Starting phenix.real_space_refine on Mon Oct 26 15:29:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s5y_24843/10_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s5y_24843/10_2026/7s5y_24843.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/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: 4.40, per 1000 atoms: 0.21 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS E 7 " - pdb=" SG CYS E 27 " distance=2.03 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: 1.54 Conformation dependent library (CDL) restraints added in 858.8 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: 0.60 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: 4.47 Time building geometry restraints manager: 2.10 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: 11719 24.98 - 49.96: 897 49.96 - 74.93: 156 74.93 - 99.91: 5 99.91 - 124.89: 1 Dihedral angle restraints: 12778 sinusoidal: 4978 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 12775 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: 2.16 - 2.71: 946 2.71 - 3.26: 19130 3.26 - 3.80: 36422 3.80 - 4.35: 43749 4.35 - 4.90: 71285 Nonbonded interactions: 171532 Sorted by model distance: 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 nonbonded pdb="MG MG E1602 " pdb=" O3B ATP E1604 " model vdw 2.175 2.170 ... (remaining 171527 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: 4.980 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: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 19.340 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.220 ------------------------------------------------------------------------------- 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 21568 Z= 0.453 Angle : 1.484 19.636 29312 Z= 0.813 Chirality : 0.083 0.704 3469 Planarity : 0.012 0.095 3646 Dihedral : 17.609 124.888 7707 Min Nonbonded Distance : 2.160 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) SS BOND : bond 0.00091 / 0.05 ( 1) SS BOND : angle 1.71628 / 0.91 ( 2) 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 : 0.591 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: 0.1403 time to fit residues: 148.0963 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 : 0.822 ------------------------------------------------------------------------------- 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: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 111] 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 = 0.3310 r_free = 0.3310 target = 0.069755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057493 restraints weight = 89763.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.059369 restraints weight = 44935.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.060636 restraints weight = 27862.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.061490 restraints weight = 19868.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.062036 restraints weight = 15617.711| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21568 Z= 0.155 Angle : 0.736 11.699 29312 Z= 0.380 Chirality : 0.046 0.255 3469 Planarity : 0.006 0.057 3646 Dihedral : 8.647 110.893 2956 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 3.75 % Allowed : 17.62 % Favored : 78.63 % 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: -2.61 (0.14), residues: 2662 helix: -1.59 (0.12), residues: 1316 sheet: -0.81 (0.32), residues: 260 loop : -1.99 (0.17), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 34 TYR 0.025 0.002 TYR E 124 PHE 0.018 0.001 PHE E 6 TRP 0.024 0.001 TRP E1033 HIS 0.005 0.001 HIS C 234 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (21567) covalent geometry : angle 0.73619 / 0.38 (29310) SS BOND : bond 0.00335 / 0.18 ( 1) SS BOND : angle 0.89198 / 0.49 ( 2) hydrogen bonds : bond 0.04518 / 3.05 ( 1065) hydrogen bonds : angle 5.14867 / 3.63 ( 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 492 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 406 time to evaluate : 0.796 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: 0.8704 (tttp) cc_final: 0.7801 (ttpp) REVERT: A 43 ASN cc_start: 0.8604 (t0) cc_final: 0.8125 (t0) REVERT: A 65 ASP cc_start: 0.8987 (t0) cc_final: 0.8648 (t0) REVERT: A 83 TRP cc_start: 0.9399 (m-10) cc_final: 0.9190 (m-90) REVERT: A 158 MET cc_start: 0.8135 (tmm) cc_final: 0.7839 (tmm) REVERT: A 163 MET cc_start: 0.9256 (mmm) cc_final: 0.8921 (mmm) REVERT: A 209 MET cc_start: 0.8880 (tpp) cc_final: 0.8644 (tpp) REVERT: A 247 ASN cc_start: 0.8514 (p0) cc_final: 0.8240 (p0) REVERT: A 250 PHE cc_start: 0.8836 (t80) cc_final: 0.8609 (t80) REVERT: B 48 ASN cc_start: 0.8855 (m110) cc_final: 0.8568 (p0) REVERT: B 56 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9104 (mm) REVERT: B 84 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9092 (mm) REVERT: B 170 LYS cc_start: 0.8554 (tptt) cc_final: 0.8347 (tptt) REVERT: B 247 ASN cc_start: 0.7698 (p0) cc_final: 0.7295 (p0) REVERT: B 313 GLN cc_start: 0.7661 (OUTLIER) cc_final: 0.7047 (mp10) REVERT: C 65 ASP cc_start: 0.7914 (t0) cc_final: 0.7583 (t0) REVERT: C 77 MET cc_start: 0.8703 (tpp) cc_final: 0.8070 (ttt) REVERT: C 170 LYS cc_start: 0.8854 (tptt) cc_final: 0.8605 (tptm) REVERT: C 179 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7837 (mt-10) REVERT: C 209 MET cc_start: 0.8820 (tpp) cc_final: 0.8490 (mmm) REVERT: C 237 ASP cc_start: 0.8469 (m-30) cc_final: 0.8108 (m-30) REVERT: C 240 MET cc_start: 0.8016 (tmm) cc_final: 0.7773 (tmm) REVERT: C 247 ASN cc_start: 0.8254 (p0) cc_final: 0.7966 (p0) REVERT: C 292 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7583 (tm-30) REVERT: C 313 GLN cc_start: 0.8986 (mt0) cc_final: 0.8177 (mm110) REVERT: D 43 ASN cc_start: 0.8050 (t0) cc_final: 0.7397 (t0) REVERT: D 110 CYS cc_start: 0.8677 (m) cc_final: 0.8367 (m) REVERT: D 160 ASN cc_start: 0.8478 (m-40) cc_final: 0.8209 (m-40) REVERT: D 163 MET cc_start: 0.9084 (mmm) cc_final: 0.8308 (mmm) REVERT: D 166 SER cc_start: 0.9420 (t) cc_final: 0.9031 (p) REVERT: D 185 LYS cc_start: 0.9098 (ttpp) cc_final: 0.8674 (ttpt) REVERT: D 198 PHE cc_start: 0.8803 (t80) cc_final: 0.8387 (t80) REVERT: D 199 MET cc_start: 0.8081 (mtm) cc_final: 0.6615 (mpp) REVERT: D 217 MET cc_start: 0.8766 (mtp) cc_final: 0.8503 (mtm) REVERT: D 240 MET cc_start: 0.8853 (ptm) cc_final: 0.8539 (ppp) REVERT: D 286 ILE cc_start: 0.9323 (mp) cc_final: 0.9005 (mp) REVERT: D 288 GLU cc_start: 0.7894 (pt0) cc_final: 0.7527 (pt0) REVERT: D 334 ASP cc_start: 0.8609 (p0) cc_final: 0.7938 (t70) REVERT: E 35 VAL cc_start: 0.9638 (m) cc_final: 0.9435 (p) REVERT: E 75 ARG cc_start: 0.8583 (mtp85) cc_final: 0.8310 (ttm-80) REVERT: E 146 LEU cc_start: 0.9565 (mm) cc_final: 0.9273 (mm) REVERT: E 168 LEU cc_start: 0.8876 (pt) cc_final: 0.8536 (tp) REVERT: E 353 LEU cc_start: 0.9386 (mm) cc_final: 0.8887 (pp) REVERT: E 364 PHE cc_start: 0.8840 (t80) cc_final: 0.8396 (t80) REVERT: E 425 ASP cc_start: 0.8021 (m-30) cc_final: 0.7762 (m-30) REVERT: E 546 PHE cc_start: 0.8879 (t80) cc_final: 0.8644 (t80) REVERT: E 603 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.5593 (mtmm) REVERT: E 857 PHE cc_start: 0.8287 (m-80) cc_final: 0.8085 (m-80) REVERT: E 1020 GLN cc_start: 0.8947 (mm110) cc_final: 0.8343 (mm-40) REVERT: E 1140 LEU cc_start: 0.9579 (OUTLIER) cc_final: 0.9283 (mm) REVERT: E 1194 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8534 (t0) REVERT: E 1261 LEU cc_start: 0.8846 (tp) cc_final: 0.8619 (tp) REVERT: E 1290 MET cc_start: 0.9392 (tpp) cc_final: 0.9153 (tpp) REVERT: E 1293 ASN cc_start: 0.9115 (m-40) cc_final: 0.8630 (t0) REVERT: E 1296 ASN cc_start: 0.9183 (p0) cc_final: 0.8976 (p0) REVERT: E 1389 SER cc_start: 0.9529 (t) cc_final: 0.9247 (p) REVERT: E 1395 MET cc_start: 0.8677 (mmt) cc_final: 0.8195 (mmp) REVERT: E 1428 ASP cc_start: 0.8604 (t0) cc_final: 0.8280 (m-30) outliers start: 86 outliers final: 44 residues processed: 463 average time/residue: 0.1350 time to fit residues: 99.4943 Evaluate side-chains 386 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 335 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 142 CYS 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 56 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 182 ILE Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 292 GLU 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 65 ASP Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 142 CYS Chi-restraints excluded: chain D residue 169 MET Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 294 THR Chi-restraints excluded: chain D residue 316 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 196 TYR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 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: [216, 247, 167, 244, 255, 16, 184, 188, 224, 62, 77] chunk 216 optimal weight: 0.7980 chunk 247 optimal weight: 0.8980 chunk 167 optimal weight: 3.9990 chunk 244 optimal weight: 5.9990 chunk 255 optimal weight: 0.4980 chunk 16 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 188 optimal weight: 0.9990 chunk 224 optimal weight: 8.9990 chunk 62 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN ** B 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 46 HIS C 128 GLN C 186 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 173 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.069281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057010 restraints weight = 89915.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.058875 restraints weight = 44959.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.060136 restraints weight = 27925.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060950 restraints weight = 19922.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.061554 restraints weight = 15750.727| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 21568 Z= 0.128 Angle : 0.680 10.748 29312 Z= 0.343 Chirality : 0.045 0.230 3469 Planarity : 0.004 0.043 3646 Dihedral : 7.070 105.659 2907 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.17 % Favored : 95.79 % Rotamer: Outliers : 3.36 % Allowed : 20.24 % 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: -1.51 (0.15), residues: 2662 helix: -0.44 (0.14), residues: 1340 sheet: -0.42 (0.32), residues: 275 loop : -1.81 (0.17), residues: 1047 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 703 TYR 0.020 0.001 TYR E 124 PHE 0.024 0.001 PHE C 250 TRP 0.020 0.001 TRP B 311 HIS 0.020 0.001 HIS E 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (21567) covalent geometry : angle 0.67958 / 0.34 (29310) SS BOND : bond 0.00221 / 0.12 ( 1) SS BOND : angle 0.69408 / 0.38 ( 2) hydrogen bonds : bond 0.04065 / 2.75 ( 1065) hydrogen bonds : angle 4.58509 / 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 442 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 365 time to evaluate : 0.821 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: 0.8575 (t0) cc_final: 0.8115 (t0) REVERT: A 48 ASN cc_start: 0.8836 (t0) cc_final: 0.8596 (t0) REVERT: A 56 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8827 (pp) REVERT: A 65 ASP cc_start: 0.9127 (t0) cc_final: 0.8616 (t0) REVERT: A 158 MET cc_start: 0.8200 (tmm) cc_final: 0.7841 (tmm) REVERT: A 163 MET cc_start: 0.9271 (mmm) cc_final: 0.8903 (mmm) REVERT: A 247 ASN cc_start: 0.8438 (p0) cc_final: 0.8061 (p0) REVERT: A 250 PHE cc_start: 0.8864 (t80) cc_final: 0.8607 (t80) REVERT: B 247 ASN cc_start: 0.7939 (p0) cc_final: 0.7633 (p0) REVERT: B 287 LEU cc_start: 0.9423 (tp) cc_final: 0.9119 (pt) REVERT: C 65 ASP cc_start: 0.8207 (t0) cc_final: 0.7775 (t0) REVERT: C 170 LYS cc_start: 0.8795 (tptt) cc_final: 0.8573 (tptm) REVERT: C 179 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7800 (mt-10) REVERT: C 237 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.8063 (m-30) REVERT: C 240 MET cc_start: 0.8063 (tmm) cc_final: 0.7781 (tmm) REVERT: C 247 ASN cc_start: 0.8465 (p0) cc_final: 0.8117 (p0) REVERT: C 292 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7638 (tm-30) REVERT: C 332 LYS cc_start: 0.9101 (tppt) cc_final: 0.8812 (tppt) REVERT: D 43 ASN cc_start: 0.8063 (t0) cc_final: 0.7361 (t0) REVERT: D 110 CYS cc_start: 0.8637 (m) cc_final: 0.7970 (m) REVERT: D 163 MET cc_start: 0.9218 (mmm) cc_final: 0.8520 (mmm) REVERT: D 166 SER cc_start: 0.9491 (t) cc_final: 0.9110 (p) REVERT: D 170 LYS cc_start: 0.9027 (tppt) cc_final: 0.8682 (tptm) REVERT: D 185 LYS cc_start: 0.9098 (ttpp) cc_final: 0.8662 (ttpt) REVERT: D 198 PHE cc_start: 0.8806 (t80) cc_final: 0.8303 (t80) REVERT: D 199 MET cc_start: 0.8165 (mtm) cc_final: 0.6678 (mpp) REVERT: D 240 MET cc_start: 0.8818 (ptm) cc_final: 0.8458 (ppp) REVERT: D 281 LEU cc_start: 0.9210 (tt) cc_final: 0.8722 (tp) REVERT: D 334 ASP cc_start: 0.8566 (p0) cc_final: 0.7858 (t70) REVERT: D 348 GLN cc_start: 0.9252 (mt0) cc_final: 0.8894 (mt0) REVERT: E 32 LEU cc_start: 0.9688 (OUTLIER) cc_final: 0.9481 (mm) REVERT: E 75 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8317 (ttm-80) REVERT: E 124 TYR cc_start: 0.9300 (t80) cc_final: 0.8963 (t80) REVERT: E 146 LEU cc_start: 0.9624 (mm) cc_final: 0.9392 (mt) REVERT: E 364 PHE cc_start: 0.8810 (t80) cc_final: 0.8491 (t80) REVERT: E 368 LEU cc_start: 0.9299 (mm) cc_final: 0.8637 (mm) REVERT: E 603 LYS cc_start: 0.7844 (OUTLIER) cc_final: 0.5801 (mtmm) REVERT: E 683 MET cc_start: 0.8468 (mpp) cc_final: 0.7962 (mpp) REVERT: E 723 LEU cc_start: 0.9400 (mt) cc_final: 0.9198 (mt) REVERT: E 857 PHE cc_start: 0.8518 (m-80) cc_final: 0.8153 (m-80) REVERT: E 919 ARG cc_start: 0.8964 (ptm160) cc_final: 0.8522 (ptm-80) REVERT: E 1020 GLN cc_start: 0.8970 (mm110) cc_final: 0.8302 (mm-40) REVERT: E 1066 MET cc_start: 0.6652 (tpt) cc_final: 0.6052 (ptm) REVERT: E 1140 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9072 (mm) REVERT: E 1194 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8621 (t0) REVERT: E 1293 ASN cc_start: 0.9073 (m-40) cc_final: 0.8511 (t0) REVERT: E 1305 MET cc_start: 0.8809 (tpp) cc_final: 0.8598 (mmt) REVERT: E 1395 MET cc_start: 0.8815 (mmt) cc_final: 0.8216 (mmp) REVERT: E 1428 ASP cc_start: 0.8591 (t0) cc_final: 0.8303 (m-30) REVERT: E 1507 GLU cc_start: 0.8320 (mt-10) cc_final: 0.7819 (mp0) outliers start: 77 outliers final: 43 residues processed: 414 average time/residue: 0.1376 time to fit residues: 91.5380 Evaluate side-chains 361 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 312 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 244 VAL Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 56 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 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 147 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 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 32 LEU Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 817 HIS Chi-restraints excluded: chain E residue 941 LYS Chi-restraints excluded: chain E residue 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: [95, 92, 78, 264, 229, 51, 145, 192, 221, 100, 203] chunk 95 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 4.9990 chunk 264 optimal weight: 0.9990 chunk 229 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 221 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 203 optimal weight: 3.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 97 HIS C 186 HIS D 97 HIS D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 160 ASN D 216 HIS D 242 ASN E 12 HIS E 60 HIS E 220 GLN E 235 ASN E 263 ASN ** E 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 817 HIS ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1197 GLN E1427 GLN E1439 ASN E1518 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.064082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.052312 restraints weight = 90774.