Starting phenix.real_space_refine on Fri Jun 20 05:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ezj_28743/06_2025/8ezj_28743.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ezj_28743/06_2025/8ezj_28743.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ezj_28743/06_2025/8ezj_28743.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ezj_28743/06_2025/8ezj_28743.map" model { file = "/net/cci-nas-00/data/ceres_data/8ezj_28743/06_2025/8ezj_28743.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ezj_28743/06_2025/8ezj_28743.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 80 5.16 5 C 14868 2.51 5 N 3780 2.21 5 O 4481 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 23215 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1285, 10319 Classifications: {'peptide': 1285} Link IDs: {'PTRANS': 39, 'TRANS': 1245} Chain breaks: 5 Chain: "B" Number of atoms: 10248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1276, 10248 Classifications: {'peptide': 1276} Link IDs: {'PTRANS': 39, 'TRANS': 1236} Chain breaks: 5 Chain: "C" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "D" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1292 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 3, 'TRANS': 161} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 17.64, per 1000 atoms: 0.76 Number of scatterers: 23215 At special positions: 0 Unit cell: (123.372, 143.244, 305.532, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 80 16.00 P 6 15.00 O 4481 8.00 N 3780 7.00 C 14868 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.17 Conformation dependent library (CDL) restraints added in 2.8 seconds 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5568 Finding SS restraints... Secondary structure from input PDB file: 149 helices and 8 sheets defined 69.5% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.38 Creating SS restraints... Processing helix chain 'A' and resid 10 through 30 removed outlier: 3.910A pdb=" N ILE A 14 " --> pdb=" O ASP A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.530A pdb=" N ILE A 97 " --> pdb=" O ASP A 93 " (cutoff:3.500A) Proline residue: A 100 - end of helix Processing helix chain 'A' and resid 111 through 129 Processing helix chain 'A' and resid 137 through 151 Processing helix chain 'A' and resid 158 through 179 removed outlier: 3.639A pdb=" N ASP A 162 " --> pdb=" O GLN A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 184 Processing helix chain 'A' and resid 186 through 202 Processing helix chain 'A' and resid 207 through 231 removed outlier: 3.860A pdb=" N THR A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 344 removed outlier: 3.523A pdb=" N VAL A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 348 removed outlier: 3.698A pdb=" N GLU A 348 " --> pdb=" O PRO A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 345 through 348' Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 377 through 386 Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 401 through 419 Processing helix chain 'A' and resid 420 through 422 No H-bonds generated for 'chain 'A' and resid 420 through 422' Processing helix chain 'A' and resid 423 through 439 Processing helix chain 'A' and resid 455 through 472 removed outlier: 3.531A pdb=" N LYS A 459 " --> pdb=" O PRO A 455 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU A 469 " --> pdb=" O GLN A 465 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N TRP A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 472 " --> pdb=" O ILE A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 484 Processing helix chain 'A' and resid 493 through 506 removed outlier: 3.755A pdb=" N LEU A 506 " --> pdb=" O THR A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 516 through 535 removed outlier: 3.894A pdb=" N ILE A 520 " --> pdb=" O SER A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 546 Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 559 through 573 Processing helix chain 'A' and resid 573 through 584 Proline residue: A 579 - end of helix Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 607 through 615 Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 637 through 648 removed outlier: 4.449A pdb=" N LYS A 648 " --> pdb=" O ILE A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 672 Processing helix chain 'A' and resid 695 through 713 removed outlier: 3.529A pdb=" N THR A 710 " --> pdb=" O ILE A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 731 removed outlier: 3.869A pdb=" N LEU A 730 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS A 731 " --> pdb=" O GLY A 728 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 727 through 731' Processing helix chain 'A' and resid 740 through 753 Processing helix chain 'A' and resid 768 through 777 Processing helix chain 'A' and resid 793 through 797 Processing helix chain 'A' and resid 798 through 828 Proline residue: A 815 - end of helix Processing helix chain 'A' and resid 830 through 852 Processing helix chain 'A' and resid 853 through 867 Processing helix chain 'A' and resid 906 through 914 Processing helix chain 'A' and resid 915 through 932 Processing helix chain 'A' and resid 939 through 956 Processing helix chain 'A' and resid 964 through 971 Processing helix chain 'A' and resid 1010 through 1026 Processing helix chain 'A' and resid 1027 through 1033 Processing helix chain 'A' and resid 1040 through 1050 removed outlier: 3.528A pdb=" N ILE A1044 " --> pdb=" O THR A1040 " (cutoff:3.500A) Processing helix chain 'A' and resid 1059 through 1061 No H-bonds generated for 'chain 'A' and resid 1059 through 1061' Processing helix chain 'A' and resid 1062 through 1081 Processing helix chain 'A' and resid 1084 through 1100 Processing helix chain 'A' and resid 1105 through 1123 Processing helix chain 'A' and resid 1126 through 1141 removed outlier: 3.533A pdb=" N LYS A1140 " --> pdb=" O ASP A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1147 through 1151 Processing helix chain 'A' and resid 1154 through 1166 Processing helix chain 'A' and resid 1172 through 1177 Processing helix chain 'A' and resid 1179 through 1190 Processing helix chain 'A' and resid 1194 through 1209 removed outlier: 3.692A pdb=" N ASP A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1217 through 1230 Processing helix chain 'A' and resid 1231 through 1247 removed outlier: 4.114A pdb=" N GLU A1241 " --> pdb=" O HIS A1237 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1276 Processing helix chain 'A' and resid 1284 through 1299 Processing helix chain 'A' and resid 1302 through 1320 Processing helix chain 'A' and resid 1330 through 1338 removed outlier: 3.596A pdb=" N LEU A1334 " --> pdb=" O SER A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1338 through 1344 removed outlier: 3.593A pdb=" N LEU A1342 " --> pdb=" O GLY A1338 " (cutoff:3.500A) Processing helix chain 'A' and resid 1348 through 1350 No H-bonds generated for 'chain 'A' and resid 1348 through 1350' Processing helix chain 'A' and resid 1351 through 1373 removed outlier: 3.731A pdb=" N LEU A1355 " --> pdb=" O ASP A1351 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1373 " --> pdb=" O HIS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1378 through 1391 Processing helix chain 'A' and resid 1395 through 1417 Processing helix chain 'B' and resid 11 through 30 Processing helix chain 'B' and resid 71 through 84 Processing helix chain 'B' and resid 93 through 107 Proline residue: B 100 - end of helix Processing helix chain 'B' and resid 111 through 128 Processing helix chain 'B' and resid 137 through 150 Processing helix chain 'B' and resid 159 through 178 Processing helix chain 'B' and resid 179 through 184 Processing helix chain 'B' and resid 186 through 202 Processing helix chain 'B' and resid 208 through 230 Processing helix chain 'B' and resid 328 through 343 removed outlier: 3.535A pdb=" N VAL B 332 " --> pdb=" O GLY B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 348 Processing helix chain 'B' and resid 352 through 371 Processing helix chain 'B' and resid 373 through 376 Processing helix chain 'B' and resid 377 through 386 Processing helix chain 'B' and resid 386 through 398 Processing helix chain 'B' and resid 401 through 419 Processing helix chain 'B' and resid 424 through 439 Processing helix chain 'B' and resid 456 through 471 removed outlier: 4.964A pdb=" N LEU B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TRP B 470 " --> pdb=" O ILE B 466 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 493 through 505 Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 516 through 536 removed outlier: 3.624A pdb=" N ILE B 520 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N MET B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.843A pdb=" N GLN B 547 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 559 through 573 Processing helix chain 'B' and resid 573 through 584 Proline residue: B 579 - end of helix Processing helix chain 'B' and resid 591 through 601 Processing helix chain 'B' and resid 607 through 616 Processing helix chain 'B' and resid 621 through 630 Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 656 through 673 removed outlier: 3.697A pdb=" N GLN B 673 " --> pdb=" O TYR B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 696 through 713 Processing helix chain 'B' and resid 722 through 730 Processing helix chain 'B' and resid 740 through 754 removed outlier: 3.571A pdb=" N LEU B 744 " --> pdb=" O PRO B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 767 through 778 Processing helix chain 'B' and resid 792 through 797 removed outlier: 3.637A pdb=" N LYS B 796 " --> pdb=" O VAL B 793 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 797 " --> pdb=" O MET B 794 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 828 Proline residue: B 815 - end of helix Processing helix chain 'B' and resid 830 through 851 Processing helix chain 'B' and resid 853 through 868 Processing helix chain 'B' and resid 906 through 914 Processing helix chain 'B' and resid 915 through 932 Processing helix chain 'B' and resid 939 through 956 Processing helix chain 'B' and resid 964 through 971 removed outlier: 3.762A pdb=" N GLN B 968 " --> pdb=" O PHE B 964 " (cutoff:3.500A) Processing helix chain 'B' and resid 1009 through 1027 removed outlier: 3.804A pdb=" N ILE B1013 " --> pdb=" O THR B1009 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1033 Processing helix chain 'B' and resid 1040 through 1050 Processing helix chain 'B' and resid 1062 through 1081 Processing helix chain 'B' and resid 1085 through 1100 removed outlier: 3.743A pdb=" N LYS B1089 " --> pdb=" O LYS B1085 " (cutoff:3.500A) Processing helix chain 'B' and resid 1105 through 1123 Processing helix chain 'B' and resid 1126 through 1137 Processing helix chain 'B' and resid 1146 through 1151 removed outlier: 3.661A pdb=" N PHE B1150 " --> pdb=" O THR B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1152 through 1167 removed outlier: 3.689A pdb=" N GLU B1167 " --> pdb=" O PHE B1163 " (cutoff:3.500A) Processing helix chain 'B' and resid 1171 through 1176 Processing helix chain 'B' and resid 1178 through 1190 removed outlier: 3.782A pdb=" N TRP B1182 " --> pdb=" O ASN B1178 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA B1190 " --> pdb=" O ARG B1186 " (cutoff:3.500A) Processing helix chain 'B' and resid 1194 through 1209 removed outlier: 4.175A pdb=" N ASP B1209 " --> pdb=" O SER B1205 " (cutoff:3.500A) Processing helix chain 'B' and resid 1210 through 1213 removed outlier: 3.741A pdb=" N LEU B1213 " --> pdb=" O SER B1210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1210 through 1213' Processing helix chain 'B' and resid 1217 through 1232 removed outlier: 3.586A pdb=" N VAL B1221 " --> pdb=" O ASN B1217 " (cutoff:3.500A) Processing helix chain 'B' and resid 1233 through 1247 Processing helix chain 'B' and resid 1258 through 1277 Processing helix chain 'B' and resid 1284 through 1299 Processing helix chain 'B' and resid 1303 through 1320 Processing helix chain 'B' and resid 1330 through 1344 Proline residue: B1341 - end of helix Processing helix chain 'B' and resid 1349 through 1374 removed outlier: 3.557A pdb=" N LYS B1353 " --> pdb=" O GLN B1349 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ILE B1354 " --> pdb=" O GLU B1350 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B1373 " --> pdb=" O HIS B1369 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY B1374 " --> pdb=" O TYR B1370 " (cutoff:3.500A) Processing helix chain 