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 292 GLU Chi-restraints excluded: chain C residue 294 THR 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 138 VAL Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain E residue 7 CYS Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 265 GLN Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 358 VAL 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 547 MET Chi-restraints excluded: chain E residue 557 LEU 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 1016 LEU Chi-restraints excluded: chain E residue 1249 GLU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: chunk 35 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 92 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 60 optimal weight: 0.6980 chunk 109 optimal weight: 0.0570 chunk 150 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 103 optimal weight: 0.0370 chunk 165 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.3754 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 299 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.067365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.055097 restraints weight = 90723.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.056897 restraints weight = 45256.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.058112 restraints weight = 28111.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.058940 restraints weight = 20124.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059473 restraints weight = 15845.668| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.5163 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= 0.125 Angle : 0.720 13.827 29310 Z= 0.347 Chirality : 0.045 0.261 3469 Planarity : 0.004 0.069 3646 Dihedral : 5.444 114.954 2883 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.05 % Allowed : 25.64 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.17), residues: 2662 helix: 0.96 (0.15), residues: 1321 sheet: -0.26 (0.30), residues: 335 loop : -0.84 (0.19), residues: 1006 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E1274 TYR 0.016 0.001 TYR B 304 PHE 0.034 0.001 PHE C 168 TRP 0.013 0.001 TRP E1037 HIS 0.006 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (21567) covalent geometry : angle 0.72039 / 0.35 (29310) hydrogen bonds : bond 0.03891 / 2.60 ( 1065) hydrogen bonds : angle 4.15226 / 2.92 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.36 seconds wall clock time: 59 minutes 55.27 seconds (3595.27 seconds total)