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.054010 restraints weight = 46474.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.055168 restraints weight = 29171.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.055966 restraints weight = 21043.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.056465 restraints weight = 16632.851| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 21568 Z= 0.221 Angle : 0.721 12.287 29312 Z= 0.366 Chirality : 0.045 0.244 3469 Planarity : 0.004 0.036 3646 Dihedral : 6.390 91.876 2897 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.23 % Allowed : 20.54 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.16), residues: 2662 helix: 0.16 (0.14), residues: 1350 sheet: -0.72 (0.29), residues: 336 loop : -1.47 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 221 TYR 0.017 0.002 TYR B 258 PHE 0.019 0.002 PHE A 117 TRP 0.034 0.002 TRP A 83 HIS 0.010 0.001 HIS E 817 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.22 (21567) covalent geometry : angle 0.72137 / 0.37 (29310) SS BOND : bond 0.00281 / 0.15 ( 1) SS BOND : angle 0.75723 / 0.42 ( 2) hydrogen bonds : bond 0.04150 / 2.80 ( 1065) hydrogen bonds : angle 4.46789 / 3.17 ( 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 414 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 317 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8678 (t0) cc_final: 0.8203 (t0) REVERT: A 47 LYS cc_start: 0.8327 (tppt) cc_final: 0.8069 (tppt) REVERT: A 56 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8948 (pp) REVERT: A 65 ASP cc_start: 0.9186 (t0) cc_final: 0.8664 (t0) REVERT: A 158 MET cc_start: 0.8096 (tmm) cc_final: 0.7732 (tmm) REVERT: A 163 MET cc_start: 0.9126 (mmm) cc_final: 0.8781 (mmm) REVERT: B 77 MET cc_start: 0.9282 (tpp) cc_final: 0.9048 (tpp) REVERT: B 159 ILE cc_start: 0.9053 (pt) cc_final: 0.8703 (mm) REVERT: B 247 ASN cc_start: 0.8604 (p0) cc_final: 0.8169 (p0) REVERT: B 292 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: B 304 TYR cc_start: 0.8931 (m-10) cc_final: 0.8447 (m-10) REVERT: C 65 ASP cc_start: 0.8300 (t0) cc_final: 0.7887 (t0) REVERT: C 81 CYS cc_start: 0.9378 (m) cc_final: 0.8916 (m) REVERT: C 85 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9153 (tp) REVERT: C 88 MET cc_start: 0.8443 (tmm) cc_final: 0.8016 (tmm) REVERT: C 179 GLU cc_start: 0.8573 (mt-10) cc_final: 0.8230 (mt-10) REVERT: C 209 MET cc_start: 0.8712 (mmm) cc_final: 0.8453 (mmm) REVERT: C 240 MET cc_start: 0.8186 (tmm) cc_final: 0.7907 (tmm) REVERT: C 247 ASN cc_start: 0.8675 (p0) cc_final: 0.8146 (p0) REVERT: C 292 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7858 (tm-30) REVERT: D 110 CYS cc_start: 0.8458 (m) cc_final: 0.8086 (m) REVERT: D 115 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7124 (p-80) REVERT: D 122 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9014 (mm) REVERT: D 163 MET cc_start: 0.9347 (mmm) cc_final: 0.8751 (mmm) REVERT: D 185 LYS cc_start: 0.9160 (ttpp) cc_final: 0.8764 (ttpt) REVERT: D 199 MET cc_start: 0.8377 (mtm) cc_final: 0.6610 (mpp) REVERT: D 217 MET cc_start: 0.8587 (mtp) cc_final: 0.8368 (mtt) REVERT: D 240 MET cc_start: 0.9017 (ptm) cc_final: 0.8492 (ppp) REVERT: D 348 GLN cc_start: 0.9180 (mt0) cc_final: 0.8960 (mp10) REVERT: E 32 LEU cc_start: 0.9734 (OUTLIER) cc_final: 0.9510 (mm) REVERT: E 75 ARG cc_start: 0.8696 (mtp85) cc_final: 0.8297 (ttm-80) REVERT: E 353 LEU cc_start: 0.9205 (mm) cc_final: 0.8920 (pp) REVERT: E 368 LEU cc_start: 0.9203 (mm) cc_final: 0.8578 (mm) REVERT: E 401 MET cc_start: 0.9263 (tpp) cc_final: 0.8701 (mmm) REVERT: E 413 MET cc_start: 0.8348 (tpp) cc_final: 0.8079 (tpp) REVERT: E 425 ASP cc_start: 0.8085 (m-30) cc_final: 0.7856 (m-30) REVERT: E 683 MET cc_start: 0.8349 (mpp) cc_final: 0.7764 (mpp) REVERT: E 723 LEU cc_start: 0.9300 (mt) cc_final: 0.9083 (mt) REVERT: E 1020 GLN cc_start: 0.8933 (mm110) cc_final: 0.8280 (mm-40) REVERT: E 1066 MET cc_start: 0.7139 (tpt) cc_final: 0.6630 (ptm) REVERT: E 1140 LEU cc_start: 0.9474 (OUTLIER) cc_final: 0.9038 (mm) REVERT: E 1252 MET cc_start: 0.8448 (mpp) cc_final: 0.8213 (mpp) REVERT: E 1293 ASN cc_start: 0.9117 (m-40) cc_final: 0.8535 (t0) REVERT: E 1298 MET cc_start: 0.9313 (tmm) cc_final: 0.9019 (tmm) REVERT: E 1395 MET cc_start: 0.8671 (mmt) cc_final: 0.8114 (mmm) outliers start: 97 outliers final: 60 residues processed: 380 average time/residue: 0.1349 time to fit residues: 82.5639 Evaluate side-chains 352 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 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 166 SER 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 56 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 138 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 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 84 LEU Chi-restraints excluded: chain D residue 115 HIS 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 294 THR Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 358 VAL 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 941 LYS Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1140 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 1334 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: [18, 117, 17, 2, 64, 202, 209, 174, 23, 160, 88] chunk 18 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 209 optimal weight: 0.6980 chunk 174 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 153 ASN A 175 HIS ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 892 GLN E1521 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.064878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.052818 restraints weight = 90651.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054539 restraints weight = 45462.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.055681 restraints weight = 28426.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.056461 restraints weight = 20490.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.056952 restraints weight = 16250.303| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 21568 Z= 0.196 Angle : 0.686 11.436 29312 Z= 0.346 Chirality : 0.045 0.220 3469 Planarity : 0.004 0.033 3646 Dihedral : 6.143 81.790 2894 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.88 % Allowed : 22.85 % Favored : 73.27 % 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: -0.53 (0.16), residues: 2662 helix: 0.45 (0.14), residues: 1348 sheet: -0.56 (0.29), residues: 336 loop : -1.30 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 50 TYR 0.014 0.001 TYR E 379 PHE 0.018 0.002 PHE E 84 TRP 0.017 0.001 TRP E1033 HIS 0.022 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 (21567) covalent geometry : angle 0.68569 / 0.35 (29310) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.45234 / 0.26 ( 2) hydrogen bonds : bond 0.04063 / 2.73 ( 1065) hydrogen bonds : angle 4.38035 / 3.10 ( 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 397 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 308 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8724 (t0) cc_final: 0.8210 (t0) REVERT: A 56 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8941 (pp) REVERT: A 65 ASP cc_start: 0.9173 (t0) cc_final: 0.8672 (t0) REVERT: A 158 MET cc_start: 0.8142 (tmm) cc_final: 0.7749 (tmm) REVERT: A 163 MET cc_start: 0.9195 (mmm) cc_final: 0.8830 (mmm) REVERT: A 257 ILE cc_start: 0.9604 (mm) cc_final: 0.9386 (mm) REVERT: B 152 GLN cc_start: 0.9469 (OUTLIER) cc_final: 0.8169 (tp40) REVERT: B 159 ILE cc_start: 0.9084 (pt) cc_final: 0.8761 (mm) REVERT: B 240 MET cc_start: 0.8620 (tmm) cc_final: 0.8377 (tmm) REVERT: B 247 ASN cc_start: 0.8729 (p0) cc_final: 0.8112 (p0) REVERT: B 292 