'B' and resid 1378 through 1391 Processing helix chain 'B' and resid 1394 through 1417 Processing helix chain 'C' and resid 30 through 40 Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 97 through 99 No H-bonds generated for 'chain 'C' and resid 97 through 99' Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 115 through 118 removed outlier: 3.871A pdb=" N GLN C 118 " --> pdb=" O GLU C 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 115 through 118' Processing helix chain 'C' and resid 136 through 145 Processing helix chain 'C' and resid 146 through 149 Processing helix chain 'C' and resid 166 through 182 removed outlier: 3.665A pdb=" N GLN C 182 " --> pdb=" O ILE C 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 40 Processing helix chain 'D' and resid 75 through 82 Processing helix chain 'D' and resid 97 through 99 No H-bonds generated for 'chain 'D' and resid 97 through 99' Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 126 through 130 removed outlier: 3.613A pdb=" N GLN D 129 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ASP D 130 " --> pdb=" O ASN D 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 126 through 130' Processing helix chain 'D' and resid 136 through 144 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 165 through 182 removed outlier: 3.703A pdb=" N GLU D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN D 182 " --> pdb=" O ILE D 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 241 through 242 Processing sheet with id=AA2, first strand: chain 'A' and resid 892 through 894 Processing sheet with id=AA3, first strand: chain 'B' and resid 241 through 242 removed outlier: 3.537A pdb=" N TYR B 241 " --> pdb=" O THR B 784 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 901 through 905 Processing sheet with id=AA5, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AA6, first strand: chain 'C' and resid 52 through 54 removed outlier: 6.043A pdb=" N LEU C 19 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N TRP C 67 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE C 21 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N LEU C 69 " --> pdb=" O ILE C 21 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE C 23 " --> pdb=" O LEU C 69 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 93 through 94 removed outlier: 3.753A pdb=" N ASN C 127 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA C 126 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 52 through 57 removed outlier: 5.842A pdb=" N LEU D 19 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TRP D 67 " --> pdb=" O LEU D 19 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE D 21 " --> pdb=" O TRP D 67 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LEU D 69 " --> pdb=" O ILE D 21 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE D 23 " --> pdb=" O LEU D 69 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG D 20 " --> pdb=" O ALA D 88 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ILE D 90 " --> pdb=" O ARG D 20 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 22 " --> pdb=" O ILE D 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER D 155 " --> pdb=" O LEU D 122 " (cutoff:3.500A) 1393 hydrogen bonds defined for protein. 4119 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: 8.77 Time building geometry restraints manager: 7.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7450 1.34 - 1.46: 4454 1.46 - 1.58: 11564 1.58 - 1.69: 10 1.69 - 1.81: 124 Bond restraints: 23602 Sorted by residual: bond pdb=" C TRP A1220 " pdb=" N VAL A1221 " ideal model delta sigma weight residual 1.334 1.380 -0.046 1.26e-02 6.30e+03 1.34e+01 bond pdb=" N SER A 974 " pdb=" CA SER A 974 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.07e+00 bond pdb=" N TYR D 78 " pdb=" CA TYR D 78 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.23e-02 6.61e+03 4.77e+00 bond pdb=" N ASN A 326 " pdb=" CA ASN A 326 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.32e-02 5.74e+03 4.65e+00 bond pdb=" N ALA A 695 " pdb=" CA ALA A 695 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 4.09e+00 ... (remaining 23597 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.70: 31337 1.70 - 3.40: 477 3.40 - 5.10: 78 5.10 - 6.80: 20 6.80 - 8.50: 1 Bond angle restraints: 31913 Sorted by residual: angle pdb=" C ILE A 644 " pdb=" CA ILE A 644 " pdb=" CB ILE A 644 " ideal model delta sigma weight residual 111.77 103.27 8.50 2.27e+00 1.94e-01 1.40e+01 angle pdb=" C ASN A 326 " pdb=" N TYR A 327 " pdb=" CA TYR A 327 " ideal model delta sigma weight residual 122.09 117.15 4.94 1.48e+00 4.57e-01 1.11e+01 angle pdb=" C ILE B 232 " pdb=" CA ILE B 232 " pdb=" CB ILE B 232 " ideal model delta sigma weight residual 110.91 114.76 -3.85 1.24e+00 6.50e-01 9.63e+00 angle pdb=" CA TRP D 79 " pdb=" CB TRP D 79 " pdb=" CG TRP D 79 " ideal model delta sigma weight residual 113.60 119.42 -5.82 1.90e+00 2.77e-01 9.38e+00 angle pdb=" C ILE B 219 " pdb=" CA ILE B 219 " pdb=" CB ILE B 219 " ideal model delta sigma weight residual 112.14 108.02 4.12 1.35e+00 5.49e-01 9.32e+00 ... (remaining 31908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.77: 14268 33.77 - 67.54: 164 67.54 - 101.32: 3 101.32 - 135.09: 0 135.09 - 168.86: 2 Dihedral angle restraints: 14437 sinusoidal: 5917 harmonic: 8520 Sorted by residual: dihedral pdb=" O3B GTP D 301 " pdb=" O3A GTP D 301 " pdb=" PB GTP D 301 " pdb=" PA GTP D 301 " ideal model delta sinusoidal sigma weight residual -68.92 99.94 -168.86 1 2.00e+01 2.50e-03 4.75e+01 dihedral pdb=" O3B GTP C 301 " pdb=" O3A GTP C 301 " pdb=" PB GTP C 301 " pdb=" PA GTP C 301 " ideal model delta sinusoidal sigma weight residual 291.08 141.31 149.77 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" C8 GTP D 301 " pdb=" C1' GTP D 301 " pdb=" N9 GTP D 301 " pdb=" O4' GTP D 301 " ideal model delta sinusoidal sigma weight residual 104.59 18.73 85.86 1 2.00e+01 2.50e-03 2.23e+01 ... (remaining 14434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2339 0.032 - 0.064: 1033 0.064 - 0.097: 290 0.097 - 0.129: 96 0.129 - 0.161: 8 Chirality restraints: 3766 Sorted by residual: chirality pdb=" CA ILE A 644 " pdb=" N ILE A 644 " pdb=" C ILE A 644 " pdb=" CB ILE A 644 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA THR A 869 " pdb=" N THR A 869 " pdb=" C THR A 869 " pdb=" CB THR A 869 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.14 2.00e-01 2.50e+01 5.08e-01 chirality pdb=" CA GLN A 99 " pdb=" N GLN A 99 " pdb=" C GLN A 99 " pdb=" CB GLN A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 3763 not shown) Planarity restraints: 4009 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A1179 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C GLU A1179 " -0.044 2.00e-02 2.50e+03 pdb=" O GLU A1179 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN A1180 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1284 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C LYS B1284 " 0.042 2.00e-02 2.50e+03 pdb=" O LYS B1284 " -0.016 2.00e-02 2.50e+03 pdb=" N ASN B1285 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1010 " -0.011 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C GLU A1010 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU A1010 " -0.015 2.00e-02 2.50e+03 pdb=" N GLU A1011 " -0.013 2.00e-02 2.50e+03 ... (remaining 4006 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2270 2.74 - 3.28: 25280 3.28 - 3.82: 38392 3.82 - 4.36: 44484 4.36 - 4.90: 75540 Nonbonded interactions: 185966 Sorted by model distance: nonbonded pdb=" O ASN B1056 " pdb=" OG SER B1060 " model vdw 2.195 3.040 nonbonded pdb=" O GLU B1204 " pdb=" OG1 THR B1208 " model vdw 2.216 3.040 nonbonded pdb=" O SER B 509 " pdb=" OG1 THR B 513 " model vdw 2.216 3.040 nonbonded pdb=" O LEU B1339 " pdb=" N LEU B1343 " model vdw 2.217 3.120 nonbonded pdb=" OG1 THR B1009 " pdb=" OE2 GLU B1011 " model vdw 2.217 3.040 ... (remaining 185961 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' and (resid 7 through 871 or resid 888 through 1417)) selection = chain 'B' } ncs_group { reference = 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.920 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: 1.140 Check model and map are aligned: 0.170 Set scattering table: 0.210 Process input model: 57.120 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.100 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.004 0.046 23602 Z= 0.200 Angle : 0.554 8.499 31913 Z= 0.300 Chirality : 0.040 0.161 3766 Planarity : 0.004 0.051 4009 Dihedral : 11.204 168.859 8869 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 0.23 % Allowed : 7.90 % Favored : 91.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.16), residues: 2863 helix: 1.59 (0.12), residues: 1879 sheet: -0.97 (0.58), residues: 94 loop : -2.23 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 470 HIS 0.003 0.001 HIS A 762 PHE 0.011 0.001 PHE B 926 TYR 0.027 0.001 TYR D 78 ARG 0.003 0.000 ARG A 605 Details of bonding type rmsd hydrogen bonds : bond 0.12241 ( 1391) hydrogen bonds : angle 5.12154 ( 4119) covalent geometry : bond 0.00439 (23602) covalent geometry : angle 0.55383 (31913) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 643 time to evaluate : 2.475 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 12 VAL cc_start: 0.8674 (t) cc_final: 0.8392 (m) REVERT: A 86 LEU cc_start: 0.6760 (mt) cc_final: 0.6553 (mm) REVERT: A 92 ILE cc_start: 0.8308 (tp) cc_final: 0.8082 (tp) REVERT: A 134 SER cc_start: 0.8244 (p) cc_final: 0.8040 (p) REVERT: A 171 PHE cc_start: 0.8079 (m-80) cc_final: 0.7844 (m-80) REVERT: A 184 LEU cc_start: 0.8425 (mt) cc_final: 0.8185 (mp) REVERT: A 216 SER cc_start: 0.8433 (t) cc_final: 0.8159 (t) REVERT: A 253 LYS cc_start: 0.7461 (mptt) cc_final: 0.7216 (mptt) REVERT: A 343 ILE cc_start: 0.8606 (pt) cc_final: 0.8178 (pt) REVERT: A 347 ASN cc_start: 0.8122 (p0) cc_final: 0.7503 (p0) REVERT: A 368 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7274 (mt-10) REVERT: A 415 LEU cc_start: 0.8065 (mt) cc_final: 0.7688 (mp) REVERT: A 487 ASN cc_start: 0.8393 (t0) cc_final: 0.8164 (t0) REVERT: A 515 GLU cc_start: 0.7227 (tm-30) cc_final: 0.6931 (tm-30) REVERT: A 523 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6643 (mm-30) REVERT: A 559 ARG cc_start: 0.7679 (mtp85) cc_final: 0.7362 (mtm110) REVERT: A 563 PHE cc_start: 0.7720 (t80) cc_final: 0.7461 (t80) REVERT: A 566 CYS cc_start: 0.8100 (m) cc_final: 0.7780 (m) REVERT: A 575 LYS cc_start: 0.8434 (mptt) cc_final: 0.8186 (mmtt) REVERT: A 576 LYS cc_start: 0.7552 (tppt) cc_final: 0.6774 (tppt) REVERT: A 584 LYS cc_start: 0.8403 (mtpt) cc_final: 0.8188 (mtpp) REVERT: A 671 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7138 (tm-30) REVERT: A 673 GLN cc_start: 0.6905 (tp40) cc_final: 0.6461 (tp40) REVERT: A 738 ASP cc_start: 0.7112 (p0) cc_final: 0.6888 (p0) REVERT: A 830 ASP cc_start: 0.7718 (t0) cc_final: 0.7421 (t70) REVERT: A 862 ASN cc_start: 0.7911 (m-40) cc_final: 0.7685 (m110) REVERT: A 866 LYS cc_start: 0.8228 (ttmm) cc_final: 0.7939 (ttmm) REVERT: A 889 MET cc_start: 0.7458 (tmm) cc_final: 0.7060 (tmm) REVERT: A 1036 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7118 (mm-30) REVERT: A 1074 THR cc_start: 0.8499 (t) cc_final: 0.8211 (p) REVERT: A 1089 LYS cc_start: 0.8340 (mtpp) cc_final: 0.7951 (mtmm) REVERT: A 1093 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 1128 GLU cc_start: 0.7499 (tp30) cc_final: 0.6905 (tp30) REVERT: A 1179 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7366 (tm-30) REVERT: A 1187 LYS cc_start: 0.8541 (tptp) cc_final: 0.8337 (tptp) REVERT: A 1191 MET cc_start: 0.5573 (mmm) cc_final: 0.5009 (mmm) REVERT: A 1196 GLU cc_start: 0.8205 (tt0) cc_final: 0.7677 (tm-30) REVERT: A 1199 PHE cc_start: 0.8573 (t80) cc_final: 0.8278 (t80) REVERT: A 1204 GLU cc_start: 0.7928 (tp30) cc_final: 0.7601 (mm-30) REVERT: A 1328 MET cc_start: 0.5291 (tpt) cc_final: 0.5017 (tpt) REVERT: A 1400 LYS cc_start: 0.8515 (mmtm) cc_final: 0.8188 (mmtm) REVERT: B 93 ASP cc_start: 0.7809 (t70) cc_final: 0.7511 (t70) REVERT: B 103 LEU cc_start: 0.8532 (tp) cc_final: 0.8332 (tp) REVERT: B 120 ASP cc_start: 0.7443 (m-30) cc_final: 0.7065 (m-30) REVERT: B 199 SER cc_start: 0.8839 (m) cc_final: 0.8624 (m) REVERT: B 245 GLU cc_start: 0.6629 (mp0) cc_final: 0.6407 (mp0) REVERT: B 375 GLN cc_start: 0.8197 (pt0) cc_final: 0.7989 (pt0) REVERT: B 503 LYS cc_start: 0.8333 (ttmm) cc_final: 0.8065 (ttmm) REVERT: B 533 PHE cc_start: 0.8192 (t80) cc_final: 0.7944 (t80) REVERT: B 568 ASN cc_start: 0.7638 (t0) cc_final: 0.7340 (t0) REVERT: B 625 ASN cc_start: 0.8414 (m-40) cc_final: 0.8111 (m110) REVERT: B 626 GLU cc_start: 0.7932 (tt0) cc_final: 0.7649 (tt0) REVERT: B 628 ILE cc_start: 0.8258 (tp) cc_final: 0.7997 (tt) REVERT: B 660 ARG cc_start: 0.8447 (mtt90) cc_final: 0.8176 (mtt90) REVERT: B 663 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7452 (tm-30) REVERT: B 703 TYR cc_start: 0.8405 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: B 737 LYS cc_start: 0.8057 (tppt) cc_final: 0.7743 (mppt) REVERT: B 753 ASP cc_start: 0.7735 (m-30) cc_final: 0.7201 (m-30) REVERT: B 754 LYS cc_start: 0.8353 (tptp) cc_final: 0.8094 (tptp) REVERT: B 770 GLU cc_start: 0.7511 (tp30) cc_final: 0.7259 (tp30) REVERT: B 825 TYR cc_start: 0.7908 (t80) cc_final: 0.7685 (t80) REVERT: B 837 MET cc_start: 0.7720 (mmp) cc_final: 0.7412 (mmm) REVERT: B 929 ILE cc_start: 0.8693 (mm) cc_final: 0.8343 (mt) REVERT: B 1089 LYS cc_start: 0.7976 (ptpt) cc_final: 0.7626 (ptpp) REVERT: B 1128 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7854 (tm-30) REVERT: B 1132 LYS cc_start: 0.8043 (tppt) cc_final: 0.7610 (tppt) REVERT: B 1147 GLN cc_start: 0.8087 (tt0) cc_final: 0.7811 (tt0) REVERT: B 1156 LYS cc_start: 0.8103 (ttmt) cc_final: 0.7872 (ttmm) REVERT: B 1157 GLU cc_start: 0.7856 (tp30) cc_final: 0.7449 (tp30) REVERT: B 1165 LEU cc_start: 0.8282 (tp) cc_final: 0.8047 (tt) REVERT: B 1180 ASN cc_start: 0.8159 (m-40) cc_final: 0.7893 (m-40) REVERT: B 1183 LYS cc_start: 0.8189 (tptp) cc_final: 0.7901 (tptm) REVERT: B 1191 MET cc_start: 0.7123 (mtm) cc_final: 0.6580 (mtm) REVERT: B 1199 PHE cc_start: 0.8573 (t80) cc_final: 0.8152 (t80) REVERT: B 1200 GLU cc_start: 0.7733 (tp30) cc_final: 0.7370 (tp30) REVERT: B 1204 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7219 (mt-10) REVERT: B 1214 THR cc_start: 0.7690 (p) cc_final: 0.7306 (t) REVERT: B 1218 PHE cc_start: 0.7388 (m-80) cc_final: 0.7057 (t80) REVERT: B 1265 SER cc_start: 0.8032 (t) cc_final: 0.7806 (t) REVERT: B 1266 LEU cc_start: 0.8310 (mt) cc_final: 0.8093 (mt) REVERT: B 1274 HIS cc_start: 0.7516 (t-90) cc_final: 0.7301 (t-90) REVERT: B 1288 PHE cc_start: 0.8549 (m-80) cc_final: 0.8083 (m-80) REVERT: B 1332 GLU cc_start: 0.7925 (mp0) cc_final: 0.6741 (mp0) REVERT: B 1383 LYS cc_start: 0.8414 (mttt) cc_final: 0.8130 (mtmt) REVERT: C 22 LEU cc_start: 0.7541 (tp) cc_final: 0.7341 (tp) REVERT: C 24 LEU cc_start: 0.7548 (mp) cc_final: 0.7251 (mp) REVERT: C 101 MET cc_start: 0.7222 (tmm) cc_final: 0.6927 (mmm) REVERT: C 111 MET cc_start: 0.7262 (ttm) cc_final: 0.7023 (ttm) REVERT: D 101 MET cc_start: 0.8144 (mmt) cc_final: 0.7922 (mmt) REVERT: D 111 MET cc_start: 0.7249 (tmm) cc_final: 0.6961 (tmm) REVERT: D 173 TRP cc_start: 0.7743 (t60) cc_final: 0.7463 (t60) outliers start: 6 outliers final: 3 residues processed: 647 average time/residue: 0.3690 time to fit residues: 368.0510 Evaluate side-chains 572 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 568 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 703 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 242 optimal weight: 0.9990 chunk 217 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 74 optimal weight: 0.4980 chunk 146 optimal weight: 0.4980 chunk 116 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 167 optimal weight: 0.0970 chunk 260 optimal weight: 4.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 129 ASN A 132 ASN A 547 GLN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 919 GLN A1194 GLN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 571 ASN B 968 GLN B1180 ASN B1285 ASN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.154903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.131716 restraints weight = 41080.973| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.62 r_work: 0.3534 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 23602 Z= 0.150 Angle : 0.579 11.160 31913 Z= 0.304 Chirality : 0.040 0.191 3766 Planarity : 0.004 0.047 4009 Dihedral : 7.033 164.410 3086 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 1.96 % Allowed : 12.19 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2863 helix: 1.61 (0.12), residues: 1911 sheet: -1.07 (0.58), residues: 94 loop : -2.26 (0.22), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 470 HIS 0.009 0.001 HIS B1369 PHE 0.027 0.002 PHE A1069 TYR 0.023 0.001 TYR D 78 ARG 0.005 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04660 ( 1391) hydrogen bonds : angle 4.37683 ( 4119) covalent geometry : bond 0.00332 (23602) covalent geometry : angle 0.57944 (31913) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 586 time to evaluate : 2.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8430 (t) cc_final: 0.8191 (m) REVERT: A 86 LEU cc_start: 0.6634 (mt) cc_final: 0.6418 (mm) REVERT: A 92 ILE cc_start: 0.8255 (tp) cc_final: 0.8044 (tp) REVERT: A 107 THR cc_start: 0.8550 (m) cc_final: 0.8277 (p) REVERT: A 184 LEU cc_start: 0.8265 (mt) cc_final: 0.8017 (mp) REVERT: A 253 LYS cc_start: 0.7388 (mptt) cc_final: 0.7163 (mptt) REVERT: A 343 ILE cc_start: 0.8535 (pt) cc_final: 0.8206 (pt) REVERT: A 347 ASN cc_start: 0.8028 (p0) cc_final: 0.7360 (p0) REVERT: A 368 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7210 (mt-10) REVERT: A 487 ASN cc_start: 0.8348 (t0) cc_final: 0.8099 (t0) REVERT: A 515 GLU cc_start: 0.7254 (tm-30) cc_final: 0.6888 (tm-30) REVERT: A 523 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6728 (mm-30) REVERT: A 559 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7216 (mtm110) REVERT: A 563 PHE cc_start: 0.7601 (t80) cc_final: 0.7337 (t80) REVERT: A 566 CYS cc_start: 0.8093 (m) cc_final: 0.7723 (m) REVERT: A 575 LYS cc_start: 0.8455 (mptt) cc_final: 0.8184 (mmtt) REVERT: A 576 LYS cc_start: 0.7692 (tppt) cc_final: 0.6896 (tppt) REVERT: A 578 ILE cc_start: 0.7845 (mm) cc_final: 0.7598 (mm) REVERT: A 584 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7831 (mtpp) REVERT: A 630 LEU cc_start: 0.8833 (tp) cc_final: 0.8624 (tp) REVERT: A 671 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7254 (tm-30) REVERT: A 673 GLN cc_start: 0.6945 (tp40) cc_final: 0.6457 (tp40) REVERT: A 738 ASP cc_start: 0.6975 (p0) cc_final: 0.6758 (p0) REVERT: A 783 ILE cc_start: 0.8213 (tt) cc_final: 0.7895 (pt) REVERT: A 862 ASN cc_start: 0.7748 (m-40) cc_final: 0.7483 (m-40) REVERT: A 866 LYS cc_start: 0.8200 (ttmm) cc_final: 0.7907 (ttmm) REVERT: A 889 MET cc_start: 0.7521 (tmm) cc_final: 0.6764 (tmm) REVERT: A 902 GLU cc_start: 0.7287 (mm-30) cc_final: 0.7025 (mm-30) REVERT: A 1022 CYS cc_start: 0.7687 (t) cc_final: 0.7075 (t) REVERT: A 1066 GLU cc_start: 0.7782 (tp30) cc_final: 0.7537 (tp30) REVERT: A 1074 THR cc_start: 0.8210 (t) cc_final: 0.7979 (p) REVERT: A 1089 LYS cc_start: 0.8271 (mtpp) cc_final: 0.7878 (mtmm) REVERT: A 1093 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 1128 GLU cc_start: 0.7594 (tp30) cc_final: 0.6998 (tp30) REVERT: A 1179 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7352 (tm-30) REVERT: A 1187 LYS cc_start: 0.8599 (tptp) cc_final: 0.8394 (tptp) REVERT: A 1196 GLU cc_start: 0.8446 (tt0) cc_final: 0.7822 (tm-30) REVERT: A 1199 PHE cc_start: 0.8575 (t80) cc_final: 0.8222 (t80) REVERT: A 1204 GLU cc_start: 0.8079 (tp30) cc_final: 0.7781 (mm-30) REVERT: A 1263 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 1328 MET cc_start: 0.5274 (tpt) cc_final: 0.5074 (tpp) REVERT: A 1400 LYS cc_start: 0.8618 (mmtm) cc_final: 0.8241 (mmtm) REVERT: B 10 ASP cc_start: 0.6702 (OUTLIER) cc_final: 0.6415 (p0) REVERT: B 29 TYR cc_start: 0.7634 (t80) cc_final: 0.7387 (t80) REVERT: B 120 ASP cc_start: 0.7488 (m-30) cc_final: 0.7165 (m-30) REVERT: B 199 SER cc_start: 0.8792 (m) cc_final: 0.8197 (p) REVERT: B 205 ARG cc_start: 0.8083 (mmm-85) cc_final: 0.7668 (mmm-85) REVERT: B 228 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8124 (ttmm) REVERT: B 245 GLU cc_start: 0.6755 (mp0) cc_final: 0.6462 (mp0) REVERT: B 253 LYS cc_start: 0.7561 (mttm) cc_final: 0.7067 (mttm) REVERT: B 368 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7084 (mp0) REVERT: B 503 LYS cc_start: 0.8425 (ttmm) cc_final: 0.8213 (ttmm) REVERT: B 533 PHE cc_start: 0.8194 (t80) cc_final: 0.7986 (t80) REVERT: B 543 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7096 (mp0) REVERT: B 551 MET cc_start: 0.7471 (mtp) cc_final: 0.7048 (mtp) REVERT: B 625 ASN cc_start: 0.8364 (m-40) cc_final: 0.8055 (m110) REVERT: B 626 GLU cc_start: 0.8153 (tt0) cc_final: 0.7885 (tt0) REVERT: B 632 ASP cc_start: 0.7980 (p0) cc_final: 0.7759 (p0) REVERT: B 663 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7560 (tm-30) REVERT: B 737 LYS cc_start: 0.8100 (tppt) cc_final: 0.7807 (mppt) REVERT: B 753 ASP cc_start: 0.7769 (m-30) cc_final: 0.7342 (m-30) REVERT: B 754 LYS cc_start: 0.8041 (tptp) cc_final: 0.7791 (tptp) REVERT: B 770 GLU cc_start: 0.7562 (tp30) cc_final: 0.7289 (tp30) REVERT: B 837 MET cc_start: 0.7656 (mmp) cc_final: 0.7178 (mmt) REVERT: B 934 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7585 (m-30) REVERT: B 1052 LYS cc_start: 0.7897 (ptpt) cc_final: 0.7585 (mttp) REVERT: B 1072 GLU cc_start: 0.8039 (tt0) cc_final: 0.7507 (tt0) REVERT: B 1089 LYS cc_start: 0.8048 (ptpt) cc_final: 0.7702 (ptpp) REVERT: B 1128 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7832 (tm-30) REVERT: B 1132 LYS cc_start: 0.8140 (tppt) cc_final: 0.7672 (tppt) REVERT: B 1147 GLN cc_start: 0.8339 (tt0) cc_final: 0.8132 (tt0) REVERT: B 1157 GLU cc_start: 0.7613 (tp30) cc_final: 0.7278 (tp30) REVERT: B 1180 ASN cc_start: 0.7859 (m110) cc_final: 0.7571 (m-40) REVERT: B 1191 MET cc_start: 0.7035 (mtm) cc_final: 0.6522 (mtm) REVERT: B 1199 PHE cc_start: 0.8499 (t80) cc_final: 0.8096 (t80) REVERT: B 1200 GLU cc_start: 0.7960 (tp30) cc_final: 0.7568 (tp30) REVERT: B 1204 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 1214 THR cc_start: 0.7641 (p) cc_final: 0.7136 (t) REVERT: B 1218 PHE cc_start: 0.7405 (m-80) cc_final: 0.7082 (t80) REVERT: B 1265 SER cc_start: 0.8064 (t) cc_final: 0.7828 (t) REVERT: B 1266 LEU cc_start: 0.8215 (mt) cc_final: 0.8008 (mt) REVERT: B 1288 PHE cc_start: 0.8624 (m-80) cc_final: 0.8236 (m-80) REVERT: B 1332 GLU cc_start: 0.7747 (mp0) cc_final: 0.7146 (mp0) REVERT: B 1350 GLU cc_start: 0.6592 (OUTLIER) cc_final: 0.6283 (pm20) REVERT: B 1383 LYS cc_start: 0.8378 (mttt) cc_final: 0.8041 (mtmt) REVERT: C 24 LEU cc_start: 0.7547 (mp) cc_final: 0.7310 (mp) REVERT: C 101 MET cc_start: 0.7201 (OUTLIER) cc_final: 0.6768 (mmm) REVERT: C 111 MET cc_start: 0.7196 (ttm) cc_final: 0.6995 (ttm) REVERT: D 101 MET cc_start: 0.8276 (mmt) cc_final: 0.8006 (mmt) REVERT: D 111 MET cc_start: 0.7303 (tmm) cc_final: 0.6928 (tmm) REVERT: D 173 TRP cc_start: 0.7666 (t60) cc_final: 0.7335 (t60) outliers start: 52 outliers final: 30 residues processed: 616 average time/residue: 0.3505 time to fit residues: 337.5641 Evaluate side-chains 597 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 562 time to evaluate : 2.