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 304 TYR cc_start: 0.8943 (m-10) cc_final: 0.8422 (m-10) REVERT: B 313 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8101 (mp10) REVERT: B 316 VAL cc_start: 0.9208 (OUTLIER) cc_final: 0.8980 (m) REVERT: B 326 TYR cc_start: 0.8822 (m-80) cc_final: 0.8483 (m-80) REVERT: B 338 LYS cc_start: 0.8624 (tptm) cc_final: 0.8135 (tptt) REVERT: C 36 VAL cc_start: 0.8403 (OUTLIER) cc_final: 0.8103 (p) REVERT: C 81 CYS cc_start: 0.9441 (m) cc_final: 0.8982 (m) REVERT: C 88 MET cc_start: 0.8501 (tmm) cc_final: 0.8040 (tmm) REVERT: C 126 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8391 (mt-10) REVERT: C 152 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8630 (tp-100) REVERT: C 199 MET cc_start: 0.8424 (mtt) cc_final: 0.8146 (mtt) REVERT: C 209 MET cc_start: 0.8579 (mmm) cc_final: 0.8283 (mmm) REVERT: C 247 ASN cc_start: 0.8762 (p0) cc_final: 0.8177 (p0) REVERT: C 292 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7873 (tm-30) REVERT: D 110 CYS cc_start: 0.8545 (m) cc_final: 0.8189 (m) REVERT: D 115 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7546 (p-80) REVERT: D 163 MET cc_start: 0.9206 (mmm) cc_final: 0.8861 (mmm) REVERT: D 185 LYS cc_start: 0.9261 (ttpp) cc_final: 0.8815 (ttpt) REVERT: D 199 MET cc_start: 0.8327 (mtm) cc_final: 0.7185 (mpp) REVERT: D 240 MET cc_start: 0.9094 (ptm) cc_final: 0.8554 (ppp) REVERT: E 32 LEU cc_start: 0.9753 (OUTLIER) cc_final: 0.9506 (mm) REVERT: E 353 LEU cc_start: 0.9217 (mm) cc_final: 0.8906 (pp) REVERT: E 364 PHE cc_start: 0.8974 (t80) cc_final: 0.8530 (t80) REVERT: E 368 LEU cc_start: 0.9206 (mm) cc_final: 0.8488 (mm) REVERT: E 401 MET cc_start: 0.9258 (tpp) cc_final: 0.8632 (mmm) REVERT: E 683 MET cc_start: 0.8318 (mpp) cc_final: 0.7909 (mpp) REVERT: E 1016 LEU cc_start: 0.9494 (OUTLIER) cc_final: 0.9191 (tp) REVERT: E 1020 GLN cc_start: 0.8966 (mm110) cc_final: 0.8274 (mm-40) REVERT: E 1066 MET cc_start: 0.7141 (tpt) cc_final: 0.6652 (ptm) REVERT: E 1136 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8705 (tp) REVERT: E 1140 LEU cc_start: 0.9496 (OUTLIER) cc_final: 0.9033 (mm) REVERT: E 1293 ASN cc_start: 0.9036 (m-40) cc_final: 0.8534 (t0) REVERT: E 1298 MET cc_start: 0.9314 (tmm) cc_final: 0.8956 (tmm) REVERT: E 1395 MET cc_start: 0.8743 (mmt) cc_final: 0.8133 (mmp) outliers start: 89 outliers final: 59 residues processed: 376 average time/residue: 0.1320 time to fit residues: 79.5469 Evaluate side-chains 350 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 280 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 281 LEU Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 56 LEU 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 138 VAL Chi-restraints excluded: chain B residue 152 GLN 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 236 VAL Chi-restraints excluded: chain B residue 291 VAL 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 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 294 THR Chi-restraints excluded: chain D residue 44 VAL Chi-restraints excluded: chain D residue 59 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 294 THR Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 358 VAL 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 844 LEU 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 1136 ILE Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1193 ASP Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1390 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: [57, 178, 75, 234, 138, 187, 218, 108, 251, 232, 3] chunk 57 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 234 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 187 optimal weight: 0.0370 chunk 218 optimal weight: 9.9990 chunk 108 optimal weight: 0.9980 chunk 251 optimal weight: 4.9990 chunk 232 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 242 ASN ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 HIS ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.066278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.054112 restraints weight = 89513.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.055884 restraints weight = 45270.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.057074 restraints weight = 28265.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.057869 restraints weight = 20289.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.058378 restraints weight = 16093.071| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 21568 Z= 0.130 Angle : 0.675 12.502 29312 Z= 0.332 Chirality : 0.044 0.203 3469 Planarity : 0.004 0.103 3646 Dihedral : 5.823 90.801 2887 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.14 % Allowed : 23.46 % Favored : 72.39 % 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: -0.28 (0.16), residues: 2662 helix: 0.63 (0.14), residues: 1361 sheet: -0.50 (0.30), residues: 324 loop : -1.13 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 192 TYR 0.036 0.001 TYR D 258 PHE 0.020 0.001 PHE E 84 TRP 0.011 0.001 TRP E1037 HIS 0.012 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (21567) covalent geometry : angle 0.67527 / 0.33 (29310) SS BOND : bond 0.00194 / 0.10 ( 1) SS BOND : angle 0.43669 / 0.25 ( 2) hydrogen bonds : bond 0.03958 / 2.66 ( 1065) hydrogen bonds : angle 4.24115 / 3.00 ( 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 419 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 324 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8646 (t0) cc_final: 0.8156 (t0) REVERT: A 56 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8945 (pp) REVERT: A 65 ASP cc_start: 0.9155 (t0) cc_final: 0.8631 (t0) REVERT: A 152 GLN cc_start: 0.9466 (OUTLIER) cc_final: 0.9195 (tm-30) REVERT: A 158 MET cc_start: 0.8110 (tmm) cc_final: 0.7727 (tmm) REVERT: A 163 MET cc_start: 0.9180 (mmm) cc_final: 0.8807 (mmm) REVERT: A 250 PHE cc_start: 0.8942 (t80) cc_final: 0.8630 (t80) REVERT: B 50 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7817 (ptp-110) REVERT: B 152 GLN cc_start: 0.9477 (OUTLIER) cc_final: 0.8305 (tp40) REVERT: B 159 ILE cc_start: 0.9104 (pt) cc_final: 0.8859 (mm) REVERT: B 240 MET cc_start: 0.8700 (tmm) cc_final: 0.8349 (tmm) REVERT: B 247 ASN cc_start: 0.8767 (p0) cc_final: 0.8132 (p0) REVERT: B 292 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: B 304 TYR cc_start: 0.8888 (m-10) cc_final: 0.8372 (m-10) REVERT: B 313 GLN cc_start: 0.8429 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: B 326 TYR cc_start: 0.8864 (m-80) cc_final: 0.8582 (m-80) REVERT: B 338 LYS cc_start: 0.8670 (tptm) cc_final: 0.8079 (tptt) REVERT: C 36 VAL cc_start: 0.8287 (OUTLIER) cc_final: 0.7913 (p) REVERT: C 81 CYS cc_start: 0.9372 (m) cc_final: 0.8930 (m) REVERT: C 88 MET cc_start: 0.8414 (tmm) cc_final: 0.7987 (tmm) REVERT: C 179 GLU cc_start: 0.8408 (mt-10) cc_final: 0.7560 (tp30) REVERT: C 199 MET cc_start: 0.8433 (mtt) cc_final: 0.8171 (mtt) REVERT: C 207 LYS cc_start: 0.8806 (ttmt) cc_final: 0.8404 (tppt) REVERT: C 209 MET cc_start: 0.8526 (mmm) cc_final: 0.8251 (mmm) REVERT: C 247 ASN cc_start: 0.8740 (p0) cc_final: 0.8186 (p0) REVERT: C 292 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7884 (tm-30) REVERT: D 110 CYS cc_start: 0.8523 (m) cc_final: 0.8023 (m) REVERT: D 115 HIS cc_start: 0.7802 (OUTLIER) cc_final: 0.7184 (p-80) REVERT: D 163 MET cc_start: 0.9277 (mmm) cc_final: 0.8939 (mmm) REVERT: D 170 LYS cc_start: 0.9177 (tppt) cc_final: 0.8591 (tptm) REVERT: D 185 LYS cc_start: 0.9230 (ttpp) cc_final: 0.8784 (ttpt) REVERT: D 199 MET cc_start: 0.8319 (mtm) cc_final: 0.7217 (mpp) REVERT: D 240 MET cc_start: 0.9101 (ptm) cc_final: 0.8712 (ppp) REVERT: D 258 TYR cc_start: 0.8746 (p90) cc_final: 0.8383 (p90) REVERT: D 318 ILE cc_start: 0.9220 (pt) cc_final: 0.8346 (mm) REVERT: E 32 LEU cc_start: 0.9744 (OUTLIER) cc_final: 