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 976 LEU Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 800 LEU Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1194 GLN Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 41 optimal weight: 0.9990 chunk 129 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 155 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 0.3980 chunk 210 optimal weight: 0.5980 chunk 231 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN B1296 HIS ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.154808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.131714 restraints weight = 40985.475| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.62 r_work: 0.3525 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 23602 Z= 0.169 Angle : 0.582 12.108 31913 Z= 0.302 Chirality : 0.041 0.225 3766 Planarity : 0.004 0.046 4009 Dihedral : 6.970 164.896 3084 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.29 % Allowed : 13.69 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.16), residues: 2863 helix: 1.55 (0.12), residues: 1912 sheet: -1.08 (0.58), residues: 94 loop : -2.26 (0.21), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.022 0.002 PHE B1090 TYR 0.018 0.001 TYR A 327 ARG 0.008 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04690 ( 1391) hydrogen bonds : angle 4.37285 ( 4119) covalent geometry : bond 0.00382 (23602) covalent geometry : angle 0.58197 (31913) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 576 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8445 (t) cc_final: 0.8192 (m) REVERT: A 78 GLN cc_start: 0.7602 (tt0) cc_final: 0.7321 (tt0) REVERT: A 86 LEU cc_start: 0.6642 (mt) cc_final: 0.6403 (mm) REVERT: A 92 ILE cc_start: 0.8250 (tp) cc_final: 0.8029 (tp) REVERT: A 253 LYS cc_start: 0.7374 (mptt) cc_final: 0.7174 (mptt) REVERT: A 343 ILE cc_start: 0.8540 (pt) cc_final: 0.8180 (pt) REVERT: A 347 ASN cc_start: 0.8147 (p0) cc_final: 0.7467 (p0) REVERT: A 368 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7228 (mt-10) REVERT: A 487 ASN cc_start: 0.8333 (t0) cc_final: 0.8078 (t0) REVERT: A 523 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6710 (mm-30) REVERT: A 559 ARG cc_start: 0.7722 (mtp85) cc_final: 0.7203 (mtm110) REVERT: A 563 PHE cc_start: 0.7596 (t80) cc_final: 0.7338 (t80) REVERT: A 566 CYS cc_start: 0.8099 (m) cc_final: 0.7740 (m) REVERT: A 570 PHE cc_start: 0.7858 (t80) cc_final: 0.7464 (t80) REVERT: A 575 LYS cc_start: 0.8450 (mptt) cc_final: 0.8179 (mmtt) REVERT: A 576 LYS cc_start: 0.7727 (tppt) cc_final: 0.6883 (tppt) REVERT: A 578 ILE cc_start: 0.7894 (mm) cc_final: 0.7624 (mm) REVERT: A 580 MET cc_start: 0.8183 (mtp) cc_final: 0.7826 (mtp) REVERT: A 584 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7827 (mtpp) REVERT: A 671 GLU cc_start: 0.7507 (tm-30) cc_final: 0.7280 (tm-30) REVERT: A 673 GLN cc_start: 0.6958 (tp40) cc_final: 0.6414 (tp40) REVERT: A 738 ASP cc_start: 0.6936 (p0) cc_final: 0.6674 (p0) REVERT: A 866 LYS cc_start: 0.8231 (ttmm) cc_final: 0.7921 (ttmm) REVERT: A 889 MET cc_start: 0.7541 (tmm) cc_final: 0.6806 (tmm) REVERT: A 1066 GLU cc_start: 0.7819 (tp30) cc_final: 0.7559 (tp30) REVERT: A 1074 THR cc_start: 0.8219 (t) cc_final: 0.8004 (p) REVERT: A 1093 GLN cc_start: 0.8430 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 1128 GLU cc_start: 0.7664 (tp30) cc_final: 0.7178 (tp30) REVERT: A 1179 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 1186 ARG cc_start: 0.8292 (mtp85) cc_final: 0.7958 (mtp85) REVERT: A 1196 GLU cc_start: 0.8424 (tt0) cc_final: 0.7834 (tm-30) REVERT: A 1199 PHE cc_start: 0.8562 (t80) cc_final: 0.8237 (t80) REVERT: A 1204 GLU cc_start: 0.8085 (tp30) cc_final: 0.7776 (mm-30) REVERT: A 1263 GLU cc_start: 0.8433 (mm-30) cc_final: 0.8115 (mm-30) REVERT: A 1328 MET cc_start: 0.5305 (tpt) cc_final: 0.5094 (tpp) REVERT: A 1383 LYS cc_start: 0.8558 (mmtt) cc_final: 0.8150 (mmtm) REVERT: B 10 ASP cc_start: 0.6686 (OUTLIER) cc_final: 0.6377 (p0) REVERT: B 29 TYR cc_start: 0.7615 (t80) cc_final: 0.7371 (t80) REVERT: B 93 ASP cc_start: 0.7404 (t70) cc_final: 0.7076 (t70) REVERT: B 120 ASP cc_start: 0.7458 (m-30) cc_final: 0.7140 (m-30) REVERT: B 124 LYS cc_start: 0.8029 (ttmt) cc_final: 0.7764 (ttmt) REVERT: B 199 SER cc_start: 0.8743 (m) cc_final: 0.8201 (p) REVERT: B 205 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7741 (mmm-85) REVERT: B 228 LYS cc_start: 0.8396 (ttmm) cc_final: 0.8090 (ttmm) REVERT: B 253 LYS cc_start: 0.7507 (mttm) cc_final: 0.7056 (mttm) REVERT: B 368 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: B 503 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8230 (ttmm) REVERT: B 533 PHE cc_start: 0.8188 (t80) cc_final: 0.7951 (t80) REVERT: B 543 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7138 (mp0) REVERT: B 551 MET cc_start: 0.7480 (mtp) cc_final: 0.6931 (mtp) REVERT: B 575 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8491 (mmmt) REVERT: B 621 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7142 (p) REVERT: B 625 ASN cc_start: 0.8360 (m-40) cc_final: 0.8045 (m110) REVERT: B 626 GLU cc_start: 0.8113 (tt0) cc_final: 0.7815 (tt0) REVERT: B 632 ASP cc_start: 0.8015 (p0) cc_final: 0.7766 (p0) REVERT: B 663 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7537 (tm-30) REVERT: B 737 LYS cc_start: 0.8105 (tppt) cc_final: 0.7830 (mppt) REVERT: B 753 ASP cc_start: 0.7775 (m-30) cc_final: 0.7319 (m-30) REVERT: B 754 LYS cc_start: 0.8054 (tptp) cc_final: 0.7844 (tptp) REVERT: B 770 GLU cc_start: 0.7584 (tp30) cc_final: 0.7299 (tp30) REVERT: B 837 MET cc_start: 0.7606 (mmp) cc_final: 0.7139 (mmp) REVERT: B 934 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7679 (t0) REVERT: B 1072 GLU cc_start: 0.8037 (tt0) cc_final: 0.7532 (tt0) REVERT: B 1089 LYS cc_start: 0.8043 (ptpt) cc_final: 0.7704 (ptpp) REVERT: B 1128 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 1132 LYS cc_start: 0.8125 (tppt) cc_final: 0.7688 (tppt) REVERT: B 1157 GLU cc_start: 0.7608 (tp30) cc_final: 0.7272 (tp30) REVERT: B 1180 ASN cc_start: 0.7896 (m110) cc_final: 0.7615 (m-40) REVERT: B 1186 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7755 (mmm160) REVERT: B 1191 MET cc_start: 0.7048 (mtm) cc_final: 0.6503 (mtm) REVERT: B 1199 PHE cc_start: 0.8508 (t80) cc_final: 0.8109 (t80) REVERT: B 1200 GLU cc_start: 0.7936 (tp30) cc_final: 0.7562 (tp30) REVERT: B 1204 GLU cc_start: 0.7754 (mt-10) cc_final: 0.7337 (mt-10) REVERT: B 1214 THR cc_start: 0.7635 (p) cc_final: 0.7119 (t) REVERT: B 1218 PHE cc_start: 0.7433 (m-80) cc_final: 0.7077 (t80) REVERT: B 1265 SER cc_start: 0.8059 (t) cc_final: 0.7850 (t) REVERT: B 1288 PHE cc_start: 0.8635 (m-80) cc_final: 0.8411 (m-80) REVERT: B 1332 GLU cc_start: 0.7771 (mp0) cc_final: 0.7276 (mp0) REVERT: B 1350 GLU cc_start: 0.6501 (OUTLIER) cc_final: 0.6166 (pm20) REVERT: C 101 MET cc_start: 0.7171 (OUTLIER) cc_final: 0.6787 (mmm) REVERT: D 101 MET cc_start: 0.8245 (mmt) cc_final: 0.7992 (mmt) REVERT: D 111 MET cc_start: 0.7319 (tmm) cc_final: 0.6945 (tmm) REVERT: D 173 TRP cc_start: 0.7737 (t60) cc_final: 0.7350 (t60) outliers start: 61 outliers final: 44 residues processed: 609 average time/residue: 0.3594 time to fit residues: 343.0563 Evaluate side-chains 612 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 562 time to evaluate : 2.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1202 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1267 LYS Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 898 ASP Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1340 LEU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 35 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 200 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 77 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN ** A 858 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 862 ASN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 421 ASN ** B 932 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 968 GLN B1296 HIS ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.154195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.130984 restraints weight = 41416.573| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.61 r_work: 0.3517 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23602 Z= 0.189 Angle : 0.592 11.345 31913 Z= 0.308 Chirality : 0.041 0.212 3766 Planarity : 0.004 0.047 4009 Dihedral : 6.999 165.006 3084 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer: Outliers : 2.97 % Allowed : 14.74 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.16), residues: 2863 helix: 1.45 (0.12), residues: 1921 sheet: -1.07 (0.58), residues: 94 loop : -2.27 (0.21), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.028 0.002 PHE A1069 TYR 0.021 0.002 TYR A 327 ARG 0.009 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04846 ( 1391) hydrogen bonds : angle 4.40775 ( 4119) covalent geometry : bond 0.00429 (23602) covalent geometry : angle 0.59208 (31913) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 572 time to evaluate : 3.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8492 (t) cc_final: 0.8234 (m) REVERT: A 78 GLN cc_start: 0.7736 (tt0) cc_final: 0.7448 (tt0) REVERT: A 86 LEU cc_start: 0.6673 (mt) cc_final: 0.6419 (mm) REVERT: A 92 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.8050 (tp) REVERT: A 107 THR cc_start: 0.8523 (m) cc_final: 0.8317 (p) REVERT: A 134 SER cc_start: 0.8286 (p) cc_final: 0.8049 (p) REVERT: A 153 ARG cc_start: 0.7752 (mtm-85) cc_final: 0.7529 (mtm-85) REVERT: A 253 LYS cc_start: 0.7370 (mptt) cc_final: 0.7152 (mptt) REVERT: A 343 ILE cc_start: 0.8543 (pt) cc_final: 0.8137 (pt) REVERT: A 347 ASN cc_start: 0.8227 (p0) cc_final: 0.7494 (p0) REVERT: A 368 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7256 (mt-10) REVERT: A 487 ASN cc_start: 0.8331 (t0) cc_final: 0.8076 (t0) REVERT: A 523 GLU cc_start: 0.7189 (mm-30) cc_final: 0.6769 (mm-30) REVERT: A 559 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7282 (mtm110) REVERT: A 563 PHE cc_start: 0.7579 (t80) cc_final: 0.7339 (t80) REVERT: A 566 CYS cc_start: 0.8144 (m) cc_final: 0.7800 (m) REVERT: A 575 LYS cc_start: 0.8464 (mptt) cc_final: 0.8182 (mmtt) REVERT: A 576 LYS cc_start: 0.7771 (tppt) cc_final: 0.6821 (tppt) REVERT: A 578 ILE cc_start: 0.7902 (mm) cc_final: 0.7410 (mt) REVERT: A 580 MET cc_start: 0.8189 (mtp) cc_final: 0.7534 (mtm) REVERT: A 584 LYS cc_start: 0.8083 (mtpt) cc_final: 0.7823 (mtpp) REVERT: A 593 LYS cc_start: 0.7976 (ttpp) cc_final: 0.7733 (tttp) REVERT: A 671 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7197 (tm-30) REVERT: A 673 GLN cc_start: 0.6919 (tp40) cc_final: 0.6299 (tp40) REVERT: A 738 ASP cc_start: 0.6935 (p0) cc_final: 0.6677 (p0) REVERT: A 866 LYS cc_start: 0.8282 (ttmm) cc_final: 0.7986 (ttmm) REVERT: A 889 MET cc_start: 0.7512 (tmm) cc_final: 0.6731 (tmm) REVERT: A 1074 THR cc_start: 0.8246 (t) cc_final: 0.8028 (p) REVERT: A 1093 GLN cc_start: 0.8435 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 1128 GLU cc_start: 0.7601 (tp30) cc_final: 0.7042 (tp30) REVERT: A 1196 GLU cc_start: 0.8417 (tt0) cc_final: 0.7851 (tm-30) REVERT: A 1199 PHE cc_start: 0.8552 (t80) cc_final: 0.8214 (t80) REVERT: A 1204 GLU cc_start: 0.8116 (tp30) cc_final: 0.7814 (mm-30) REVERT: A 1263 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 1299 ILE cc_start: 0.8466 (OUTLIER) cc_final: 0.8229 (mm) REVERT: A 1328 MET cc_start: 0.5298 (tpt) cc_final: 0.5097 (tpp) REVERT: A 1383 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8186 (mmtm) REVERT: A 1400 LYS cc_start: 0.8649 (mttm) cc_final: 0.8386 (mmtm) REVERT: B 10 ASP cc_start: 0.6721 (OUTLIER) cc_final: 0.6423 (p0) REVERT: B 29 TYR cc_start: 0.7627 (t80) cc_final: 0.7414 (t80) REVERT: B 93 ASP cc_start: 0.7359 (t70) cc_final: 0.7022 (t70) REVERT: B 120 ASP cc_start: 0.7499 (m-30) cc_final: 0.7149 (m-30) REVERT: B 199 SER cc_start: 0.8798 (m) cc_final: 0.8586 (m) REVERT: B 205 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7760 (mmm-85) REVERT: B 228 LYS cc_start: 0.8435 (ttmm) cc_final: 0.8161 (ttmm) REVERT: B 253 LYS cc_start: 0.7521 (mttm) cc_final: 0.7098 (mttm) REVERT: B 368 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7130 (mp0) REVERT: B 488 LEU cc_start: 0.8202 (mp) cc_final: 0.7916 (mt) REVERT: B 533 PHE cc_start: 0.8218 (t80) cc_final: 0.7951 (t80) REVERT: B 543 GLU cc_start: 0.7438 (mt-10) cc_final: 0.7134 (mp0) REVERT: B 551 MET cc_start: 0.7484 (mtp) cc_final: 0.6941 (mtp) REVERT: B 575 LYS cc_start: 0.8773 (mmmt) cc_final: 0.8523 (mmmt) REVERT: B 625 ASN cc_start: 0.8376 (m-40) cc_final: 0.8056 (m110) REVERT: B 626 GLU cc_start: 0.8140 (tt0) cc_final: 0.7907 (tt0) REVERT: B 632 ASP cc_start: 0.8043 (p0) cc_final: 0.7794 (p0) REVERT: B 657 GLN cc_start: 0.7556 (mp10) cc_final: 0.7129 (mp-120) REVERT: B 663 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7562 (tm-30) REVERT: B 737 LYS cc_start: 0.8094 (tppt) cc_final: 0.7805 (mppt) REVERT: B 753 ASP cc_start: 0.7776 (m-30) cc_final: 0.7317 (m-30) REVERT: B 754 LYS cc_start: 0.8052 (tptp) cc_final: 0.7845 (tptp) REVERT: B 770 GLU cc_start: 0.7566 (tp30) cc_final: 0.7300 (tp30) REVERT: B 775 ASN cc_start: 0.8348 (m-40) cc_final: 0.8112 (m-40) REVERT: B 837 MET cc_start: 0.7637 (mmp) cc_final: 0.7172 (mmp) REVERT: B 934 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7698 (t0) REVERT: B 1052 LYS cc_start: 0.7859 (ptpt) cc_final: 0.7561 (mttp) REVERT: B 1072 GLU cc_start: 0.8037 (tt0) cc_final: 0.7547 (tt0) REVERT: B 1089 LYS cc_start: 0.8077 (ptpt) cc_final: 0.7755 (ptpp) REVERT: B 1128 GLU cc_start: 0.8095 (tm-30) cc_final: 0.7833 (tm-30) REVERT: B 1132 LYS cc_start: 0.8107 (tppt) cc_final: 0.7696 (tppt) REVERT: B 1157 GLU cc_start: 0.7602 (tp30) cc_final: 0.7287 (tp30) REVERT: B 1180 ASN cc_start: 0.7865 (m110) cc_final: 0.7606 (m-40) REVERT: B 1199 PHE cc_start: 0.8539 (t80) cc_final: 0.8127 (t80) REVERT: B 1200 GLU cc_start: 0.7907 (tp30) cc_final: 0.7585 (tp30) REVERT: B 1204 GLU cc_start: 0.7703 (mt-10) cc_final: 0.7318 (mt-10) REVERT: B 1214 THR cc_start: 0.7517 (p) cc_final: 0.7033 (t) REVERT: B 1218 PHE cc_start: 0.7458 (m-80) cc_final: 0.7098 (t80) REVERT: B 1265 SER cc_start: 0.8056 (t) cc_final: 0.7848 (t) REVERT: B 1332 GLU cc_start: 0.7669 (mp0) cc_final: 0.7226 (mp0) REVERT: B 1334 LEU cc_start: 0.8428 (mt) cc_final: 0.7964 (mt) REVERT: B 1350 GLU cc_start: 0.6563 (OUTLIER) cc_final: 0.6185 (pm20) REVERT: C 101 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6973 (mmm) REVERT: D 101 MET cc_start: 0.8490 (mmt) cc_final: 0.8089 (mmt) REVERT: D 111 MET cc_start: 0.7209 (tmm) cc_final: 0.6854 (tmm) REVERT: D 173 TRP cc_start: 0.7763 (t60) cc_final: 0.7278 (t60) outliers start: 79 outliers final: 52 residues processed: 615 average time/residue: 0.4147 time to fit residues: 402.4091 Evaluate side-chains 609 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 550 time to evaluate : 2.