0.9510 (mm) REVERT: E 62 HIS cc_start: 0.6482 (m-70) cc_final: 0.6126 (m-70) REVERT: E 138 ILE cc_start: 0.9614 (mm) cc_final: 0.9272 (tp) REVERT: E 153 ILE cc_start: 0.9402 (mm) cc_final: 0.9193 (mm) REVERT: E 353 LEU cc_start: 0.9279 (mm) cc_final: 0.8943 (pp) REVERT: E 364 PHE cc_start: 0.8988 (t80) cc_final: 0.8563 (t80) REVERT: E 368 LEU cc_start: 0.9325 (mm) cc_final: 0.8652 (mm) REVERT: E 401 MET cc_start: 0.9262 (tpp) cc_final: 0.8618 (mmm) REVERT: E 442 MET cc_start: 0.8683 (tpp) cc_final: 0.8475 (tpt) REVERT: E 603 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.6682 (mtmm) REVERT: E 683 MET cc_start: 0.8367 (mpp) cc_final: 0.8026 (mpp) REVERT: E 903 MET cc_start: 0.7466 (ptp) cc_final: 0.6828 (ptt) REVERT: E 1020 GLN cc_start: 0.8930 (mm110) cc_final: 0.8136 (mm-40) REVERT: E 1066 MET cc_start: 0.7149 (tpt) cc_final: 0.6622 (ptm) REVERT: E 1136 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8708 (tt) REVERT: E 1140 LEU cc_start: 0.9495 (OUTLIER) cc_final: 0.9002 (mm) REVERT: E 1173 ILE cc_start: 0.9186 (mm) cc_final: 0.8849 (pt) REVERT: E 1293 ASN cc_start: 0.8993 (m-40) cc_final: 0.8461 (t0) REVERT: E 1298 MET cc_start: 0.9357 (tmm) cc_final: 0.9019 (tmm) REVERT: E 1395 MET cc_start: 0.8763 (mmt) cc_final: 0.8216 (mmp) REVERT: E 1507 GLU cc_start: 0.8570 (mt-10) cc_final: 0.7895 (mp0) REVERT: E 1514 MET cc_start: 0.8617 (mtt) cc_final: 0.8343 (mtm) outliers start: 95 outliers final: 56 residues processed: 394 average time/residue: 0.1292 time to fit residues: 82.0696 Evaluate side-chains 360 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 0.515 ------------------------------------------------------------------------------- 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 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 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 50 ARG Chi-restraints excluded: chain B residue 56 LEU 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 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 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 294 THR Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 83 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 222 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 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 943 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1136 ILE Chi-restraints excluded: chain E residue 1140 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [25, 41, 50, 241, 161, 51, 234, 227, 132, 61, 117] chunk 25 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 161 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 234 optimal weight: 0.9980 chunk 227 optimal weight: 3.9990 chunk 132 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 117 optimal weight: 0.4980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.066499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.054252 restraints weight = 89957.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.056010 restraints weight = 45556.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.057204 restraints weight = 28602.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.058009 restraints weight = 20597.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.058528 restraints weight = 16336.513| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21568 Z= 0.129 Angle : 0.682 12.672 29312 Z= 0.333 Chirality : 0.044 0.261 3469 Planarity : 0.004 0.090 3646 Dihedral : 5.616 97.773 2885 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.62 % Allowed : 24.42 % Favored : 71.96 % 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: -0.14 (0.16), residues: 2662 helix: 0.74 (0.14), residues: 1358 sheet: -0.44 (0.30), residues: 324 loop : -1.05 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 919 TYR 0.026 0.001 TYR D 258 PHE 0.021 0.001 PHE E 84 TRP 0.012 0.001 TRP E1037 HIS 0.022 0.001 HIS D 115 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 (21567) covalent geometry : angle 0.68241 / 0.33 (29310) SS BOND : bond 0.00152 / 0.08 ( 1) SS BOND : angle 0.43965 / 0.25 ( 2) hydrogen bonds : bond 0.03926 / 2.63 ( 1065) hydrogen bonds : angle 4.20859 / 2.97 ( 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 394 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 311 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8678 (t0) cc_final: 0.8267 (t0) REVERT: A 47 LYS cc_start: 0.8430 (tppt) cc_final: 0.7947 (tppt) REVERT: A 56 LEU cc_start: 0.9197 (OUTLIER) cc_final: 0.8918 (pp) REVERT: A 65 ASP cc_start: 0.9162 (t0) cc_final: 0.8640 (t0) REVERT: A 152 GLN cc_start: 0.9471 (OUTLIER) cc_final: 0.9196 (tm-30) REVERT: A 158 MET cc_start: 0.8389 (tmm) cc_final: 0.7969 (tmm) REVERT: A 163 MET cc_start: 0.9190 (mmm) cc_final: 0.8800 (mmm) REVERT: A 250 PHE cc_start: 0.8956 (t80) cc_final: 0.8653 (t80) REVERT: B 152 GLN cc_start: 0.9484 (OUTLIER) cc_final: 0.8372 (tp40) REVERT: B 159 ILE cc_start: 0.9093 (pt) cc_final: 0.8874 (mm) REVERT: B 240 MET cc_start: 0.8697 (tmm) cc_final: 0.8275 (tmm) REVERT: B 247 ASN cc_start: 0.8800 (p0) cc_final: 0.8134 (p0) REVERT: B 292 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8098 (tm-30) REVERT: B 304 TYR cc_start: 0.8927 (m-10) cc_final: 0.8413 (m-10) REVERT: B 313 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8170 (mp10) REVERT: B 326 TYR cc_start: 0.8833 (m-80) cc_final: 0.8584 (m-80) REVERT: B 338 LYS cc_start: 0.8711 (tptm) cc_final: 0.8079 (tptt) REVERT: C 36 VAL cc_start: 0.8258 (OUTLIER) cc_final: 0.7873 (p) REVERT: C 88 MET cc_start: 0.8387 (tmm) cc_final: 0.7944 (tmm) REVERT: C 179 GLU cc_start: 0.8459 (mt-10) cc_final: 0.8066 (mt-10) REVERT: C 199 MET cc_start: 0.8457 (mtt) cc_final: 0.8200 (mtt) REVERT: C 209 MET cc_start: 0.8480 (mmm) cc_final: 0.8187 (mmm) REVERT: C 247 ASN cc_start: 0.8758 (p0) cc_final: 0.8193 (p0) REVERT: C 292 GLU cc_start: 0.8243 (tm-30) cc_final: 0.7914 (tm-30) REVERT: C 313 GLN cc_start: 0.9046 (mt0) cc_final: 0.8067 (mm110) REVERT: D 43 ASN cc_start: 0.7894 (m-40) cc_final: 0.7263 (p0) REVERT: D 110 CYS cc_start: 0.8508 (m) cc_final: 0.8001 (m) REVERT: D 115 HIS cc_start: 0.7841 (OUTLIER) cc_final: 0.6975 (p90) REVERT: D 163 MET cc_start: 0.9245 (mmm) cc_final: 0.8937 (mmm) REVERT: D 170 LYS cc_start: 0.9176 (tppt) cc_final: 0.8607 (tptm) REVERT: D 185 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8771 (ttpt) REVERT: D 240 MET cc_start: 0.9030 (ptm) cc_final: 0.8763 (ppp) REVERT: D 258 TYR cc_start: 0.8741 (p90) cc_final: 0.8451 (p90) REVERT: D 281 LEU cc_start: 0.9190 (tt) cc_final: 0.8700 (tp) REVERT: D 318 ILE cc_start: 0.9222 (pt) cc_final: 0.8351 (mm) REVERT: D 332 LYS cc_start: 0.9038 (mtmm) cc_final: 0.8603 (mptt) REVERT: E 32 LEU cc_start: 0.9730 (OUTLIER) cc_final: 0.9490 (mm) REVERT: E 63 HIS cc_start: 0.7897 (p90) cc_final: 0.7390 (p90) REVERT: E 138 ILE cc_start: 0.9616 (mm) cc_final: 0.9257 (tp) REVERT: E 153 ILE cc_start: 0.9396 (mm) cc_final: 0.9187 (mm) REVERT: E 353 LEU cc_start: 0.9284 (mm) cc_final: 0.8938 (pp) REVERT: E 364 PHE cc_start: 0.9015 (t80) cc_final: 0.8531 (t80) REVERT: E 368 LEU cc_start: 0.9315 (mm) cc_final: 0.8671 (mm) REVERT: E 603 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.6988 (mtmm) REVERT: E 683 MET cc_start: 0.8322 (mpp) cc_final: 0.8004 (mpp) REVERT: E 903 MET cc_start: 0.7527 (ptp) cc_final: 0.6872 (ptt) REVERT: E 1020 GLN cc_start: 0.8964 (mm110) cc_final: 0.8182 (mm-40) REVERT: E 1066 MET cc_start: 0.7215 (tpt) cc_final: 0.6695 (ptm) REVERT: E 1173 ILE cc_start: 0.9218 (mm) cc_final: 0.8835 (pt) REVERT: E 1252 MET cc_start: 0.8523 (mpp) cc_final: 0.8317 (mpp) REVERT: E 1261 LEU cc_start: 0.9120 (tp) cc_final: 0.8913 (tp) REVERT: E 1293 ASN cc_start: 0.8981 (m-40) cc_final: 0.8473 (t0) REVERT: E 1298 MET cc_start: 0.9388 (tmm) cc_final: 0.9054 (tmm) REVERT: E 1395 