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 401 LYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 183 optimal weight: 0.0970 chunk 277 optimal weight: 0.2980 chunk 269 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 143 optimal weight: 0.4980 chunk 111 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 79 optimal weight: 0.0980 chunk 166 optimal weight: 0.9980 chunk 207 optimal weight: 0.0010 overall best weight: 0.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 547 GLN A 862 ASN A 948 ASN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 968 GLN B1147 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.156794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.133599 restraints weight = 41277.047| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.63 r_work: 0.3562 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7324 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 23602 Z= 0.118 Angle : 0.567 12.465 31913 Z= 0.290 Chirality : 0.039 0.210 3766 Planarity : 0.004 0.044 4009 Dihedral : 6.923 163.250 3084 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.78 % Allowed : 15.72 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.16), residues: 2863 helix: 1.70 (0.12), residues: 1913 sheet: -1.13 (0.56), residues: 94 loop : -2.19 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 173 HIS 0.007 0.001 HIS B1369 PHE 0.031 0.001 PHE A1158 TYR 0.024 0.001 TYR A1201 ARG 0.009 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 1391) hydrogen bonds : angle 4.14728 ( 4119) covalent geometry : bond 0.00253 (23602) covalent geometry : angle 0.56670 (31913) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 575 time to evaluate : 2.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8383 (t) cc_final: 0.8149 (m) REVERT: A 78 GLN cc_start: 0.7546 (tt0) cc_final: 0.7198 (tt0) REVERT: A 86 LEU cc_start: 0.6625 (mt) cc_final: 0.6385 (mm) REVERT: A 92 ILE cc_start: 0.8203 (tp) cc_final: 0.7990 (tp) REVERT: A 107 THR cc_start: 0.8505 (m) cc_final: 0.8302 (p) REVERT: A 192 ASP cc_start: 0.7479 (m-30) cc_final: 0.7168 (m-30) REVERT: A 253 LYS cc_start: 0.7368 (mptt) cc_final: 0.7158 (mptt) REVERT: A 343 ILE cc_start: 0.8469 (pt) cc_final: 0.8140 (pt) REVERT: A 347 ASN cc_start: 0.8095 (p0) cc_final: 0.7746 (p0) REVERT: A 368 GLU cc_start: 0.7414 (mt-10) cc_final: 0.7181 (mt-10) REVERT: A 487 ASN cc_start: 0.8322 (t0) cc_final: 0.8081 (t0) REVERT: A 523 GLU cc_start: 0.7054 (mm-30) cc_final: 0.6518 (mm-30) REVERT: A 559 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7168 (mtm110) REVERT: A 563 PHE cc_start: 0.7526 (t80) cc_final: 0.7272 (t80) REVERT: A 566 CYS cc_start: 0.8104 (m) cc_final: 0.7736 (m) REVERT: A 575 LYS cc_start: 0.8439 (mptt) cc_final: 0.8155 (mmtt) REVERT: A 576 LYS cc_start: 0.7759 (tppt) cc_final: 0.6962 (tppt) REVERT: A 578 ILE cc_start: 0.7810 (mm) cc_final: 0.7316 (mt) REVERT: A 580 MET cc_start: 0.8170 (mtp) cc_final: 0.7930 (mtp) REVERT: A 584 LYS cc_start: 0.8008 (mtpt) cc_final: 0.7760 (mtpp) REVERT: A 593 LYS cc_start: 0.7952 (ttpp) cc_final: 0.7723 (tttp) REVERT: A 626 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7765 (mt-10) REVERT: A 636 LEU cc_start: 0.7960 (mt) cc_final: 0.7684 (mp) REVERT: A 671 GLU cc_start: 0.7454 (tm-30) cc_final: 0.7151 (tm-30) REVERT: A 738 ASP cc_start: 0.6844 (p0) cc_final: 0.6583 (p0) REVERT: A 866 LYS cc_start: 0.8238 (ttmm) cc_final: 0.7945 (ttmm) REVERT: A 889 MET cc_start: 0.7546 (tmm) cc_final: 0.6656 (tmm) REVERT: A 902 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6894 (mm-30) REVERT: A 944 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8085 (tt) REVERT: A 1066 GLU cc_start: 0.7786 (tp30) cc_final: 0.7554 (tp30) REVERT: A 1093 GLN cc_start: 0.8413 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 1113 LEU cc_start: 0.8031 (tp) cc_final: 0.7765 (tp) REVERT: A 1128 GLU cc_start: 0.7565 (tp30) cc_final: 0.7046 (tp30) REVERT: A 1186 ARG cc_start: 0.8255 (mtp85) cc_final: 0.7935 (mtp85) REVERT: A 1196 GLU cc_start: 0.8396 (tt0) cc_final: 0.7704 (tm-30) REVERT: A 1199 PHE cc_start: 0.8512 (t80) cc_final: 0.8180 (t80) REVERT: A 1204 GLU cc_start: 0.8094 (tp30) cc_final: 0.7827 (tp30) REVERT: A 1263 GLU cc_start: 0.8463 (mm-30) cc_final: 0.8121 (mm-30) REVERT: A 1299 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8169 (mm) REVERT: A 1400 LYS cc_start: 0.8615 (mttm) cc_final: 0.8358 (mmtm) REVERT: B 10 ASP cc_start: 0.6662 (OUTLIER) cc_final: 0.6367 (p0) REVERT: B 29 TYR cc_start: 0.7611 (t80) cc_final: 0.7385 (t80) REVERT: B 120 ASP cc_start: 0.7461 (m-30) cc_final: 0.7098 (m-30) REVERT: B 124 LYS cc_start: 0.8016 (ttmt) cc_final: 0.7765 (ttmt) REVERT: B 199 SER cc_start: 0.8736 (m) cc_final: 0.8179 (p) REVERT: B 205 ARG cc_start: 0.8093 (mmm-85) cc_final: 0.7710 (mmm-85) REVERT: B 228 LYS cc_start: 0.8299 (ttmm) cc_final: 0.7964 (ttmm) REVERT: B 245 GLU cc_start: 0.6728 (mp0) cc_final: 0.6502 (mp0) REVERT: B 253 LYS cc_start: 0.7554 (mttm) cc_final: 0.7077 (mttm) REVERT: B 368 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7095 (mp0) REVERT: B 488 LEU cc_start: 0.8120 (mp) cc_final: 0.7838 (mt) REVERT: B 533 PHE cc_start: 0.8169 (t80) cc_final: 0.7964 (t80) REVERT: B 543 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7067 (mp0) REVERT: B 575 LYS cc_start: 0.8751 (mmmt) cc_final: 0.8387 (tppt) REVERT: B 621 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7052 (p) REVERT: B 625 ASN cc_start: 0.8318 (m-40) cc_final: 0.7977 (m110) REVERT: B 626 GLU cc_start: 0.8096 (tt0) cc_final: 0.7850 (tt0) REVERT: B 632 ASP cc_start: 0.8027 (p0) cc_final: 0.7767 (p0) REVERT: B 657 GLN cc_start: 0.7524 (mp10) cc_final: 0.7127 (mp-120) REVERT: B 663 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7553 (tm-30) REVERT: B 737 LYS cc_start: 0.8089 (tppt) cc_final: 0.7866 (mppt) REVERT: B 753 ASP cc_start: 0.7730 (m-30) cc_final: 0.7242 (m-30) REVERT: B 770 GLU cc_start: 0.7610 (tp30) cc_final: 0.7327 (tp30) REVERT: B 837 MET cc_start: 0.7531 (mmp) cc_final: 0.7151 (mmp) REVERT: B 903 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7572 (tp) REVERT: B 929 ILE cc_start: 0.8424 (mm) cc_final: 0.8057 (mt) REVERT: B 1089 LYS cc_start: 0.8019 (ptpt) cc_final: 0.7662 (ptpp) REVERT: B 1107 ARG cc_start: 0.7928 (ttm-80) cc_final: 0.7679 (ttm-80) REVERT: B 1128 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 1132 LYS cc_start: 0.8051 (tppt) cc_final: 0.7611 (tppt) REVERT: B 1148 LYS cc_start: 0.8398 (mtmm) cc_final: 0.8177 (mtmm) REVERT: B 1157 GLU cc_start: 0.7545 (tp30) cc_final: 0.7241 (tp30) REVERT: B 1180 ASN cc_start: 0.7879 (m110) cc_final: 0.7627 (m-40) REVERT: B 1186 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7647 (mmm160) REVERT: B 1188 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8264 (p) REVERT: B 1191 MET cc_start: 0.7150 (mtm) cc_final: 0.6732 (mtm) REVERT: B 1199 PHE cc_start: 0.8468 (t80) cc_final: 0.8079 (t80) REVERT: B 1200 GLU cc_start: 0.7924 (tp30) cc_final: 0.7526 (tp30) REVERT: B 1204 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7320 (mt-10) REVERT: B 1214 THR cc_start: 0.7488 (p) cc_final: 0.7032 (t) REVERT: B 1218 PHE cc_start: 0.7370 (m-80) cc_final: 0.7034 (t80) REVERT: B 1265 SER cc_start: 0.8030 (t) cc_final: 0.7813 (t) REVERT: B 1288 PHE cc_start: 0.8622 (m-80) cc_final: 0.8409 (m-80) REVERT: B 1332 GLU cc_start: 0.7605 (mp0) cc_final: 0.7156 (mp0) REVERT: B 1350 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.6141 (pm20) REVERT: C 101 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6813 (mmm) REVERT: D 101 MET cc_start: 0.8219 (mmt) cc_final: 0.7978 (mmt) REVERT: D 111 MET cc_start: 0.7293 (tmm) cc_final: 0.6972 (tmm) REVERT: D 173 TRP cc_start: 0.7754 (t60) cc_final: 0.7357 (t60) outliers start: 74 outliers final: 53 residues processed: 616 average time/residue: 0.3556 time to fit residues: 342.9739 Evaluate side-chains 619 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 555 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 995 LEU Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1285 ASN Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 29 optimal weight: 0.6980 chunk 276 optimal weight: 0.5980 chunk 36 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 271 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 188 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 193 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 862 ASN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.154736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.131573 restraints weight = 41011.575| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.61 r_work: 0.3537 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 23602 Z= 0.161 Angle : 0.591 13.055 31913 Z= 0.302 Chirality : 0.041 0.219 3766 Planarity : 0.004 0.045 4009 Dihedral : 6.932 164.531 3084 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 3.05 % Allowed : 16.10 % Favored : 80.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2863 helix: 1.60 (0.12), residues: 1916 sheet: -1.12 (0.57), residues: 94 loop : -2.26 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 173 HIS 0.008 0.001 HIS B1369 PHE 0.023 0.001 PHE A1158 TYR 0.026 0.001 TYR A1201 ARG 0.006 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 1391) hydrogen bonds : angle 4.23276 ( 4119) covalent geometry : bond 0.00368 (23602) covalent geometry : angle 0.59107 (31913) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 570 time to evaluate : 2.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8468 (t) cc_final: 0.8214 (m) REVERT: A 78 GLN cc_start: 0.7661 (tt0) cc_final: 0.7332 (tt0) REVERT: A 86 LEU cc_start: 0.6644 (mt) cc_final: 0.6398 (mm) REVERT: A 92 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.8012 (tp) REVERT: A 107 THR cc_start: 0.8514 (m) cc_final: 0.8297 (p) REVERT: A 253 LYS cc_start: 0.7354 (mptt) cc_final: 0.7141 (mptt) REVERT: A 343 ILE cc_start: 0.8524 (pt) cc_final: 0.8188 (pt) REVERT: A 347 ASN cc_start: 0.8214 (p0) cc_final: 0.7815 (p0) REVERT: A 368 GLU cc_start: 0.7504 (mt-10) cc_final: 0.7264 (mt-10) REVERT: A 487 ASN cc_start: 0.8329 (t0) cc_final: 0.8092 (t0) REVERT: A 523 GLU cc_start: 0.7121 (mm-30) cc_final: 0.6616 (mm-30) REVERT: A 559 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7215 (mtm110) REVERT: A 575 LYS cc_start: 0.8454 (mptt) cc_final: 0.8159 (mmtt) REVERT: A 576 LYS cc_start: 0.7784 (tppt) cc_final: 0.6911 (tppt) REVERT: A 578 ILE cc_start: 0.7867 (mm) cc_final: 0.7352 (mt) REVERT: A 580 MET cc_start: 0.8195 (mtp) cc_final: 0.7607 (mtm) REVERT: A 584 LYS cc_start: 0.8031 (mtpt) cc_final: 0.7754 (mtpp) REVERT: A 671 GLU cc_start: 0.7467 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 738 ASP cc_start: 0.6872 (p0) cc_final: 0.6624 (p0) REVERT: A 746 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7235 (mpt90) REVERT: A 866 LYS cc_start: 0.8275 (ttmm) cc_final: 0.7994 (ttmm) REVERT: A 889 MET cc_start: 0.7578 (tmm) cc_final: 0.6748 (tmm) REVERT: A 902 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.6867 (mm-30) REVERT: A 944 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8207 (tt) REVERT: A 1093 GLN cc_start: 0.8439 (tm-30) cc_final: 0.8014 (tm-30) REVERT: A 1113 LEU cc_start: 0.8232 (tp) cc_final: 0.8007 (tp) REVERT: A 1128 GLU cc_start: 0.7599 (tp30) cc_final: 0.7066 (tp30) REVERT: A 1186 ARG cc_start: 0.8296 (mtp85) cc_final: 0.7943 (mtp85) REVERT: A 1196 GLU cc_start: 0.8408 (tt0) cc_final: 0.7757 (tm-30) REVERT: A 1199 PHE cc_start: 0.8496 (t80) cc_final: 0.8160 (t80) REVERT: A 1204 GLU cc_start: 0.8087 (tp30) cc_final: 0.7826 (tp30) REVERT: A 1299 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8194 (mm) REVERT: A 1383 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8145 (mmtm) REVERT: A 1400 LYS cc_start: 0.8603 (mttm) cc_final: 0.8335 (mmtm) REVERT: B 10 ASP cc_start: 0.6704 (OUTLIER) cc_final: 0.6398 (p0) REVERT: B 29 TYR cc_start: 0.7627 (t80) cc_final: 0.7408 (t80) REVERT: B 120 ASP cc_start: 0.7474 (m-30) cc_final: 0.7112 (m-30) REVERT: B 205 ARG cc_start: 0.8127 (mmm-85) cc_final: 0.7724 (mmm-85) REVERT: B 228 LYS cc_start: 0.8342 (ttmm) cc_final: 0.7996 (ttmm) REVERT: B 231 THR cc_start: 0.8113 (OUTLIER) cc_final: 0.7713 (p) REVERT: B 245 GLU cc_start: 0.6694 (mp0) cc_final: 0.6471 (mp0) REVERT: B 253 LYS cc_start: 0.7563 (mttm) cc_final: 0.7125 (mttm) REVERT: B 368 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 488 LEU cc_start: 0.8140 (mp) cc_final: 0.7864 (mt) REVERT: B 543 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7116 (mp0) REVERT: B 551 MET cc_start: 0.7781 (mmm) cc_final: 0.7531 (mmt) REVERT: B 575 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8508 (mmmt) REVERT: B 625 ASN cc_start: 0.8340 (m-40) cc_final: 0.7989 (m110) REVERT: B 626 GLU cc_start: 0.8125 (tt0) cc_final: 0.7860 (tt0) REVERT: B 632 ASP cc_start: 0.8059 (p0) cc_final: 0.7769 (p0) REVERT: B 663 GLU cc_start: 0.8019 (tm-30) cc_final: 0.7547 (tm-30) REVERT: B 737 LYS cc_start: 0.8098 (tppt) cc_final: 0.7848 (mppt) REVERT: B 753 ASP cc_start: 0.7768 (m-30) cc_final: 0.7262 (m-30) REVERT: B 770 GLU cc_start: 0.7571 (tp30) cc_final: 0.7301 (tp30) REVERT: B 775 ASN cc_start: 0.8346 (m-40) cc_final: 0.8097 (m-40) REVERT: B 837 MET cc_start: 0.7568 (mmp) cc_final: 0.7318 (mmp) REVERT: B 929 ILE cc_start: 0.8508 (mm) cc_final: 0.8136 (mt) REVERT: B 934 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7675 (t70) REVERT: B 958 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8632 (tt) REVERT: B 1089 LYS cc_start: 0.8034 (ptpt) cc_final: 0.7698 (ptpp) REVERT: B 1107 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7779 (ttm-80) REVERT: B 1128 GLU cc_start: 0.8080 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 1132 LYS cc_start: 0.8081 (tppt) cc_final: 0.7667 (tppt) REVERT: B 1157 GLU cc_start: 0.7606 (tp30) cc_final: 0.7327 (tp30) REVERT: B 1180 ASN cc_start: 0.7868 (m110) cc_final: 0.7644 (m-40) REVERT: B 1186 ARG cc_start: 0.8033 (mmm160) cc_final: 0.7823 (mmm160) REVERT: B 1188 VAL cc_start: 0.8707 (OUTLIER) cc_final: 0.8385 (p) REVERT: B 1191 MET cc_start: 0.7036 (mtm) cc_final: 0.6597 (mtm) REVERT: B 1199 PHE cc_start: 0.8498 (t80) cc_final: 0.8092 (t80) REVERT: B 1200 GLU cc_start: 0.7902 (tp30) cc_final: 0.7543 (tp30) REVERT: B 1204 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7307 (mt-10) REVERT: B 1214 THR cc_start: 0.7530 (OUTLIER) cc_final: 0.7087 (t) REVERT: B 1218 PHE cc_start: 0.7405 (m-80) cc_final: 0.7040 (t80) REVERT: B 1265 SER cc_start: 0.8036 (t) cc_final: 0.7816 (t) REVERT: B 1288 PHE cc_start: 0.8655 (m-80) cc_final: 0.8374 (m-80) REVERT: B 1332 GLU cc_start: 0.7616 (mp0) cc_final: 0.7194 (mp0) REVERT: B 1350 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6154 (pm20) REVERT: B 1383 LYS cc_start: 0.8315 (mttt) cc_final: 0.8073 (mtmt) REVERT: C 101 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.6996 (mmm) REVERT: D 101 MET cc_start: 0.8479 (mmt) cc_final: 0.8094 (mmt) REVERT: D 111 MET cc_start: 0.7196 (tmm) cc_final: 0.6861 (tmm) REVERT: D 173 TRP cc_start: 0.7771 (t60) cc_final: 0.7344 (t60) outliers start: 81 outliers final: 52 residues processed: 616 average time/residue: 0.3396 time to fit residues: 329.4925 Evaluate side-chains 620 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 554 time to evaluate : 2.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 958 ILE Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 281 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 169 optimal weight: 1.9990 chunk 218 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 157 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 125 optimal weight: 0.5980 chunk 113 optimal weight: 0.6980 chunk 102 optimal weight: 0.4980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN A 398 ASN A 862 ASN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 968 GLN ** B1369 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 = 0.4005 r_free = 0.4005 target = 0.154424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.131164 restraints weight = 41319.152| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.61 r_work: 0.3524 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 23602 Z= 0.178 Angle : 0.614 13.515 31913 Z= 0.312 Chirality : 0.042 0.231 3766 Planarity : 0.004 0.046 4009 Dihedral : 6.977 164.599 3084 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.12 % Allowed : 17.07 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2863 helix: 1.55 (0.12), residues: 1906 sheet: -1.11 (0.57), residues: 94 loop : -2.18 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 173 HIS 0.008 0.001 HIS B1369 PHE 0.030 0.002 PHE A 563 TYR 0.023 0.002 TYR A1201 ARG 0.007 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 1391) hydrogen bonds : angle 4.29591 ( 4119) covalent geometry : bond 0.00408 (23602) covalent geometry : angle 0.61407 (31913) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 565 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8497 (t) cc_final: 0.8241 (m) REVERT: A 78 GLN cc_start: 0.7665 (tt0) cc_final: 0.7354 (tt0) REVERT: A 86 LEU cc_start: 0.6645 (mt) cc_final: 0.6380 (mm) REVERT: A 92 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8023 (tp) REVERT: A 107 THR cc_start: 0.8511 (m) cc_final: 0.8279 (p) REVERT: A 153 ARG cc_start: 0.7728 (mtm-85) cc_final: 0.7503 (mtm-85) REVERT: A 211 ARG cc_start: 0.7478 (mtp85) cc_final: 0.6983 (mtt180) REVERT: A 253 LYS cc_start: 0.7359 (mptt) cc_final: 0.7146 (mptt) REVERT: A 343 ILE cc_start: 0.8520 (pt) cc_final: 0.8096 (pt) REVERT: A 347 ASN cc_start: 0.8235 (OUTLIER) cc_final: 0.7853 (p0) REVERT: A 368 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7286 (mt-10) REVERT: A 487 ASN cc_start: 0.8342 (t0) cc_final: 0.8096 (t0) REVERT: A 523 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6697 (mm-30) REVERT: A 559 ARG cc_start: 0.7784 (mtp85) cc_final: 0.7282 (mtm110) REVERT: A 575 LYS cc_start: 0.8455 (mptt) cc_final: 0.8162 (mmtt) REVERT: A 576 LYS cc_start: 0.7805 (tppt) cc_final: 0.6938 (tppt) REVERT: A 578 ILE cc_start: 0.7899 (mm) cc_final: 0.7389 (mt) REVERT: A 580 MET cc_start: 0.8201 (mtp) cc_final: 0.7624 (mtm) REVERT: A 584 LYS cc_start: 0.8043 (mtpt) cc_final: 0.7775 (mtpp) REVERT: A 671 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7252 (tm-30) REVERT: A 738 ASP cc_start: 0.6882 (p0) cc_final: 0.6639 (p0) REVERT: A 746 ARG cc_start: 0.7531 (OUTLIER) cc_final: 0.7221 (mpt90) REVERT: A 866 LYS cc_start: 0.8269 (ttmm) cc_final: 0.7989 (ttmm) REVERT: A 889 MET cc_start: 0.7584 (tmm) cc_final: 0.7295 (tmm) REVERT: A 902 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.6917 (mm-30) REVERT: A 944 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8203 (tt) REVERT: A 1080 PHE cc_start: 0.7556 (m-80) cc_final: 0.7280 (t80) REVERT: A 1092 LEU cc_start: 0.8580 (tp) cc_final: 0.8334 (tp) REVERT: A 1093 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8013 (tm-30) REVERT: A 1128 GLU cc_start: 0.7614 (tp30) cc_final: 0.7106 (tp30) REVERT: A 1186 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7924 (mtp85) REVERT: A 1196 GLU cc_start: 0.8395 (tt0) cc_final: 0.8056 (tp30) REVERT: A 1199 PHE cc_start: 0.8508 (t80) cc_final: 0.8180 (t80) REVERT: A 1204 GLU cc_start: 0.8106 (tp30) cc_final: 0.7849 (tp30) REVERT: A 1263 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8192 (mm-30) REVERT: A 1299 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8235 (mm) REVERT: A 1383 LYS cc_start: 0.8571 (mmtt) cc_final: 0.8176 (mmtm) REVERT: A 1400 LYS cc_start: 0.8603 (mttm) cc_final: 0.8336 (mmtm) REVERT: B 10 ASP cc_start: 0.6719 (OUTLIER) cc_final: 0.6415 (p0) REVERT: B 120 ASP cc_start: 0.7475 (m-30) cc_final: 0.7115 (m-30) REVERT: B 205 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7728 (mmm-85) REVERT: B 228 LYS cc_start: 0.8364 (ttmm) cc_final: 0.8007 (ttmm) REVERT: B 231 THR cc_start: 0.8104 (OUTLIER) cc_final: 0.7739 (p) REVERT: B 245 GLU cc_start: 0.6699 (mp0) cc_final: 0.6471 (mp0) REVERT: B 253 LYS cc_start: 0.7591 (mttm) cc_final: 0.7107 (mttm) REVERT: B 368 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: B 488 LEU cc_start: 0.8121 (mp) cc_final: 0.7839 (mt) REVERT: B 543 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7139 (mp0) REVERT: B 551 MET cc_start: 0.7778 (mmm) cc_final: 0.7562 (mmt) REVERT: B 575 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8502 (mmmt) REVERT: B 625 ASN cc_start: 0.8350 (m-40) cc_final: 0.8000 (m110) REVERT: B 626 GLU cc_start: 0.8103 (tt0) cc_final: 0.7827 (tt0) REVERT: B 632 ASP cc_start: 0.8061 (p0) cc_final: 0.7776 (p0) REVERT: B 663 GLU cc_start: 0.8034 (tm-30) cc_final: 0.7559 (tm-30) REVERT: B 737 LYS cc_start: 0.8094 (tppt) cc_final: 0.7840 (mppt) REVERT: B 753 ASP cc_start: 0.7756 (m-30) cc_final: 0.7254 (m-30) REVERT: B 770 GLU cc_start: 0.7582 (tp30) cc_final: 0.7311 (tp30) REVERT: B 775 ASN cc_start: 0.8339 (m-40) cc_final: 0.8098 (m-40) REVERT: B 837 MET cc_start: 0.7564 (mmp) cc_final: 0.7168 (mmt) REVERT: B 929 ILE cc_start: 0.8531 (mm) cc_final: 0.8169 (mt) REVERT: B 934 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7590 (t0) REVERT: B 1089 LYS cc_start: 0.8051 (ptpt) cc_final: 0.7713 (ptpp) REVERT: B 1107 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7842 (ttm-80) REVERT: B 1128 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7809 (tm-30) REVERT: B 1132 LYS cc_start: 0.8106 (tppt) cc_final: 0.7698 (tppt) REVERT: B 1157 GLU cc_start: 0.7595 (tp30) cc_final: 0.7302 (tp30) REVERT: B 1180 ASN cc_start: 0.7881 (m110) cc_final: 0.7662 (m-40) REVERT: B 1188 VAL cc_start: 0.8719 (OUTLIER) cc_final: 0.8409 (p) REVERT: B 1191 MET cc_start: 0.7054 (mtm) cc_final: 0.6636 (mtm) REVERT: B 1199 PHE cc_start: 0.8505 (t80) cc_final: 0.8076 (t80) REVERT: B 1200 GLU cc_start: 0.7925 (tp30) cc_final: 0.7578 (tp30) REVERT: B 1204 GLU cc_start: 0.7748 (mt-10) cc_final: 0.7328 (mt-10) REVERT: B 1214 THR cc_start: 0.7550 (OUTLIER) cc_final: 0.7089 (t) REVERT: B 1218 PHE cc_start: 0.7419 (m-80) cc_final: 0.7049 (t80) REVERT: B 1265 SER cc_start: 0.8046 (t) cc_final: 0.7838 (t) REVERT: B 1288 PHE cc_start: 0.8669 (m-80) cc_final: 0.8355 (m-80) REVERT: B 1350 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6142 (pm20) REVERT: B 1383 LYS cc_start: 0.8390 (mttt) cc_final: 0.8170 (mtmt) REVERT: C 101 MET cc_start: 0.7351 (OUTLIER) cc_final: 0.7007 (mmm) REVERT: D 101 MET cc_start: 0.8496 (mmt) cc_final: 0.8116 (mmt) REVERT: D 111 MET cc_start: 0.7201 (tmm) cc_final: 0.6885 (tmm) REVERT: D 173 TRP cc_start: 0.7782 (t60) cc_final: 0.7343 (t60) outliers start: 83 outliers final: 58 residues processed: 611 average time/residue: 0.3439 time to fit residues: 329.0649 Evaluate side-chains 622 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 550 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 746 ARG Chi-restraints excluded: chain A residue 768 TRP Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1206 ILE Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 8 optimal weight: 0.9990 chunk 197 optimal weight: 0.5980 chunk 246 optimal weight: 2.9990 chunk 56 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 214 optimal weight: 0.0570 chunk 271 optimal weight: 0.9990 chunk 170 optimal weight: 0.3980 chunk 276 optimal weight: 0.8980 chunk 220 optimal weight: 1.9990 chunk 188 optimal weight: 0.6980 overall best weight: 0.3898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN A 547 GLN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 347 ASN B 968 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.155788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.132487 restraints weight = 41100.634| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.62 r_work: 0.3549 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 23602 Z= 0.139 Angle : 0.607 14.951 31913 Z= 0.307 Chirality : 0.041 0.241 3766 Planarity : 0.004 0.044 4009 Dihedral : 6.954 163.821 3084 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.68 % Favored : 92.32 % Rotamer: Outliers : 2.86 % Allowed : 18.05 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.16), residues: 2863 helix: 1.64 (0.12), residues: 1901 sheet: -1.10 (0.57), residues: 94 loop : -2.14 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 173 HIS 0.008 0.001 HIS B1369 PHE 0.032 0.001 PHE A1158 TYR 0.024 0.001 TYR A1201 ARG 0.007 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 1391) hydrogen bonds : angle 4.22758 ( 4119) covalent geometry : bond 0.00313 (23602) covalent geometry : angle 0.60693 (31913) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 565 time to evaluate : 2.