MET cc_start: 0.8779 (mmt) cc_final: 0.8312 (mmp) REVERT: E 1507 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7902 (mp0) REVERT: E 1514 MET cc_start: 0.8618 (mtt) cc_final: 0.8357 (mtm) outliers start: 83 outliers final: 56 residues processed: 371 average time/residue: 0.1337 time to fit residues: 80.0379 Evaluate side-chains 359 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 294 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 230 VAL Chi-restraints excluded: chain A residue 236 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 50 ARG Chi-restraints excluded: chain B residue 56 LEU 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 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL 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 294 THR Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 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 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 943 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1283 LEU Chi-restraints excluded: chain E residue 1390 LEU Chi-restraints excluded: chain E residue 1509 THR Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [57, 243, 34, 267, 191, 225, 116, 111, 66, 65, 2] chunk 57 optimal weight: 0.9990 chunk 243 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 chunk 267 optimal weight: 5.9990 chunk 191 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 116 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 65 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN ** E 889 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1541 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.063525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.051524 restraints weight = 90416.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.053210 restraints weight = 45985.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.054332 restraints weight = 29136.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.055138 restraints weight = 21173.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.055698 restraints weight = 16858.352| |-----------------------------------------------------------------------------| r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 21568 Z= 0.204 Angle : 0.717 12.568 29312 Z= 0.358 Chirality : 0.045 0.240 3469 Planarity : 0.004 0.079 3646 Dihedral : 5.685 106.604 2885 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.79 % Allowed : 24.55 % Favored : 71.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.16), residues: 2662 helix: 0.74 (0.14), residues: 1360 sheet: -0.43 (0.29), residues: 336 loop : -0.99 (0.20), residues: 966 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 919 TYR 0.024 0.001 TYR D 258 PHE 0.022 0.002 PHE E 84 TRP 0.017 0.001 TRP E1033 HIS 0.009 0.001 HIS E 63 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (21567) covalent geometry : angle 0.71681 / 0.36 (29310) SS BOND : bond 0.00054 / 0.03 ( 1) SS BOND : angle 0.37742 / 0.22 ( 2) hydrogen bonds : bond 0.04039 / 2.72 ( 1065) hydrogen bonds : angle 4.33290 / 3.06 ( 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 376 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 289 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ASN cc_start: 0.8835 (t0) cc_final: 0.8415 (t0) REVERT: A 47 LYS cc_start: 0.8572 (tppt) cc_final: 0.8081 (tppt) REVERT: A 56 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8927 (pp) REVERT: A 65 ASP cc_start: 0.9204 (t0) cc_final: 0.8635 (t0) REVERT: A 158 MET cc_start: 0.8454 (tmm) cc_final: 0.8011 (tmm) REVERT: A 163 MET cc_start: 0.9194 (mmm) cc_final: 0.8821 (mmm) REVERT: B 65 ASP cc_start: 0.8854 (t70) cc_final: 0.8524 (t70) REVERT: B 152 GLN cc_start: 0.9502 (OUTLIER) cc_final: 0.8178 (tp40) REVERT: B 159 ILE cc_start: 0.9209 (pt) cc_final: 0.8943 (mm) REVERT: B 240 MET cc_start: 0.8820 (tmm) cc_final: 0.8395 (tmm) REVERT: B 247 ASN cc_start: 0.8825 (p0) cc_final: 0.8079 (p0) REVERT: B 292 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8347 (tm-30) REVERT: B 304 TYR cc_start: 0.8989 (m-10) cc_final: 0.8486 (m-10) REVERT: B 313 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8213 (mp10) REVERT: B 326 TYR cc_start: 0.8938 (m-80) cc_final: 0.8727 (m-80) REVERT: C 36 VAL cc_start: 0.8538 (OUTLIER) cc_final: 0.8140 (p) REVERT: C 81 CYS cc_start: 0.9459 (m) cc_final: 0.8979 (m) REVERT: C 88 MET cc_start: 0.8532 (tmm) cc_final: 0.8035 (tmm) REVERT: C 152 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8586 (tp-100) REVERT: C 179 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8179 (mt-10) REVERT: C 185 LYS cc_start: 0.9151 (tptp) cc_final: 0.8929 (tptp) REVERT: C 199 MET cc_start: 0.8497 (mtt) cc_final: 0.8268 (mtt) REVERT: C 209 MET cc_start: 0.8570 (mmm) cc_final: 0.8370 (mmm) REVERT: C 218 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7382 (mm-40) REVERT: C 247 ASN cc_start: 0.8953 (p0) cc_final: 0.8508 (p0) REVERT: C 292 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7980 (tm-30) REVERT: D 43 ASN cc_start: 0.7955 (m-40) cc_final: 0.7372 (p0) REVERT: D 110 CYS cc_start: 0.8422 (m) cc_final: 0.7749 (m) REVERT: D 122 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8996 (mm) REVERT: D 163 MET cc_start: 0.9256 (mmm) cc_final: 0.8963 (mmm) REVERT: D 170 LYS cc_start: 0.9191 (tppt) cc_final: 0.8543 (tptm) REVERT: D 185 LYS cc_start: 0.9258 (ttpp) cc_final: 0.8858 (ttpt) REVERT: D 199 MET cc_start: 0.8351 (mtm) cc_final: 0.7320 (mpp) REVERT: D 240 MET cc_start: 0.9181 (ptm) cc_final: 0.8744 (ppp) REVERT: D 258 TYR cc_start: 0.8772 (p90) cc_final: 0.8438 (p90) REVERT: D 318 ILE cc_start: 0.9251 (pt) cc_final: 0.8428 (mm) REVERT: E 32 LEU cc_start: 0.9704 (OUTLIER) cc_final: 0.9434 (mm) REVERT: E 153 ILE cc_start: 0.9396 (mm) cc_final: 0.9187 (mm) REVERT: E 353 LEU cc_start: 0.9297 (mm) cc_final: 0.8958 (pp) REVERT: E 364 PHE cc_start: 0.9052 (t80) cc_final: 0.8612 (t80) REVERT: E 368 LEU cc_start: 0.9310 (mm) cc_final: 0.8650 (mm) REVERT: E 683 MET cc_start: 0.8305 (mpp) cc_final: 0.7881 (mpp) REVERT: E 903 MET cc_start: 0.7577 (ptp) cc_final: 0.7007 (ptt) REVERT: E 1020 GLN cc_start: 0.9064 (mm110) cc_final: 0.8355 (mm-40) REVERT: E 1066 MET cc_start: 0.7286 (tpt) cc_final: 0.6840 (ptm) REVERT: E 1149 LEU cc_start: 0.9679 (OUTLIER) cc_final: 0.9453 (mt) REVERT: E 1173 ILE cc_start: 0.9222 (mm) cc_final: 0.8856 (pt) REVERT: E 1292 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9120 (p) REVERT: E 1293 ASN cc_start: 0.9014 (m-40) cc_final: 0.8585 (t0) REVERT: E 1298 MET cc_start: 0.9449 (tmm) cc_final: 0.9220 (tmm) REVERT: E 1395 MET cc_start: 0.8674 (mmt) cc_final: 0.8222 (mmp) outliers start: 87 outliers final: 63 residues processed: 352 average time/residue: 0.1350 time to fit residues: 76.2240 Evaluate side-chains 347 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 56 LEU 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 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL 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 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 219 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 266 ARG Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 PHE Chi-restraints excluded: chain E residue 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 523 VAL Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 830 LEU Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1013 LEU Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1149 LEU 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 Chi-restraints excluded: chain E residue 1551 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [169, 126, 244, 130, 202, 89, 42, 138, 146, 154, 155] chunk 169 optimal weight: 0.7980 chunk 126 optimal weight: 0.4980 chunk 244 optimal weight: 9.9990 chunk 130 optimal weight: 0.0030 chunk 202 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 42 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 155 optimal weight: 0.6980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN E 892 GLN E1234 ASN E1541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.066584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.054402 restraints weight = 89606.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.056181 restraints weight = 44638.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.057394 restraints weight = 27732.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.058163 restraints weight = 19758.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.058761 restraints weight = 15674.179| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 21568 Z= 0.125 Angle : 0.697 13.279 29312 Z= 0.339 Chirality : 0.044 0.232 3469 Planarity : 0.003 0.035 3646 Dihedral : 5.515 112.954 2884 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.27 % Allowed : 25.25 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.16), residues: 2662 helix: 0.97 (0.15), residues: 1323 sheet: -0.44 (0.29), residues: 334 loop : -0.88 (0.19), residues: 1005 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 919 TYR 0.022 0.001 TYR D 258 PHE 0.024 0.001 PHE E 84 TRP 0.011 0.001 TRP E1037 HIS 0.008 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (21567) covalent geometry : angle 0.69663 / 0.34 (29310) SS BOND : bond 0.00157 / 0.08 ( 1) SS BOND : angle 0.30352 / 0.17 ( 2) hydrogen bonds : bond 0.03916 / 2.62 ( 1065) hydrogen bonds : angle 4.20569 / 2.96 ( 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 395 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 320 time to evaluate : 0.847 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: 0.8859 (tttt) cc_final: 0.8553 (tttp) REVERT: A 43 ASN cc_start: 0.8874 (t0) cc_final: 0.8459 (t0) REVERT: A 47 LYS cc_start: 0.8336 (tppt) cc_final: 0.7937 (tppt) REVERT: A 56 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8923 (pp) REVERT: A 65 ASP cc_start: 0.9164 (t0) cc_final: 0.8540 (t0) REVERT: A 152 GLN cc_start: 0.9422 (OUTLIER) cc_final: 0.8858 (tm-30) REVERT: A 158 MET cc_start: 0.8576 (tmm) cc_final: 0.8093 (tmm) REVERT: A 163 MET cc_start: 0.9192 (mmm) cc_final: 0.8783 (mmm) REVERT: A 250 PHE cc_start: 0.8917 (t80) cc_final: 0.8598 (t80) REVERT: B 65 ASP cc_start: 0.8886 (t70) cc_final: 0.8520 (t0) REVERT: B 152 GLN cc_start: 0.9457 (OUTLIER) cc_final: 0.8373 (tp40) REVERT: B 240 MET cc_start: 0.8849 (tmm) cc_final: 0.8395 (tmm) REVERT: B 247 ASN cc_start: 0.8812 (p0) cc_final: 0.8035 (p0) REVERT: B 292 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8318 (tm-30) REVERT: B 304 TYR cc_start: 0.8943 (m-10) cc_final: 0.8485 (m-10) REVERT: B 313 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8095 (mp10) REVERT: B 326 TYR cc_start: 0.8923 (m-80) cc_final: 0.8708 (m-80) REVERT: B 338 LYS cc_start: 0.8740 (tptm) cc_final: 0.8034 (tptt) REVERT: C 36 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.7890 (p) REVERT: C 39 LYS cc_start: 0.8681 (tttp) cc_final: 0.8232 (tttp) REVERT: C 81 CYS cc_start: 0.9399 (m) cc_final: 0.8908 (m) REVERT: C 88 MET cc_start: 0.8443 (tmm) cc_final: 0.7986 (tmm) REVERT: C 163 MET cc_start: 0.9330 (mmm) cc_final: 0.9112 (mmp) REVERT: C 179 GLU cc_start: 0.8465 (mt-10) cc_final: 0.8026 (mt-10) REVERT: C 185 LYS cc_start: 0.9138 (tptp) cc_final: 0.8902 (tptp) REVERT: C 199 MET cc_start: 0.8495 (mtt) cc_final: 0.8247 (mtt) REVERT: C 218 GLN cc_start: 0.7692 (mm-40) cc_final: 0.7172 (mm-40) REVERT: C 236 VAL cc_start: 0.9073 (OUTLIER) cc_final: 0.8789 (m) REVERT: C 247 ASN cc_start: 0.8937 (p0) cc_final: 0.8523 (p0) REVERT: C 292 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7953 (tm-30) REVERT: D 43 ASN cc_start: 0.7963 (m-40) cc_final: 0.7192 (p0) REVERT: D 110 CYS cc_start: 0.8457 (m) cc_final: 0.7731 (m) REVERT: D 163 MET cc_start: 0.9254 (mmm) cc_final: 0.8931 (mmm) REVERT: D 170 LYS cc_start: 0.9160 (tppt) cc_final: 0.8534 (tptm) REVERT: D 185 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8837 (tmtt) REVERT: D 240 MET cc_start: 0.9038 (ptm) cc_final: 0.8804 (ppp) REVERT: D 258 TYR cc_start: 0.8728 (p90) cc_final: 0.8402 (p90) REVERT: D 281 LEU cc_start: 0.9198 (tt) cc_final: 0.8702 (tp) REVERT: D 318 ILE cc_start: 0.9222 (pt) cc_final: 0.8362 (mm) REVERT: E 32 LEU cc_start: 0.9696 (OUTLIER) cc_final: 0.9420 (mm) REVERT: E 138 ILE cc_start: 0.9639 (mm) cc_final: 0.9300 (tp) REVERT: E 153 ILE cc_start: 0.9384 (mm) cc_final: 0.9179 (mm) REVERT: E 353 LEU cc_start: 0.9304 (mm) cc_final: 0.8927 (pp) REVERT: E 364 PHE cc_start: 0.9039 (t80) cc_final: 0.8541 (t80) REVERT: E 368 LEU cc_start: 0.9316 (mm) cc_final: 0.8671 (mm) REVERT: E 599 ARG cc_start: 0.9238 (OUTLIER) cc_final: 0.8845 (tpp80) REVERT: E 683 MET cc_start: 0.8289 (mpp) cc_final: 0.8018 (mpp) REVERT: E 1016 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9167 (tp) REVERT: E 1020 GLN cc_start: 0.9037 (mm110) cc_final: 0.8334 (mm-40) REVERT: E 1066 MET cc_start: 0.7238 (tpt) cc_final: 0.6790 (ptm) REVERT: E 1149 LEU cc_start: 0.9665 (OUTLIER) cc_final: 0.9456 (mt) REVERT: E 1173 ILE cc_start: 0.9240 (mm) cc_final: 0.8879 (pt) REVERT: E 1261 LEU cc_start: 0.9101 (tp) cc_final: 0.8867 (tp) REVERT: E 1292 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9139 (p) REVERT: E 1293 ASN cc_start: 0.9005 (m-40) cc_final: 0.8538 (t0) REVERT: E 1298 MET cc_start: 0.9408 (tmm) cc_final: 0.9185 (tmm) REVERT: E 1395 MET cc_start: 0.8736 (mmt) cc_final: 0.8332 (mmp) outliers start: 75 outliers final: 48 residues processed: 375 average time/residue: 0.1337 time to fit residues: 80.7336 Evaluate side-chains 353 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 293 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 169 MET 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 42 CYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL 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 138 VAL 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 332 LYS Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 271 PHE Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 350 GLN Chi-restraints excluded: chain E residue 358 VAL Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1149 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [175, 255, 256, 246, 1, 212, 240, 215, 167, 13, 257] chunk 175 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 256 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 240 optimal weight: 9.9990 chunk 215 optimal weight: 0.9990 chunk 167 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 257 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.066125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.053887 restraints weight = 90171.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.055641 restraints weight = 45375.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.056845 restraints weight = 28274.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.057651 restraints weight = 20267.