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8457 (t) cc_final: 0.8211 (m) REVERT: A 78 GLN cc_start: 0.7628 (tt0) cc_final: 0.7295 (tt0) REVERT: A 86 LEU cc_start: 0.6631 (mt) cc_final: 0.6377 (mm) REVERT: A 92 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 109 SER cc_start: 0.8552 (m) cc_final: 0.8290 (p) REVERT: A 153 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7522 (mtm-85) REVERT: A 253 LYS cc_start: 0.7352 (mptt) cc_final: 0.7133 (mptt) REVERT: A 343 ILE cc_start: 0.8494 (pt) cc_final: 0.8155 (pt) REVERT: A 347 ASN cc_start: 0.8194 (OUTLIER) cc_final: 0.7831 (p0) REVERT: A 368 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7235 (mt-10) REVERT: A 487 ASN cc_start: 0.8357 (t0) cc_final: 0.8078 (t0) REVERT: A 523 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6564 (mm-30) REVERT: A 559 ARG cc_start: 0.7799 (mtp85) cc_final: 0.7236 (mtm110) REVERT: A 575 LYS cc_start: 0.8453 (mptt) cc_final: 0.8136 (mmtt) REVERT: A 576 LYS cc_start: 0.7807 (tppt) cc_final: 0.6997 (tppt) REVERT: A 578 ILE cc_start: 0.7835 (mm) cc_final: 0.7319 (mt) REVERT: A 580 MET cc_start: 0.8189 (mtp) cc_final: 0.7624 (mtm) REVERT: A 584 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7733 (mtpp) REVERT: A 671 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7208 (tm-30) REVERT: A 738 ASP cc_start: 0.6821 (p0) cc_final: 0.6572 (p0) REVERT: A 866 LYS cc_start: 0.8250 (ttmm) cc_final: 0.7970 (ttmm) REVERT: A 889 MET cc_start: 0.7594 (tmm) cc_final: 0.6735 (tmm) REVERT: A 902 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: A 944 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8187 (tt) REVERT: A 1092 LEU cc_start: 0.8545 (tp) cc_final: 0.8296 (tp) REVERT: A 1093 GLN cc_start: 0.8440 (tm-30) cc_final: 0.8010 (tm-30) REVERT: A 1128 GLU cc_start: 0.7605 (tp30) cc_final: 0.7080 (tp30) REVERT: A 1186 ARG cc_start: 0.8269 (mtp85) cc_final: 0.7912 (mtp85) REVERT: A 1196 GLU cc_start: 0.8366 (tt0) cc_final: 0.8038 (tp30) REVERT: A 1199 PHE cc_start: 0.8471 (t80) cc_final: 0.8094 (t80) REVERT: A 1204 GLU cc_start: 0.8116 (tp30) cc_final: 0.7853 (tp30) REVERT: A 1227 GLU cc_start: 0.7963 (tp30) cc_final: 0.7663 (tp30) REVERT: A 1299 ILE cc_start: 0.8445 (OUTLIER) cc_final: 0.8206 (mm) REVERT: A 1383 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8150 (mmtm) REVERT: A 1400 LYS cc_start: 0.8611 (mttm) cc_final: 0.8332 (mmtm) REVERT: B 10 ASP cc_start: 0.6707 (OUTLIER) cc_final: 0.6415 (p0) REVERT: B 120 ASP cc_start: 0.7483 (m-30) cc_final: 0.7109 (m-30) REVERT: B 199 SER cc_start: 0.8741 (m) cc_final: 0.8382 (p) REVERT: B 205 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7714 (mmm-85) REVERT: B 228 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7966 (ttmm) REVERT: B 231 THR cc_start: 0.8095 (OUTLIER) cc_final: 0.7685 (p) REVERT: B 241 TYR cc_start: 0.7980 (t80) cc_final: 0.7544 (t80) REVERT: B 245 GLU cc_start: 0.6707 (mp0) cc_final: 0.6467 (mp0) REVERT: B 253 LYS cc_start: 0.7591 (mttm) cc_final: 0.7107 (mttm) REVERT: B 368 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 488 LEU cc_start: 0.8079 (mp) cc_final: 0.7799 (mt) REVERT: B 551 MET cc_start: 0.7759 (mmm) cc_final: 0.7520 (mmt) REVERT: B 575 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8494 (mmmt) REVERT: B 625 ASN cc_start: 0.8318 (m-40) cc_final: 0.7964 (m110) REVERT: B 626 GLU cc_start: 0.8102 (tt0) cc_final: 0.7888 (tt0) REVERT: B 632 ASP cc_start: 0.8059 (p0) cc_final: 0.7763 (p0) REVERT: B 663 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 737 LYS cc_start: 0.8098 (tppt) cc_final: 0.7840 (mppt) REVERT: B 753 ASP cc_start: 0.7732 (m-30) cc_final: 0.7235 (m-30) REVERT: B 770 GLU cc_start: 0.7607 (tp30) cc_final: 0.7335 (tp30) REVERT: B 775 ASN cc_start: 0.8332 (m-40) cc_final: 0.8085 (m-40) REVERT: B 837 MET cc_start: 0.7526 (mmp) cc_final: 0.7305 (mmp) REVERT: B 929 ILE cc_start: 0.8500 (mm) cc_final: 0.8124 (mt) REVERT: B 934 ASP cc_start: 0.7980 (OUTLIER) cc_final: 0.7590 (t0) REVERT: B 1089 LYS cc_start: 0.8029 (ptpt) cc_final: 0.7691 (ptpp) REVERT: B 1107 ARG cc_start: 0.7977 (ttm-80) cc_final: 0.7755 (ttm-80) REVERT: B 1128 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 1132 LYS cc_start: 0.8076 (tppt) cc_final: 0.7656 (tppt) REVERT: B 1157 GLU cc_start: 0.7565 (tp30) cc_final: 0.7242 (tp30) REVERT: B 1180 ASN cc_start: 0.7834 (m110) cc_final: 0.7606 (m-40) REVERT: B 1186 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7763 (mmm160) REVERT: B 1191 MET cc_start: 0.6994 (mtm) cc_final: 0.6536 (mtm) REVERT: B 1199 PHE cc_start: 0.8472 (t80) cc_final: 0.8050 (t80) REVERT: B 1200 GLU cc_start: 0.7899 (tp30) cc_final: 0.7527 (tp30) REVERT: B 1204 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 1214 THR cc_start: 0.7509 (OUTLIER) cc_final: 0.7088 (t) REVERT: B 1218 PHE cc_start: 0.7360 (m-80) cc_final: 0.7004 (t80) REVERT: B 1265 SER cc_start: 0.8006 (t) cc_final: 0.7804 (t) REVERT: B 1288 PHE cc_start: 0.8636 (m-80) cc_final: 0.8396 (m-80) REVERT: B 1350 GLU cc_start: 0.6412 (OUTLIER) cc_final: 0.6081 (pm20) REVERT: B 1383 LYS cc_start: 0.8349 (mttt) cc_final: 0.8113 (mtmt) REVERT: C 101 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.7013 (mmm) REVERT: D 101 MET cc_start: 0.8479 (mmt) cc_final: 0.8105 (mmt) REVERT: D 111 MET cc_start: 0.7197 (tmm) cc_final: 0.6911 (tmm) REVERT: D 173 TRP cc_start: 0.7798 (t60) cc_final: 0.7352 (t60) outliers start: 76 outliers final: 57 residues processed: 605 average time/residue: 0.3509 time to fit residues: 333.2841 Evaluate side-chains 628 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 559 time to evaluate : 2.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1100 HIS Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1104 LEU Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 133 optimal weight: 0.8980 chunk 258 optimal weight: 0.0770 chunk 246 optimal weight: 0.0870 chunk 245 optimal weight: 0.5980 chunk 121 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 257 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 968 GLN ** B1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.155738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.132466 restraints weight = 41231.944| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.66 r_work: 0.3542 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7386 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 23602 Z= 0.148 Angle : 0.621 15.416 31913 Z= 0.313 Chirality : 0.041 0.324 3766 Planarity : 0.004 0.045 4009 Dihedral : 6.954 164.028 3084 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 3.05 % Allowed : 18.24 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.16), residues: 2863 helix: 1.60 (0.12), residues: 1904 sheet: -1.18 (0.56), residues: 94 loop : -2.16 (0.21), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 173 HIS 0.009 0.001 HIS B1369 PHE 0.029 0.001 PHE A1158 TYR 0.024 0.001 TYR A1201 ARG 0.007 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04260 ( 1391) hydrogen bonds : angle 4.22931 ( 4119) covalent geometry : bond 0.00337 (23602) covalent geometry : angle 0.62066 (31913) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 561 time to evaluate : 2.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8481 (t) cc_final: 0.8231 (m) REVERT: A 78 GLN cc_start: 0.7625 (tt0) cc_final: 0.7302 (tt0) REVERT: A 86 LEU cc_start: 0.6628 (mt) cc_final: 0.6373 (mm) REVERT: A 92 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7998 (tp) REVERT: A 104 ILE cc_start: 0.8426 (mm) cc_final: 0.8165 (mt) REVERT: A 153 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7516 (mtm-85) REVERT: A 253 LYS cc_start: 0.7359 (mptt) cc_final: 0.7138 (mptt) REVERT: A 343 ILE cc_start: 0.8507 (pt) cc_final: 0.8163 (pt) REVERT: A 347 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7840 (p0) REVERT: A 368 GLU cc_start: 0.7472 (mt-10) cc_final: 0.7251 (mt-10) REVERT: A 487 ASN cc_start: 0.8356 (t0) cc_final: 0.8074 (t0) REVERT: A 523 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6553 (mm-30) REVERT: A 559 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7231 (mtm110) REVERT: A 575 LYS cc_start: 0.8449 (mptt) cc_final: 0.8137 (mmtt) REVERT: A 576 LYS cc_start: 0.7829 (tppt) cc_final: 0.7058 (tppt) REVERT: A 578 ILE cc_start: 0.7843 (mm) cc_final: 0.7318 (mt) REVERT: A 580 MET cc_start: 0.8195 (mtp) cc_final: 0.7649 (mtm) REVERT: A 584 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7743 (mtpp) REVERT: A 671 GLU cc_start: 0.7460 (tm-30) cc_final: 0.7205 (tm-30) REVERT: A 738 ASP cc_start: 0.6829 (p0) cc_final: 0.6581 (p0) REVERT: A 866 LYS cc_start: 0.8248 (ttmm) cc_final: 0.7968 (ttmm) REVERT: A 889 MET cc_start: 0.7593 (tmm) cc_final: 0.7359 (tmm) REVERT: A 902 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6844 (mm-30) REVERT: A 944 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8208 (tt) REVERT: A 1092 LEU cc_start: 0.8556 (tp) cc_final: 0.8306 (tp) REVERT: A 1093 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7997 (tm-30) REVERT: A 1128 GLU cc_start: 0.7615 (tp30) cc_final: 0.7084 (tp30) REVERT: A 1186 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7940 (mtp85) REVERT: A 1196 GLU cc_start: 0.8405 (tt0) cc_final: 0.8060 (tp30) REVERT: A 1199 PHE cc_start: 0.8484 (t80) cc_final: 0.8135 (t80) REVERT: A 1204 GLU cc_start: 0.8120 (tp30) cc_final: 0.7858 (tp30) REVERT: A 1299 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 1383 LYS cc_start: 0.8554 (mmtt) cc_final: 0.8155 (mmtm) REVERT: A 1400 LYS cc_start: 0.8612 (mttm) cc_final: 0.8332 (mmtm) REVERT: B 10 ASP cc_start: 0.6701 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 120 ASP cc_start: 0.7493 (m-30) cc_final: 0.7120 (m-30) REVERT: B 199 SER cc_start: 0.8744 (m) cc_final: 0.8381 (p) REVERT: B 205 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7707 (mmm-85) REVERT: B 228 LYS cc_start: 0.8332 (ttmm) cc_final: 0.7976 (ttmm) REVERT: B 231 THR cc_start: 0.8102 (OUTLIER) cc_final: 0.7685 (p) REVERT: B 241 TYR cc_start: 0.7979 (t80) cc_final: 0.7557 (t80) REVERT: B 245 GLU cc_start: 0.6722 (mp0) cc_final: 0.6481 (mp0) REVERT: B 253 LYS cc_start: 0.7595 (mttm) cc_final: 0.7107 (mttm) REVERT: B 368 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: B 488 LEU cc_start: 0.8063 (mp) cc_final: 0.7783 (mt) REVERT: B 551 MET cc_start: 0.7771 (mmm) cc_final: 0.7532 (mmt) REVERT: B 575 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8502 (mmmt) REVERT: B 625 ASN cc_start: 0.8329 (m-40) cc_final: 0.7978 (m110) REVERT: B 626 GLU cc_start: 0.8107 (tt0) cc_final: 0.7874 (mt-10) REVERT: B 631 PHE cc_start: 0.8023 (m-80) cc_final: 0.7404 (m-80) REVERT: B 632 ASP cc_start: 0.8064 (p0) cc_final: 0.7804 (p0) REVERT: B 663 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7541 (tm-30) REVERT: B 737 LYS cc_start: 0.8096 (tppt) cc_final: 0.7837 (mppt) REVERT: B 753 ASP cc_start: 0.7736 (m-30) cc_final: 0.7273 (m-30) REVERT: B 770 GLU cc_start: 0.7627 (tp30) cc_final: 0.7353 (tp30) REVERT: B 837 MET cc_start: 0.7528 (mmp) cc_final: 0.7300 (mmp) REVERT: B 903 ILE cc_start: 0.7727 (OUTLIER) cc_final: 0.7472 (tp) REVERT: B 929 ILE cc_start: 0.8525 (mm) cc_final: 0.8153 (mt) REVERT: B 934 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7692 (t70) REVERT: B 989 LYS cc_start: 0.5723 (OUTLIER) cc_final: 0.5345 (pttt) REVERT: B 1089 LYS cc_start: 0.8033 (ptpt) cc_final: 0.7705 (ptpp) REVERT: B 1107 ARG cc_start: 0.7994 (ttm-80) cc_final: 0.7763 (ttm-80) REVERT: B 1128 GLU cc_start: 0.8077 (tm-30) cc_final: 0.7804 (tm-30) REVERT: B 1132 LYS cc_start: 0.8081 (tppt) cc_final: 0.7665 (tppt) REVERT: B 1147 GLN cc_start: 0.8166 (tp-100) cc_final: 0.7813 (tp-100) REVERT: B 1157 GLU cc_start: 0.7582 (tp30) cc_final: 0.7253 (tp30) REVERT: B 1180 ASN cc_start: 0.7869 (m110) cc_final: 0.7638 (m-40) REVERT: B 1186 ARG cc_start: 0.7978 (mmm160) cc_final: 0.7714 (mmm160) REVERT: B 1191 MET cc_start: 0.6970 (mtm) cc_final: 0.6575 (mtm) REVERT: B 1199 PHE cc_start: 0.8472 (t80) cc_final: 0.8056 (t80) REVERT: B 1200 GLU cc_start: 0.7901 (tp30) cc_final: 0.7533 (tp30) REVERT: B 1204 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7339 (mt-10) REVERT: B 1214 THR cc_start: 0.7519 (OUTLIER) cc_final: 0.7067 (t) REVERT: B 1218 PHE cc_start: 0.7367 (m-80) cc_final: 0.7011 (t80) REVERT: B 1288 PHE cc_start: 0.8660 (m-80) cc_final: 0.8399 (m-80) REVERT: B 1343 LEU cc_start: 0.7950 (tp) cc_final: 0.7602 (tp) REVERT: B 1350 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.6083 (pm20) REVERT: B 1383 LYS cc_start: 0.8443 (mttt) cc_final: 0.8214 (mtmt) REVERT: C 101 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.7066 (mmm) REVERT: D 101 MET cc_start: 0.8488 (mmt) cc_final: 0.8109 (mmt) REVERT: D 111 MET cc_start: 0.7208 (tmm) cc_final: 0.6913 (tmm) REVERT: D 173 TRP cc_start: 0.7816 (t60) cc_final: 0.7369 (t60) outliers start: 81 outliers final: 64 residues processed: 603 average time/residue: 0.3423 time to fit residues: 324.0499 Evaluate side-chains 632 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 554 time to evaluate : 2.