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.058211 restraints weight = 16007.770| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 21568 Z= 0.143 Angle : 0.716 13.567 29312 Z= 0.349 Chirality : 0.045 0.280 3469 Planarity : 0.004 0.093 3646 Dihedral : 5.429 113.777 2882 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.83 % Allowed : 25.77 % Favored : 71.39 % 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: 0.25 (0.17), residues: 2662 helix: 1.10 (0.15), residues: 1299 sheet: -0.43 (0.29), residues: 334 loop : -0.75 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.000 ARG E1274 TYR 0.021 0.001 TYR D 258 PHE 0.028 0.001 PHE E 84 TRP 0.011 0.001 TRP E1037 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (21567) covalent geometry : angle 0.71634 / 0.35 (29310) SS BOND : bond 0.00089 / 0.05 ( 1) SS BOND : angle 0.23957 / 0.13 ( 2) hydrogen bonds : bond 0.03921 / 2.62 ( 1065) hydrogen bonds : angle 4.23310 / 2.98 ( 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 357 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 292 time to evaluate : 0.796 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: 0.8873 (tttt) cc_final: 0.8577 (tttp) REVERT: A 43 ASN cc_start: 0.8897 (t0) cc_final: 0.8462 (t0) REVERT: A 47 LYS cc_start: 0.8382 (tppt) cc_final: 0.8003 (tppt) REVERT: A 56 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8903 (pp) REVERT: A 65 ASP cc_start: 0.9142 (t0) cc_final: 0.8505 (t0) REVERT: A 152 GLN cc_start: 0.9483 (OUTLIER) cc_final: 0.8850 (tm-30) REVERT: A 158 MET cc_start: 0.8627 (tmm) cc_final: 0.8165 (tmm) REVERT: A 163 MET cc_start: 0.9189 (mmm) cc_final: 0.8791 (mmm) REVERT: A 207 LYS cc_start: 0.8045 (pttt) cc_final: 0.7676 (ptpt) REVERT: A 250 PHE cc_start: 0.8935 (t80) cc_final: 0.8625 (t80) REVERT: B 65 ASP cc_start: 0.8864 (t70) cc_final: 0.8472 (t0) REVERT: B 152 GLN cc_start: 0.9508 (OUTLIER) cc_final: 0.8374 (tp40) REVERT: B 240 MET cc_start: 0.8853 (tmm) cc_final: 0.8413 (tmm) REVERT: B 247 ASN cc_start: 0.8859 (p0) cc_final: 0.8063 (p0) REVERT: B 292 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8327 (tm-30) REVERT: B 304 TYR cc_start: 0.8978 (m-10) cc_final: 0.8508 (m-10) REVERT: B 313 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.8016 (mp10) REVERT: B 338 LYS cc_start: 0.8744 (tptm) cc_final: 0.8299 (tppt) REVERT: C 36 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7871 (p) REVERT: C 81 CYS cc_start: 0.9401 (m) cc_final: 0.8924 (m) REVERT: C 88 MET cc_start: 0.8408 (tmm) cc_final: 0.7945 (tmm) REVERT: C 152 GLN cc_start: 0.9289 (OUTLIER) cc_final: 0.8778 (tp40) REVERT: C 179 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8062 (mt-10) REVERT: C 185 LYS cc_start: 0.9134 (tptp) cc_final: 0.8879 (tptp) REVERT: C 199 MET cc_start: 0.8494 (mtt) cc_final: 0.8265 (mtt) REVERT: C 209 MET cc_start: 0.8467 (mmm) cc_final: 0.8065 (mmm) REVERT: C 218 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7229 (mm-40) REVERT: C 236 VAL cc_start: 0.9084 (OUTLIER) cc_final: 0.8821 (m) REVERT: C 247 ASN cc_start: 0.8939 (p0) cc_final: 0.8509 (p0) REVERT: C 292 GLU cc_start: 0.8318 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 43 ASN cc_start: 0.7713 (m-40) cc_final: 0.7175 (p0) REVERT: D 110 CYS cc_start: 0.8471 (m) cc_final: 0.7730 (m) REVERT: D 163 MET cc_start: 0.9263 (mmm) cc_final: 0.8884 (mmm) REVERT: D 185 LYS cc_start: 0.9239 (ttpp) cc_final: 0.8848 (tmtt) REVERT: D 240 MET cc_start: 0.9102 (ptm) cc_final: 0.8698 (ppp) REVERT: D 258 TYR cc_start: 0.8796 (p90) cc_final: 0.8497 (p90) REVERT: D 318 ILE cc_start: 0.9230 (pt) cc_final: 0.8384 (mm) REVERT: E 32 LEU cc_start: 0.9714 (OUTLIER) cc_final: 0.9449 (mm) REVERT: E 61 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7543 (mp) REVERT: E 153 ILE cc_start: 0.9376 (mm) cc_final: 0.9167 (mm) REVERT: E 353 LEU cc_start: 0.9229 (mm) cc_final: 0.8895 (pp) REVERT: E 364 PHE cc_start: 0.9035 (t80) cc_final: 0.8552 (t80) REVERT: E 368 LEU cc_start: 0.9300 (mm) cc_final: 0.8681 (mm) REVERT: E 442 MET cc_start: 0.8755 (mmm) cc_final: 0.8463 (mmp) REVERT: E 599 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8858 (tpp80) REVERT: E 683 MET cc_start: 0.8212 (mpp) cc_final: 0.7928 (mpp) REVERT: E 1016 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9209 (tp) REVERT: E 1020 GLN cc_start: 0.9052 (mm110) cc_final: 0.8366 (mm-40) REVERT: E 1066 MET cc_start: 0.7258 (tpt) cc_final: 0.6809 (ptm) REVERT: E 1149 LEU cc_start: 0.9668 (OUTLIER) cc_final: 0.9463 (mt) REVERT: E 1173 ILE cc_start: 0.9251 (mm) cc_final: 0.8883 (pt) REVERT: E 1252 MET cc_start: 0.8755 (mpp) cc_final: 0.8209 (mpp) REVERT: E 1261 LEU cc_start: 0.9054 (tp) cc_final: 0.8843 (tp) REVERT: E 1292 SER cc_start: 0.9332 (OUTLIER) cc_final: 0.9130 (p) REVERT: E 1293 ASN cc_start: 0.8968 (m-40) cc_final: 0.8531 (t0) REVERT: E 1298 MET cc_start: 0.9403 (tmm) cc_final: 0.9175 (tmm) REVERT: E 1395 MET cc_start: 0.8671 (mmt) cc_final: 0.8236 (mmp) outliers start: 65 outliers final: 47 residues processed: 340 average time/residue: 0.1390 time to fit residues: 75.7873 Evaluate side-chains 351 residues out of total 2323 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 290 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 352 ASP Chi-restraints excluded: chain B residue 42 CYS Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 115 HIS Chi-restraints excluded: chain B residue 152 GLN Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 291 VAL Chi-restraints excluded: chain B residue 292 GLU Chi-restraints excluded: chain B residue 313 GLN Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 231 VAL Chi-restraints excluded: chain C residue 236 VAL 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 138 VAL Chi-restraints excluded: chain D residue 146 ILE Chi-restraints excluded: chain D residue 219 VAL Chi-restraints excluded: chain D residue 332 LYS Chi-restraints excluded: chain D residue 335 ASN Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 159 LEU Chi-restraints excluded: chain E residue 175 LEU Chi-restraints excluded: chain E residue 222 PHE Chi-restraints excluded: chain E residue 232 TRP Chi-restraints excluded: chain E residue 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 452 LEU Chi-restraints excluded: chain E residue 497 LEU Chi-restraints excluded: chain E residue 557 LEU Chi-restraints excluded: chain E residue 599 ARG Chi-restraints excluded: chain E residue 603 LYS Chi-restraints excluded: chain E residue 885 VAL Chi-restraints excluded: chain E residue 943 THR Chi-restraints excluded: chain E residue 1016 LEU Chi-restraints excluded: chain E residue 1149 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 268 random chunks: [35, 82, 92, 152, 60, 109, 150, 222, 103, 165, 110] chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 152 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 150 optimal weight: 5.9990 chunk 222 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 110 optimal weight: 0.1980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 175 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.066970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.054647 restraints weight = 90680.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.056442 restraints weight = 45488.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.057655 restraints weight = 28423.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.058464 restraints weight = 20350.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.059041 restraints weight = 16083.906| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21568 Z= 0.129 Angle : 0.713 13.668 29312 Z= 0.346 Chirality : 0.045 0.273 3469 Planarity : 0.004 0.060 3646 Dihedral : 5.419 115.931 2882 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.97 % Allowed : 25.69 % 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: 0.33 (0.17), residues: 2662 helix: 1.11 (0.15), residues: 1299 sheet: -0.34 (0.31), residues: 289 loop : -0.65 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E1274 TYR 0.020 0.001 TYR D 258 PHE 0.027 0.001 PHE E 84 TRP 0.012 0.001 TRP E1037 HIS 0.007 0.001 HIS E 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (21567) covalent geometry : angle 0.71323 / 0.35 (29310) SS BOND : bond 0.00106 / 0.06 ( 1) SS BOND : angle 0.24258 / 0.13 ( 2) hydrogen bonds : bond 0.03891 / 2.58 ( 1065) hydrogen bonds : angle 4.19076 / 2.95 ( 3063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3269.48 seconds wall clock time: 57 minutes 33.38 seconds (3453.38 seconds total)