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 727 SER Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1058 ASP Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1212 ILE Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1334 LEU Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 126 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 chunk 261 optimal weight: 0.7980 chunk 217 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 195 optimal weight: 0.6980 chunk 225 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 116 optimal weight: 0.4980 chunk 73 optimal weight: 0.7980 chunk 268 optimal weight: 0.8980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.155944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132588 restraints weight = 41375.540| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.62 r_work: 0.3544 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 23602 Z= 0.151 Angle : 0.632 15.781 31913 Z= 0.320 Chirality : 0.041 0.273 3766 Planarity : 0.004 0.044 4009 Dihedral : 6.961 163.957 3084 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.93 % Favored : 92.04 % Rotamer: Outliers : 2.93 % Allowed : 18.62 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.16), residues: 2863 helix: 1.61 (0.12), residues: 1897 sheet: -1.16 (0.56), residues: 94 loop : -2.20 (0.21), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 173 HIS 0.009 0.001 HIS B1369 PHE 0.030 0.002 PHE A1158 TYR 0.024 0.001 TYR A1201 ARG 0.007 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 1391) hydrogen bonds : angle 4.23387 ( 4119) covalent geometry : bond 0.00345 (23602) covalent geometry : angle 0.63224 (31913) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5726 Ramachandran restraints generated. 2863 Oldfield, 0 Emsley, 2863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 557 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 VAL cc_start: 0.8430 (t) cc_final: 0.8178 (m) REVERT: A 26 MET cc_start: 0.8292 (mtp) cc_final: 0.8019 (mtt) REVERT: A 78 GLN cc_start: 0.7630 (tt0) cc_final: 0.7297 (tt0) REVERT: A 86 LEU cc_start: 0.6646 (mt) cc_final: 0.6376 (mm) REVERT: A 92 ILE cc_start: 0.8206 (OUTLIER) cc_final: 0.7999 (tp) REVERT: A 153 ARG cc_start: 0.7703 (mtm-85) cc_final: 0.7492 (mtm-85) REVERT: A 253 LYS cc_start: 0.7362 (mptt) cc_final: 0.7144 (mptt) REVERT: A 343 ILE cc_start: 0.8499 (pt) cc_final: 0.8147 (pt) REVERT: A 347 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7839 (p0) REVERT: A 368 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7254 (mt-10) REVERT: A 487 ASN cc_start: 0.8363 (t0) cc_final: 0.8079 (t0) REVERT: A 523 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6559 (mm-30) REVERT: A 559 ARG cc_start: 0.7800 (mtp85) cc_final: 0.7283 (mtm110) REVERT: A 575 LYS cc_start: 0.8461 (mptt) cc_final: 0.8149 (mmtt) REVERT: A 576 LYS cc_start: 0.7823 (tppt) cc_final: 0.7060 (tppt) REVERT: A 578 ILE cc_start: 0.7823 (mm) cc_final: 0.7298 (mt) REVERT: A 580 MET cc_start: 0.8202 (mtp) cc_final: 0.7650 (mtm) REVERT: A 584 LYS cc_start: 0.8002 (mtpt) cc_final: 0.7739 (mtpp) REVERT: A 671 GLU cc_start: 0.7461 (tm-30) cc_final: 0.7202 (tm-30) REVERT: A 738 ASP cc_start: 0.6828 (p0) cc_final: 0.6575 (p0) REVERT: A 866 LYS cc_start: 0.8253 (ttmm) cc_final: 0.7972 (ttmm) REVERT: A 889 MET cc_start: 0.7580 (tmm) cc_final: 0.7337 (tmm) REVERT: A 902 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6812 (mm-30) REVERT: A 944 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8198 (tt) REVERT: A 1078 PHE cc_start: 0.8536 (t80) cc_final: 0.8272 (t80) REVERT: A 1092 LEU cc_start: 0.8576 (tp) cc_final: 0.8319 (tp) REVERT: A 1093 GLN cc_start: 0.8444 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 1128 GLU cc_start: 0.7612 (tp30) cc_final: 0.7064 (tp30) REVERT: A 1152 THR cc_start: 0.7959 (p) cc_final: 0.7708 (p) REVERT: A 1186 ARG cc_start: 0.8303 (mtp85) cc_final: 0.7922 (mtp85) REVERT: A 1196 GLU cc_start: 0.8418 (tt0) cc_final: 0.8071 (tp30) REVERT: A 1199 PHE cc_start: 0.8472 (t80) cc_final: 0.8119 (t80) REVERT: A 1204 GLU cc_start: 0.8118 (tp30) cc_final: 0.7860 (tp30) REVERT: A 1227 GLU cc_start: 0.7975 (tp30) cc_final: 0.7627 (tp30) REVERT: A 1299 ILE cc_start: 0.8480 (OUTLIER) cc_final: 0.8214 (mm) REVERT: A 1317 LEU cc_start: 0.8110 (mt) cc_final: 0.7844 (mm) REVERT: A 1383 LYS cc_start: 0.8559 (mmtt) cc_final: 0.8157 (mmtm) REVERT: A 1400 LYS cc_start: 0.8603 (mttm) cc_final: 0.8318 (mmtm) REVERT: B 10 ASP cc_start: 0.6695 (OUTLIER) cc_final: 0.6409 (p0) REVERT: B 120 ASP cc_start: 0.7487 (m-30) cc_final: 0.7111 (m-30) REVERT: B 199 SER cc_start: 0.8753 (m) cc_final: 0.8425 (p) REVERT: B 205 ARG cc_start: 0.8107 (mmm-85) cc_final: 0.7692 (mmm-85) REVERT: B 228 LYS cc_start: 0.8330 (ttmm) cc_final: 0.7964 (ttmm) REVERT: B 231 THR cc_start: 0.8094 (OUTLIER) cc_final: 0.7682 (p) REVERT: B 241 TYR cc_start: 0.7969 (t80) cc_final: 0.7561 (t80) REVERT: B 245 GLU cc_start: 0.6732 (mp0) cc_final: 0.6487 (mp0) REVERT: B 253 LYS cc_start: 0.7607 (mttm) cc_final: 0.7135 (mttm) REVERT: B 368 GLU cc_start: 0.7645 (OUTLIER) cc_final: 0.7123 (mp0) REVERT: B 488 LEU cc_start: 0.8061 (mp) cc_final: 0.7769 (mt) REVERT: B 551 MET cc_start: 0.7792 (mmm) cc_final: 0.7559 (mmt) REVERT: B 575 LYS cc_start: 0.8738 (mmmt) cc_final: 0.8503 (mmmt) REVERT: B 625 ASN cc_start: 0.8314 (m-40) cc_final: 0.7965 (m110) REVERT: B 626 GLU cc_start: 0.8100 (tt0) cc_final: 0.7868 (mt-10) REVERT: B 631 PHE cc_start: 0.8024 (m-80) cc_final: 0.7448 (m-80) REVERT: B 632 ASP cc_start: 0.8066 (p0) cc_final: 0.7806 (p0) REVERT: B 663 GLU cc_start: 0.8049 (tm-30) cc_final: 0.7568 (tm-30) REVERT: B 737 LYS cc_start: 0.8087 (tppt) cc_final: 0.7815 (mppt) REVERT: B 753 ASP cc_start: 0.7720 (m-30) cc_final: 0.7126 (m-30) REVERT: B 770 GLU cc_start: 0.7611 (tp30) cc_final: 0.7333 (tp30) REVERT: B 775 ASN cc_start: 0.8344 (m-40) cc_final: 0.8081 (m-40) REVERT: B 837 MET cc_start: 0.7506 (mmp) cc_final: 0.7245 (mmp) REVERT: B 903 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7546 (tp) REVERT: B 929 ILE cc_start: 0.8532 (mm) cc_final: 0.8163 (mt) REVERT: B 934 ASP cc_start: 0.7991 (OUTLIER) cc_final: 0.7708 (t70) REVERT: B 989 LYS cc_start: 0.5725 (OUTLIER) cc_final: 0.5349 (pttt) REVERT: B 1089 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7690 (ptpp) REVERT: B 1128 GLU cc_start: 0.8063 (tm-30) cc_final: 0.7789 (tm-30) REVERT: B 1132 LYS cc_start: 0.8076 (tppt) cc_final: 0.7664 (tppt) REVERT: B 1147 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7846 (mm110) REVERT: B 1157 GLU cc_start: 0.7558 (tp30) cc_final: 0.7217 (tp30) REVERT: B 1180 ASN cc_start: 0.7874 (m110) cc_final: 0.7648 (m-40) REVERT: B 1191 MET cc_start: 0.6862 (mtm) cc_final: 0.6462 (mtm) REVERT: B 1199 PHE cc_start: 0.8465 (t80) cc_final: 0.8041 (t80) REVERT: B 1200 GLU cc_start: 0.7903 (tp30) cc_final: 0.7528 (tp30) REVERT: B 1204 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7349 (mt-10) REVERT: B 1214 THR cc_start: 0.7510 (OUTLIER) cc_final: 0.7061 (t) REVERT: B 1218 PHE cc_start: 0.7361 (m-80) cc_final: 0.7010 (t80) REVERT: B 1288 PHE cc_start: 0.8652 (m-80) cc_final: 0.8389 (m-80) REVERT: B 1343 LEU cc_start: 0.7942 (tp) cc_final: 0.7601 (tp) REVERT: B 1350 GLU cc_start: 0.6410 (OUTLIER) cc_final: 0.6105 (pm20) REVERT: B 1383 LYS cc_start: 0.8464 (mttt) cc_final: 0.8215 (mtmt) REVERT: C 101 MET cc_start: 0.7340 (OUTLIER) cc_final: 0.7034 (mmm) REVERT: D 101 MET cc_start: 0.8482 (mmt) cc_final: 0.8104 (mmt) REVERT: D 111 MET cc_start: 0.7191 (tmm) cc_final: 0.6898 (tmm) REVERT: D 173 TRP cc_start: 0.7841 (t60) cc_final: 0.7388 (t60) outliers start: 78 outliers final: 59 residues processed: 597 average time/residue: 0.3506 time to fit residues: 327.9109 Evaluate side-chains 622 residues out of total 2659 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 549 time to evaluate : 2.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 347 ASN Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 582 ILE Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 697 SER Chi-restraints excluded: chain A residue 703 TYR Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 838 ILE Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 902 GLU Chi-restraints excluded: chain A residue 905 VAL Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 944 LEU Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 1001 TYR Chi-restraints excluded: chain A residue 1020 MET Chi-restraints excluded: chain A residue 1053 THR Chi-restraints excluded: chain A residue 1067 LEU Chi-restraints excluded: chain A residue 1123 CYS Chi-restraints excluded: chain A residue 1175 LEU Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain A residue 1214 THR Chi-restraints excluded: chain A residue 1299 ILE Chi-restraints excluded: chain A residue 1331 VAL Chi-restraints excluded: chain A residue 1378 ASN Chi-restraints excluded: chain B residue 10 ASP Chi-restraints excluded: chain B residue 28 LYS Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 184 LEU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 463 ILE Chi-restraints excluded: chain B residue 580 MET Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 630 LEU Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 782 VAL Chi-restraints excluded: chain B residue 783 ILE Chi-restraints excluded: chain B residue 903 ILE Chi-restraints excluded: chain B residue 934 ASP Chi-restraints excluded: chain B residue 978 LYS Chi-restraints excluded: chain B residue 983 ILE Chi-restraints excluded: chain B residue 989 LYS Chi-restraints excluded: chain B residue 1023 ILE Chi-restraints excluded: chain B residue 1067 LEU Chi-restraints excluded: chain B residue 1070 ILE Chi-restraints excluded: chain B residue 1113 LEU Chi-restraints excluded: chain B residue 1185 LEU Chi-restraints excluded: chain B residue 1189 THR Chi-restraints excluded: chain B residue 1214 THR Chi-restraints excluded: chain B residue 1292 GLN Chi-restraints excluded: chain B residue 1300 ASN Chi-restraints excluded: chain B residue 1307 GLU Chi-restraints excluded: chain B residue 1321 ILE Chi-restraints excluded: chain B residue 1350 GLU Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain D residue 35 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 156 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 287 random chunks: chunk 135 optimal weight: 0.5980 chunk 240 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 247 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 117 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 347 ASN B 968 GLN ** B1369 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.154724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.131348 restraints weight = 41118.521| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 2.61 r_work: 0.3530 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23602 Z= 0.176 Angle : 0.654 15.186 31913 Z= 0.330 Chirality : 0.042 0.316 3766 Planarity : 0.004 0.045 4009 Dihedral : 6.999 164.459 3084 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.24 % Favored : 91.72 % Rotamer: Outliers : 2.97 % Allowed : 18.65 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.16), residues: 2863 helix: 1.49 (0.12), residues: 1906 sheet: -1.14 (0.57), residues: 94 loop : -2.23 (0.21), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 173 HIS 0.010 0.001 HIS B1369 PHE 0.029 0.002 PHE A1145 TYR 0.024 0.002 TYR A1201 ARG 0.007 0.000 ARG B 807 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 1391) hydrogen bonds : angle 4.31208 ( 4119) covalent geometry : bond 0.00404 (23602) covalent geometry : angle 0.65445 (31913) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15277.07 seconds wall clock time: 264 minutes 1.33 seconds (15841.33 seconds total)